diff --git a/README.md b/README.md
index a91b7e5edc584bd827104c04e621f2e456baf401..71abb5a53d47f565f816196d238ed9b207ed3dd2 100644
--- a/README.md
+++ b/README.md
@@ -4,6 +4,81 @@ This module contains the custom code for sample management like it is
used in GEOMAR's [Biosample Information System
BIS](https://biosamples.geomar.de/).
+## Features
+### Sample Registration
+Samples have unique identifiers (Sample ID) that can be used to persistently
+identify them. The Sample ID can for example be printed as QR Code and used to
+label the physical samples.
+
+Since online access to LinkAhead might not be available during sampling,
+Samples can be registered in advance in order to generate the Sample IDs. This
+allows to print labels for future samples and also allows to download a CSV
+template that can be filled with information about the sample for later import
+into LinkAhead.
+
+Registration is available via the menu in the webinterface "Sample
+Management" -> "Register new Sample"
+
+The CSV Template that is generated always has a set of required columns and
+possibly additional columns that can be selected during the registration. The
+set of columns can be stored for later use via the `RegisterSampleTemplates`.
+Such a template can be created using the "Create sample template" menu entry.
+
+### Sample Update
+Via the menu in the webinterface "Sample Management" -> "Upload Sample template"
+you can upload a CSV template that was created via the registration detailed
+above (or via the export, see below). This updates existing Sample Records
+according to the data contained in the CSV file. This upload possibly creates
+new Records like Events which are related to the updated Samples.
+
+**Important**: Note, that this will override the information of updated samples
+in the server and thus can possibly cause data loss if changes in LinkAhead are
+not reflected in the uploaded file.
+
+### Child Samples
+A Sample can reference another Sample as `Parent sample` to indicate, that the
+sample originated form the other one. If a sample has such a reference, we
+call it a child sample and the referenced sample a parent sample.
+A lot of information is the same
+for both child and parent Sample and this information is not duplicated but it
+is only referenced by the parent Sample.
+
+This implies that child samples are treated differently thatn parent samples
+during the upload of CSV templates: Some information that is obligatory for
+parent sample are not needed for child samples. There for you can create a
+different CSV template for child samples via the "Register new child sample"
+menu entry.
+
+### Container Registration
+Containers have a unique identifier (Container ID) that can be used to
+persistently identify them. The Container ID can for example be printed as QR
+Code and used to label physical containers.
+
+The "Register new Container" menu entry under "Storage Management" allows to
+create new Container Records with the respective IDs. In this process also
+information on Container Type, Size and parent Containers are incorporated.
+
+### Container Update
+You can upload filled CSV templates to update the information about Containers
+stored in LinkAhead
+
+### Container Export
+You can create a filled CSV template with the information about Containers as
+it is currently stored in LinkAhead.
+
+### Extensibility
+The registration, update and export does not only work with RecordTypes and
+Properties that are defined within this module, but the data model can be
+extended by users of the system: Any Property that is added to the Sample
+RecordType can also be used within the workflow. Once an additional Property
+was added to the RecordType (say "width"), you can select a corresponding
+column during registration with the same name and also upload CSV templates
+that have this column. The Sample records will be created or updated to also
+have this ("width") column.
+
+If the Property that is added is a RecordType, it must be kind of an enum, i.e.
+it should be uniquely identified either by its name or by a sole property.
+
## Usage
**TODO**: Add explanations, screenshots, ec. to explain the sample
@@ -29,11 +104,96 @@ instance's data model (e.g., by [synchronizing with the LinkAhead
advanced user
tools](https://docs.indiscale.com//caosdb-advanced-user-tools/yaml_interface.html)).
+## Customization
+
+The sample management module can be customized by overwriting
+indivdual code and config files by using files of the same name and
+with the same relative path in your LinkAhead profile's custom
+directory. E.g., if you want to overwrite how sample entities are post-processed in the sample upload, you overwrite
+
+```
+sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
+```
+
+from this repository by a
+
+```
+profile/custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
+```
+
+in your server profile. When doing so, it is important that in your
+custom file, you use the exact same function names, signatures, and
+return types as in the original file. In our example, the custom
+`sample_upload_post_processing.py` needs to contain a
+`post_process_samples` that takes the samples and the csv data as
+arguments and returns the list of post processed samples.
+
+
## Testing
There is a pre-configured `test-profile` that you can use for testing
this repository.
+
+## Data Model
+This module requires a certain data model in order to work. However, the exact
+names of RecordTypes and Properties can be configured. Below, we will use the
+default names but also reference the variable names of `constants.yml` that
+allow to change those.
+
+### Sample (`variable missing`)
+This is the central RecordType for the sample management and used to represent
+samples of various types
+
+#### `Parent_sample` (`$parent_sample_prop`)
+references the sample from which the sample at hand originated (for example by
+cutting the parent sample into multiple pieces0
+
+#### `Main User`
+references the person that mainly works with this sample
+
+#### `PI`
+references the person that is the responsible principle investigator (PI)
+
+### Event (`$event_rt`)
+A sampling event. Each sample reference the event where it was created.
+
+#### Position (`var missing`)
+The position (e.g. of an Event) that is defined via longituted, latitude and
+possibly elevation
+#### "Biome"
+#### "Campaign"
+#### "Device"
+#### "EventType"
+#### "igsn_doi_prop"
+#### "level"
+#### "locality_description_prop"
+#### "locality_name_prop"
+#### "Sphere"
+
+### Person (`variable missing`)
+a natural person
+
+#### `first_name` (`$first_name_prop`)
+#### `last_name` (`$last_name_prop`)
+#### `abbreviation` (`$abbreviation_prop`)
+
+### `Container` (`$container_rt`)
+a physical container that contains Samples and/or other Containers
+
+####`Child_Container` (`$child_container_prop`)
+references Containers that are contained in the Container at hand
+
+#### `container_label` (`$container_label_prop`)
+#### `Container size` (`$container_size_prop`)
+#### `ContainerType` (`$containertype_rt`)
+#### `custom_label` (`$custom_label_prop`)
+
+#### `Responsible_Person` (`$responsible_person_event`)
+references the person that is responsilbe for this sample, e.g. the PI
+
+### `RegisterSampleTemplates` (missing var)
+
## Further Reading
Please refer to the [official documentation](https://docs.indiscale.com/caosdb-deploy/) for more information.
diff --git a/models_and_helper_scripts/sample-management-datamodel.yml b/models_and_helper_scripts/sample-management-datamodel.yml
index f8deb9d90206c9a5b37690b233aa9ce35d6f52e6..aef3b68183e47b862b3189622822247dcb8c3ee3 100644
--- a/models_and_helper_scripts/sample-management-datamodel.yml
+++ b/models_and_helper_scripts/sample-management-datamodel.yml
@@ -1,7 +1,6 @@
#
-#
-# Copyright (C) 2024 IndiScale <info@indiscale.com>
-# Copyright (C) 2024 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+# Copyright (C) 2024-2025 IndiScale <info@indiscale.com>
+# Copyright (C) 2024-2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
@@ -26,34 +25,21 @@ ControlledRecordType:
Responsible:
inherit_from_obligatory:
- ControlledRecordType
- obligatory_properties:
+ recommended_properties:
Abbreviation:
- description: An abbreviation for this entity that is used for creating BIS labels
- datatype: TEXT
-ResearchDivision:
- inherit_from_obligatory:
- - Responsible
- obligatory_properties:
- German name:
- description: A german name for an entitiy. This can be used in queries since it is an alias.
+ description: An abbreviation for this entity that is used for identification purposes
datatype: TEXT
-ResearchUnit:
- inherit_from_obligatory:
- - Responsible
- obligatory_properties:
- German name:
- ResearchDivision:
Person:
- inherit_from_obligatory:
+ inherit_from_recommended:
- Responsible
obligatory_properties:
- First name:
+ first_name:
datatype: TEXT
- Last name:
+ last_name:
datatype: TEXT
+ recommended_properties:
Email:
datatype: TEXT
- ResearchUnit:
ContainerType:
inherit_from_obligatory:
@@ -61,63 +47,59 @@ ContainerType:
obligatory_properties:
Abbreviation:
+ConditionType:
+ inherit_from_obligatory:
+ - ControlledRecordType
+
+StorageCondition:
+ recommended_properties:
+ ConditionType:
+ condition_value:
+ datatype: TEXT
+
Container:
obligatory_properties:
Responsible:
ContainerType:
- BIS Label:
- description: A standardized label for a container in BIS.
- datatype: TEXT
suggested_properties:
- Child container:
+ container_label:
+ description: A standardized label for a container
+ datatype: TEXT
+ Child_Container:
datatype: LIST<Container>
Container size:
description: The size of the container, e.g. number of spaces or dimension
datatype: TEXT
- Custom label:
- description: A custom label for a container that doesn't have to follow the BIS labeling guidelines.
+ custom_label:
+ description: A custom label for a container that doesn't have to follow the automatic labeling guidelines.
datatype: TEXT
Container Contents:
datatype: TEXT
PI:
datatype: Person
+ StorageCondition:
Sample:
recommended_properties:
- NagoyaCase:
Container:
- FunctionalGroup:
SampleType:
- Parent sample:
+ Parent_sample:
datatype: Sample
- Sampling Person:
- datatype: Person
Main User:
datatype: Person
- suggested_properties:
- Custom ID:
- datatype: LIST<TEXT>
- Publications:
- description: DOIs of publications related to this sample.
- datatype: LIST<TEXT>
- NCBI BioProject:
- datatype: LIST<TEXT>
- NCBI BioSample:
- datatype: LIST<TEXT>
- NCBI Accession:
- datatype: LIST<TEXT>
- Sampling method:
- description: A short description of the sampling methodology used for this sample.
- datatype: TEXT
- Notes:
+ Collector:
+ datatype: LIST(Person)
+ Curator:
+ datatype: LIST(Person)
+ Device:
+ material_left:
+ datatype: BOOLEAN
+ Event:
+ SampleMethod:
+ nagoya_link:
datatype: TEXT
- Time sampled start:
- datatype: DATETIME
- Time sampled stop:
- datatype: DATETIME
- AphiaID:
- description: An ID for this taxon that allows to uniquely identify it on http://www.marinespecies.org.
- datatype: INTEGER
+ nagoya_relevance:
+ datatype: BOOLEAN
Collection:
@@ -154,65 +136,54 @@ NagoyaCase:
Position:
obligatory_properties:
- Latitude:
+ latitude:
datatype: DOUBLE
unit: °
- Longitude:
+ longitude:
datatype: DOUBLE
unit: °
- recommended_properties:
- Water depth:
- description: The depth of the water in meters as a positive value
- datatype: DOUBLE
- unit: m
- Sampling depth:
- description: The depth in meters where the sampling took place as a positive value
+ elevation:
datatype: DOUBLE
- unit: m
-FunctionalGroup:
+EventType:
inherit_from_obligatory:
- ControlledRecordType
-Gear:
+Biome:
+ inherit_from_obligatory:
+ - ControlledRecordType
+
+Device:
inherit_from_obligatory:
- ControlledRecordType
- recommended_properties:
- Configuration:
- datatype: TEXT
Event:
- obligatory_properties:
- Gear:
recommended_properties:
- Time start:
+ Parent_Event:
+ datatype: Event
+ Biome:
+ Campaign:
+ Device:
+ Position:
+ datatype: LIST(Position)
+ start_date:
description: The date and time the event started.
datatype: DATETIME
- suggested_properties:
- Time stop:
+ end_date:
description: The date and time the event ended.
datatype: DATETIME
-
-SourceEvent:
- inherit_from_suggested:
- - Event
- obligatory_properties:
- Position:
- datatype: LIST<Position>
- Gear:
- recommended_properties:
- Hol:
+ EventType:
+ igsn_doi:
datatype: TEXT
- Station Number:
+ level:
datatype: TEXT
- IGSN:
+ locality_description:
datatype: TEXT
- DOI:
- datatype: TEXT
- suggested_properties:
- Station ID:
- description: The name/identifier of a station where regular sampling activity takes place.
+ locality_name:
datatype: TEXT
+ Sphere:
+ Responsible_Person:
+ datatype: LIST(Person)
Platform:
inherit_from_obligatory:
@@ -222,9 +193,10 @@ SampleType:
inherit_from_obligatory:
- ControlledRecordType
-SampleTypeSpecific:
- inherit_from_obligatory:
- - ControlledRecordType
+SampleMethod:
+ recommended_properties:
+ Parent_SampleMethod:
+ datatype: SampleMethod
StartPosition:
inherit_from_obligatory:
@@ -239,25 +211,6 @@ RegisterSampleTemplate:
column_names:
datatype: LIST<TEXT>
-MeshPoreSize:
- inherit_from_obligatory:
- - ControlledRecordType
- recommended_properties:
- enumValue:
- datatype: TEXT
-
-Fixation:
- inherit_from_obligatory:
- - ControlledRecordType
- recommended_properties:
- enumValue:
-
-StorageTemperature:
- inherit_from_obligatory:
- - ControlledRecordType
- recommended_properties:
- enumValue:
-
Campaign:
inherit_from_obligatory:
- ControlledRecordType
@@ -267,27 +220,7 @@ Sphere:
inherit_from_obligatory:
- ControlledRecordType
-Sample context:
- inherit_from_obligatory:
- - ControlledRecordType
-
PDFReport:
inherit_from_obligatory:
- ControlledRecordType
description: PDF files which contain reports and additional information about samples, collections, or containers
-
-commonGermanName:
- inherit_from_obligatory:
- - ControlledRecordType
-
-commonEnglishName:
- inherit_from_obligatory:
- - ControlledRecordType
-
-Taxonomic group/Species:
- inherit_from_obligatory:
- - ControlledRecordType
-
-Sample container:
- inherit_from_obligatory:
- - ControlledRecordType
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf b/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
index 185d75ef202aff0b38c806fec8f0a3654be04931..6727bd1ff64c2dbb8add5a605ba9ed0a8f6e0d8a 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
+++ b/sample-management-custom/caosdb-server/caosdb-webui/build.properties.d/50.sample-management.conf
@@ -22,6 +22,8 @@ BUILD_MODULE_EXT_SSS_MARKDOWN=ENABLED
# Showing id in labels helps for the container/sample id columns
BUILD_MODULE_SHOW_ID_IN_LABEL=ENABLED
-# BIS specific variables
-BUILD_MODULE_EXT_BIS_SAMPLEMANAGEMENT=ENABLED
-BUILD_MODULE_EXT_BIS_STOCKMANAGEMENT=ENABLED
+# sample-management specific variables
+BUILD_MODULE_EXT_SAMPLEMANAGEMENT=ENABLED
+BUILD_MODULE_EXT_STOCKMANAGEMENT=ENABLED
+BUILD_MODULE_EXT_SAMPLEMANGEMENT_ID_LABEL="Sample ID"
+BUILD_MODULE_EXT_STOCKMANAGEMENT_ID_LABEL="Container ID"
\ No newline at end of file
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_sample_reference_resolver.js
similarity index 92%
rename from sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js
rename to sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_sample_reference_resolver.js
index 780a0c20983149530d8cbfdcdba34c06c9f763d2..d237d621d07fd54088234b80530471375b2447c0 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/bis_custom_reference_resolver.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_sample_reference_resolver.js
@@ -1,7 +1,8 @@
-var bis_custom_reference_resolver = new function (getEntityID, getEntityName, getParents, getProperty, query) {
+var sample_management_reference_resolver = new function (getEntityID, getEntityName, getParents, getProperty, query) {
+ // TODO note explicitly what data model assumptions are made here
- const lastname_prop_name = "Last name";
- const firstname_prop_name = "First name";
+ const lastname_prop_name = "last_name";
+ const firstname_prop_name = "first_name";
const person_rt_name = "Person";
const bis_label_prop_name = "BIS label";
const custom_label_prop_name = "Custom label"
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
similarity index 87%
rename from sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
rename to sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
index 4228d6423c37ec8d71d7608448fa4361de281c3e..e8e46e0d88ac2cc40b4fe89fe5032ecbbdd3cb82 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_samplemanagemet.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_samplemanagement.js
@@ -6,9 +6,9 @@
'use strict';
/**
- * This module adds to forms to BIS that relate to sample management.
- * One form allows to register samples.
- * The other allows to update registered samples.
+ * This module adds to forms to LinkAhead that relate to sample
+ * management; there are forms for sample registration, upload, and
+ * export.
*
* @module ext_flight_preview
* @version 0.1
@@ -16,7 +16,7 @@
* @requires nothing yet
* (pass the dependencies as arguments)
*/
-const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
+const ext_samplemanagement = function($, navbar, log, form_elements, form_panel, sample_management_reference_resolver) {
const logger = log.getLogger("samplemanagement_form");
const tool_box = "Sample Management"
const upload_sample_template_title = "Upload sample template"; // title of the form and text in the toolbox
@@ -29,6 +29,7 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
const upload_pdf_title = "Upload PDF file";
const export_csv_id = "export_sample_csv";
const export_csv_title = "Export Samples to CSV";
+ const sample_id_label = ("${BUILD_MODULE_EXT_SAMPLEMANGEMENT_ID_LABEL}" != "") ? "${BUILD_MODULE_EXT_SAMPLEMANGEMENT_ID_LABEL}" : "Sample ID";
const accepted_file_formats = [
".csv",
".CSV",
@@ -36,85 +37,47 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
"text/csv",
];
const required_column_names = [
- "BIS ID",
- "Date collected start",
+ "LinkAhead ID",
"Main User",
- "Gear",
- "Gear configuration",
"Latitude start",
"Longitude start",
- "Collection",
- "PI",
+ "Elevation start",
+ "Start date",
"Storage ID",
- "Nagoya case number",
- "Sample container",
- "Fixation",
- "StorageTemperature",
- "SampleType",
- "SampleTypeSpecific",
- "Sphere",
- "Sample Context",
+ "Device"
];
const requiredColumnNamesChildren = [
- "BIS ID",
- "Date sampled start",
- "Fixation",
+ "LinkAhead ID",
"Main User",
- "Parent BIS ID",
- "Sample Context",
- "Sample container",
+ "Parent LinkAhead ID",
"SampleType",
- "SampleTypeSpecific",
- "Sphere",
"Storage ID",
- "StorageTemperature",
];
const non_sample_rt_column_names = [
- "Platform",
+ "Biome",
"Campaign",
- "Station ID",
- "Station number",
- "Subevent",
- "Time collected start",
- "Date collected stop",
- "Time collected stop",
- "Timezone",
- "Hol",
- "Sampling depth start",
- "Sampling depth stop",
- "Water depth start",
- "Water depth stop",
+ "Start date",
+ "End date",
+ "IGSN DOI",
+ "Level",
+ "Locality description",
+ "Locality name",
+ "Sphere",
+ "Event responsible",
"Latitude stop",
"Longitude stop",
- "Taxonomic group/Species",
- "AphiaID",
- "On-board sampleID",
- "Extraction ID",
- "Duplicate number",
- "Other fixations",
- "Notes / remarks",
- "Forlmaldehyde_box",
- "OSIS URL",
- "Ecotaxa URL",
+ "Elevation stop",
"PDFReport",
- "Date sampled start",
- "Date sampled stop",
- "Time sampled start",
- "Time sampled stop",
- "Parent BIS ID"
- ]
+ "Parent LinkAhead ID",
+ ];
const allColumnNames = non_sample_rt_column_names.concat(requiredColumnNamesChildren).concat(required_column_names);
const unused_property_names = [
- 'Container',
- 'Event',
"Main User",
+ "Event",
+ "Container",
'NagoyaCase',
- "Parent Sample",
- "Person",
- "SampleType",
- "Time start",
- "Time stop"
+ "Parent_sample",
]
const upload_sample_template_form_config = {
@@ -134,12 +97,12 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
script: "export_sample_csv.py",
fields: [{
type: "text",
- name: "bis_ids",
- label: "BIS IDS",
+ name: "ids",
+ label: sample_id_label,
required: false,
pattern: "((([0-9]+\\s*-\\s*){0,1}[0-9]+)\\s*,\\s*)*(([0-9]+\\s*-\\s*){0,1}[0-9]+)",
cached: false,
- help: "Comma-separated list of single BIS IDs or ranges, e.g. '124, 126-139, 242'",
+ help: `Comma-separated list of single ${sample_id_label}s or ranges, e.g. '124, 126-139, 242'`,
}, {
type: "text",
name: "query_string",
@@ -181,7 +144,7 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
name: "responsible_person",
label: "Main user",
query: "FIND RECORD Person",
- make_desc: bis_custom_reference_resolver.resolve_person_reference,
+ make_desc: sample_management_reference_resolver.resolve_person_reference,
required: true
},
{
@@ -262,7 +225,7 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
name: "main_user",
label: "Main user",
query: "FIND RECORD Person",
- make_desc: bis_custom_reference_resolver.resolve_person_reference,
+ make_desc: sample_management_reference_resolver.resolve_person_reference,
required: true
}, {
type: "select",
@@ -398,7 +361,7 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
});
};
-
+
const is_authorized = function() {
// return true //for testing
return isAuthenticated() //&& (userHasRole("stockmanager") || userHasRole("administration"))
@@ -416,14 +379,14 @@ const ext_bis_samplemanagement = function($, navbar, log, form_elements, form_pa
return {
init: init,
};
-}($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver);
+}($, navbar, log, form_elements, form_panel, sample_management_reference_resolver);
// this will be replaced by require.js in the future.
$(document).ready(function() {
// use a variable starting with `BUILD_MODULE_` to enable your module
// the build variable has to be enabled in the `build.properties.d/` directory.
// Otherwise the module will not be activated.
- if ("${BUILD_MODULE_EXT_BIS_SAMPLEMANAGEMENT}" === "ENABLED") {
- caosdb_modules.register(ext_bis_samplemanagement);
+ if ("${BUILD_MODULE_EXT_SAMPLEMANAGEMENT}" === "ENABLED") {
+ caosdb_modules.register(ext_samplemanagement);
}
});
diff --git a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
similarity index 84%
rename from sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js
rename to sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
index b8630a40836d7bc971ffe749af898d0f583cebf1..4775b9dff5327cf026106a530da05023f0858f8d 100644
--- a/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_bis_stockmanagement.js
+++ b/sample-management-custom/caosdb-server/caosdb-webui/src/ext/js/ext_stockmanagement.js
@@ -6,18 +6,19 @@
'use strict';
/**
- * @module ext_bis_stockmanagement
+ * @module ext_stockmanagement
* @version 0.2
*
- * @requires($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver)
+ * @requires($, navbar, log, form_elements, form_panel, sample_management_reference_resolver)
*/
-const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver) {
+const ext_stockmanagement = function($, navbar, log, form_elements, form_panel, sample_management_reference_resolver) {
const tool_box = "Storage Management" // The item that is shown in the top-navbar
///////////////// REGISTER NEW CONTAINERS START
const register_new_containers_title = "Register new Containers";
const register_new_containers_panel_id = "register_new_containers_form_panel";
+ const container_id_label = ("${BUILD_MODULE_EXT_STOCKMANAGEMENT_ID_LABEL}" != "") ? "${BUILD_MODULE_EXT_STOCKMANAGEMENT_ID_LABEL}" : "Container ID";
const register_new_containers_form_config = {
// the script can be found in profiles/default/custom/caosdb-server/scripting/bin/
// it is called like ./register_new_containers.py form.json where form.json
@@ -34,7 +35,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
name: "responsible_entity",
label: "Responsible entity",
query: "FIND RECORD Responsible",
- make_desc: getEntityName,
+ make_desc: sample_management_reference_resolver.resolve_person_reference,
required: true
},
{
@@ -76,7 +77,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
name: "parent_id",
label: "Parent container",
query: "FIND RECORD Container",
- make_desc: bis_custom_reference_resolver.resolve_default,
+ make_desc: sample_management_reference_resolver.resolve_default,
required: false
},
],
@@ -114,12 +115,12 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
script: "export_container_csv.py",
fields: [{
type: "text",
- name: "bis_ids",
- label: "BIS IDS",
+ name: "container_ids",
+ label: container_id_label,
required: true,
pattern: "((([0-9]+\\s*-\\s*){0,1}[0-9]+)\\s*,\\s*)*(([0-9]+\\s*-\\s*){0,1}[0-9]+)",
cached: false,
- help: "Comma-separated list of single BIS IDs or ranges, e.g. '124, 126-139, 242'"
+ help: `Comma-separated list of single ${container_id_label}s or ranges, e.g. '124, 126-139, 242'`
}]
};
///////////////// EXPORT CONTAINER CSV END
@@ -130,7 +131,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
* dropdown for Container registration and for uploading filled-in container
* forms.
*/
- const init_show_stockmanagement_panel_buttons = function () {
+ const init_show_stockmanagement_panel_buttons = function() {
create_register_new_containers_button();
create_update_containers_button();
@@ -159,7 +160,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
});
};
- const create_register_new_containers_button = function () {
+ const create_register_new_containers_button = function() {
navbar.add_tool(register_new_containers_title, tool_box, {
callback: form_panel.create_show_form_callback(
register_new_containers_panel_id,
@@ -168,7 +169,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
});
};
- const create_update_containers_button = function () {
+ const create_update_containers_button = function() {
navbar.add_tool(update_containers_title, tool_box, {
callback: form_panel.create_show_form_callback(
update_containers_panel_id,
@@ -183,7 +184,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
* Check if the user is authenticated and has at least stockmanager or
* administrator role.
*/
- const is_authorized = function () {
+ const is_authorized = function() {
return isAuthenticated() && (userHasRole("Scientist") || userHasRole("Stock manager") || userHasRole("administration") || userHasRole("Curator"));
}
@@ -192,7 +193,7 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
* top-navbar is_authorized() returns true, i.e. the user is authenticated
* and has either stockmanager or administration role.
*/
- const init = function () {
+ const init = function() {
if (is_authorized()) {
init_show_stockmanagement_panel_buttons();
}
@@ -202,14 +203,14 @@ const ext_bis_stockmanagement = function ($, navbar, log, form_elements, form_pa
return {
init: init,
};
-}($, navbar, log, form_elements, form_panel, bis_custom_reference_resolver); // this will be replaced by require.js in the future.
+}($, navbar, log, form_elements, form_panel, sample_management_reference_resolver); // this will be replaced by require.js in the future.
-$(document).ready(function () {
+$(document).ready(function() {
// use a variable starting with `BUILD_MODULE_` to this module
// the build variable has to be enabled in the `build.properties.d/` directory.
// Otherwise the module will not be activated.
- if ("${BUILD_MODULE_EXT_BIS_STOCKMANAGEMENT}" === "ENABLED") {
- caosdb_modules.register(ext_bis_stockmanagement);
+ if ("${BUILD_MODULE_EXT_STOCKMANAGEMENT}" === "ENABLED") {
+ caosdb_modules.register(ext_stockmanagement);
}
});
// const form = form_elements.make_form(config);
diff --git a/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py b/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
index d70503062881b0df7701fff1d7e6b6fc936a6921..00699e559a62b6cbfb208f144ba83f0cdf078d01 100644
--- a/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/bis_utils.py
@@ -32,84 +32,12 @@ from caosadvancedtools.serverside.helper import send_mail
from caoscrawler.config import get_config_setting
from linkahead import get_entity_by_name
-SPECIAL_TREATMENT_SAMPLE = [
- "BIS ID",
- "Collection",
- "Date collected start",
- "Date collected stop",
- "Date sampled start",
- "Date sampled stop",
- "Gear configuration",
- "Gear",
- "Hol",
- "Latitude start",
- "Latitude stop",
- "Longitude start",
- "Longitude stop",
- "Main User",
- "Nagoya case number",
- "PDFReport",
- "PI",
- "Parent BIS ID",
- "Person",
- "Sampling Person",
- "Sampling depth start",
- "Sampling depth stop",
- "Sphere",
- "Station ID",
- "Station number",
- "Storage Container Label",
- "Storage ID",
- "Subevent",
- "Time collected start",
- "Time collected stop",
- "Time sampled start",
- "Time sampled stop",
- "Timezone",
- "Water depth start",
- "Water depth stop",
-]
-
-IGNORED_COLUMN_NAMES_SAMPLE = [
- "BIS URL",
- "Date",
- "IGSN URL",
- "IGSN", # TODO This will be relevant for external IGSNs in the future.
- "Parent Sample",
- "Sampling depth",
- "Storage chain",
- "Water depth",
-]
-
-
-# This can be used for hard-coded descriptions
-COLUMN_DESCRIPTIONS = {
- "BIS ID": "An ID generated by the BIS (either integer or URL to this entity). Do not change this column!",
- "BIS label": "The label automatically assigned by the BIS. Do not change this column.",
- "Collection": "Collection(s) to which this container or samples belongs (separated by ';')",
- "Container Contents": "Notes concerning the contents of this container",
- "Container size": "The size of the container (e.g 81 spaces)",
- "Container type": "The type of container. Do not change this column.",
- "Custom label": "Any additional custom label you put on the container",
- "Date collected start": "The start date in format YYYY-MM-DD",
- "Date collected stop": "The end date in format YYYY-MM-DD",
- "Gear configuration": "How gear is configured, meshsize of the net, filter pore size, what kind of trawl",
- "Latitude start": "Latitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for S",
- "Latitude stop": "Latitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for S",
- "Longitude start": "Longitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for W",
- "Longitude stop": "Longitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for W",
- "Notes / remarks": "Field for notes",
- "PDFReport": "A PDF containing additional information on the container or sampe contents",
- "PI": "The PI (by abbreviation) of the container or sample",
- "Parent container": "The BIS ID (integer or URL) or name or BIS label of the container where this container is stored.",
- "Sampling depth start": "The depth in meters where the sampling started as a positive value, not bottom depth",
- "Sampling depth stop": "The depth in meters where the sampling ended as a positive value,not bottom depth",
- "Storage ID": "BIS ID of the Container that holds this sample",
- "Subevent": "Subevent given by D-Ship in Stationlog. Expl. AL123_14-4",
- "Timezone": "Timezone: Either UTC, CET, .... or in the form +hh[:mm], -hh:[mm].",
- "Water depth start": "The bottom depth in meters where the sampling started as a positive value",
- "Water depth stop": "The bottom depth in meters where the sampling ended as a positive value",
-}
+from sample_helpers.sample_upload_column_definitions import (
+ IGNORED_COLUMN_NAMES_SAMPLE, SPECIAL_TREATMENT_SAMPLE)
+from sample_helpers.utils import CONSTANTS, return_value_if_not_none
+
+
+COLUMN_DESCRIPTIONS = CONSTANTS["csv_column_descriptions"]
def get_do_not_insert_type_names(override_names: list[str] = []):
@@ -203,22 +131,6 @@ def replace_entity_urls_by_ids(data: pd.DataFrame, eid_columns: list[str] = ["BI
return data
-def return_value_if_not_none(val):
- """Workaround for somewhat weird pandas behavior. Return value if actual
- value, otherwise, return None.
-
- """
- if isinstance(val, list):
- if len(val) == 0:
- return None
- if len(val) == 1:
- if pd.isnull(val[0]) or val[0] is None or f"{val[0]}".lower() == "nan" or f"{val[0]}" == "":
- return None
- elif pd.isnull(val) or val is None or f"{val}".lower() == "nan" or f"{val}" == "":
- return None
- return val
-
-
def whitespace_cleanup_in_df(df: pd.DataFrame):
"""Strip all leading and trailing whitespaces from all str values in df."""
diff --git a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
index 1c578f9e6e6b56c53805857996b13b90f4199e4b..ace23eef4c481fdc20057fce83ef44d4c45dbca5 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/crawl_sample_data_async.py
@@ -47,6 +47,11 @@ from bis_utils import (get_do_not_insert_type_names,
return_value_if_not_none,
send_mail_with_defaults,
SPECIAL_TREATMENT_SAMPLE)
+from sample_helpers.sample_upload_add_special_properties import add_special_properties
+from sample_helpers.sample_upload_get_event import add_event_to_sample
+from sample_helpers.sample_upload_get_person import get_person
+from sample_helpers.sample_upload_post_processing import post_process_samples
+from sample_helpers.utils import (get_column_header_name, get_entity_name, update_property)
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -66,373 +71,6 @@ def _is_ignored_column_name(name, parent_suffix="_parent"):
return name in IGNORED_COLUMN_NAMES_SAMPLE or name.endswith(parent_suffix)
-def _update_property(entity: db.Record, property_id: int, value, property_name="", datatype=None):
- """
- Set the property of an entity.
-
- If the entity already has the property, just the value is set.
- Else, the property is added to the entity
- """
- # TODO: Replace by assure_property_is etc.
-
- # If the value in the spreadsheet is empty (nan)
- if ((isinstance(value, list) and len(value) == 0)
- or (not isinstance(value, list) and pd.isna(value))):
- # Remove the property from te Entity if it has it
- try:
- entity.get_properties().get_by_name(property_name)
- entity.remove_property(property_name)
- except KeyError:
- pass
- return entity
- if entity.get_property(property_id) is None:
- if datatype:
- entity.add_property(id=property_id, value=value, name=property_name, datatype=datatype)
- else:
- entity.add_property(id=property_id, value=value, name=property_name)
- logger.debug("{}: Adding {} = {}".format(entity.id, property_id, value.id if
- isinstance(value, db.Entity) else value))
- else:
- if isinstance(value, list) and not entity.get_property(property_id).datatype.startswith("LIST"):
- entity.get_property(property_id).datatype = db.LIST(
- entity.get_property(property_id).datatype)
- entity.get_property(property_id).value = value
- logger.debug("{}: Setting {} = {}".format(entity.id, property_id, value.id if
- isinstance(value, db.Entity) else value))
- return entity
-
-
-def _treat_date(date_val: str):
-
- date_pattern = r"^[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2}$"
- # Check general pattern since dateutil.parse is unreliable with incomplete
- # dates (e.g., 2024-01) or wrong formats (e.g., 01.12.2024 is parsed as
- # 2024-01-12).
- if re.match(date_pattern, date_val) is None:
- # ParserError for simplified error handling down the line.
- raise dateparser.ParserError(f"{date_val} is not of the format YYYY-MM-DD.")
- # Use dateutils.parser despite having checked the pattern to exclude
- # nonsense dates like 2024-13-54.
- return str(dateparser.parse(date_val).date())
-
-
-def _append_times_to_entity(ent, data, propname_prefix="Time", colname_time_prefix="Time collected", colname_date_prefix="Date collected"):
- propname_start = f"{propname_prefix} start"
- propname_stop = f"{propname_prefix} stop"
- prop_start = cached_get_entity_by(name=propname_start)
- prop_stop = cached_get_entity_by(name=propname_stop)
- colname_time_start = f"{colname_time_prefix} start"
- colname_time_stop = f"{colname_time_prefix} stop"
- colname_date_start = f"{colname_date_prefix} start"
- colname_date_stop = f"{colname_date_prefix} stop"
-
- date_start = None
- date_stop = None
- time_start = None
- time_stop = None
- timezone = None
- # Time start
- if colname_date_start in data and return_value_if_not_none(data[colname_date_start]) is not None:
- date_start = return_value_if_not_none(data[colname_date_start])
- try:
- date_start = _treat_date(date_start)
- except dateparser.ParserError as perr:
- logger.error(
- f"There is a problem in '{colname_date_start}': {date_start}"
- f" of sample {data['BIS ID']}: {perr}"
- )
- raise DataInconsistencyError
- if colname_time_start in data and return_value_if_not_none(data[colname_time_start]) is not None:
- if not "Timezone" in data or return_value_if_not_none(data["Timezone"]) is None:
- logger.error(f"{colname_time_start} but no timezone given for sample "
- f"{data['BIS ID']}.")
- raise DataInconsistencyError
- time_start = return_value_if_not_none(data[colname_time_start])
- timezone = return_value_if_not_none(data["Timezone"])
- if date_start is None:
- logger.error(
- f"{colname_time_start} is given but {colname_date_start} is missing for sample {data['BIS ID']}.")
- raise DataInconsistencyError
- try:
- _val = str(dateparser.parse(f"{date_start}T{time_start}{timezone}"))
- ent = _update_property(ent, prop_start.id, property_name=prop_start.name, value=_val)
- except dateparser.ParserError as perr:
- logger.error(
- f"Couldn't parse {colname_time_start}: {time_start} with timezone {timezone} "
- f"of sample {data['BIS ID']}: {perr}"
- )
- raise DataInconsistencyError
- elif date_start is not None:
- ent = _update_property(ent, prop_start.id, value=date_start, property_name=prop_start.name)
-
- # Time stop; raise error in case of stop without start
- if colname_date_stop in data and return_value_if_not_none(data[colname_date_stop]) is not None:
- date_stop = return_value_if_not_none(data[colname_date_stop])
- if date_stop is not None and date_start is None:
- logger.error(
- f"{colname_date_stop} is given but {colname_date_start} is missing for sample {data['BIS ID']}.")
- raise DataInconsistencyError
- if date_stop is None:
- _date_stop = date_start
- else:
- try:
- _date_stop = _treat_date(date_stop)
- except dateparser.ParserError as perr:
- logger.error(
- f"There is a problem in '{colname_date_stop}': {date_stop}"
- f" of sample {data['BIS ID']}: {perr}"
- )
- raise DataInconsistencyError
-
- if colname_time_stop in data and return_value_if_not_none(data[colname_time_stop]) is not None:
- time_stop = return_value_if_not_none(data[colname_time_stop])
- if time_start is None:
- logger.error(
- f"{colname_time_stop} is given but {colname_time_start} is missing for sample {data['BIS ID']}.")
- raise DataInconsistencyError
- # timezone is set by time start; if it hadn't been there, we would already have an error.
- try:
- _val = str(dateparser.parse(f"{_date_stop}T{time_stop}{timezone}"))
- except dateparser.ParserError as perr:
- logger.error(
- f"Couldn't parse {colname_time_stop}: {time_stop} with timezone {timezone} "
- f"of sample {data['BIS ID']}: {perr}"
- )
- raise DataInconsistencyError
- ent = _update_property(ent, prop_stop.id, property_name=prop_stop.name, value=_val)
- elif date_stop is not None:
- # We check date_stop but we used the cleaned-up _date_stop as value
- ent = _update_property(ent, prop_stop.id, property_name=prop_stop.name, value=_date_stop)
-
- return ent
-
-
-def get_container(data):
- """
- Retrun the BIS ID of the Container Record that is identified by 'Storage contianer' in data.
- A Container can either be identified via a BIS ID or via a BIS Label.
-
- If no Container can be identified, an Error is raised, since creating/registering new
- Containers has to be done before registering samples.
- """
- identified_by_label = False
- container_identifier = data["Storage ID"]
- # If the ID is not spcified, try to get the label
- if "Storage Container Label" in data and pd.isnull(container_identifier):
- container_identifier = data["Storage Container Label"]
- identified_by_label = True
-
- if identified_by_label:
- container = _get_container_by_label(container_identifier)
- else:
- container = _get_container_by_id(container_identifier)
-
- if container is not None:
- return container
- else:
- msg = "Container: '{}' could not be identified.".format(container_identifier)
- raise DataInconsistencyError(msg)
-
-
-def _get_container_by_id(id):
- res = db.execute_query("FIND RECORD Container WITH id = '{}'".format(id))
- if len(res) > 0:
- return res[0]
- else:
- return None
-
-
-def _get_container_by_label(label):
- res = db.execute_query("FIND RECORD Container WITH 'BIS Label' = '{}'".format(label))
- if len(res) > 0:
- return res[0]
- else:
- return None
-
-
-def get_event(data, gear_id):
- # Events only have names if they have the subevent property.
- if "Subevent" in data and return_value_if_not_none(data["Subevent"]) is not None:
- event_name = f"{data['Subevent']}"
- return _create_new_source_event(event_name, data, gear_id)
-
- return _create_new_source_event(name=None, data=data, gear_id=gear_id)
-
-
-def _create_new_source_event(name, data, gear_id) -> db.Record:
- event = db.Record(name)
- event.add_parent("SourceEvent")
- event = _append_times_to_entity(event, data)
-
- event.add_property(name="Gear", value=gear_id)
- event.add_property(name="Position", value=_get_positions(
- data), datatype=db.common.datatype.LIST("Position")) # type: ignore
- if "Station ID" in data and return_value_if_not_none(data["Station ID"]) is not None:
- event.add_property(name="Station ID", value=str(data["Station ID"]))
- if "Station number" in data and return_value_if_not_none(data["Station number"]) is not None:
- event.add_property(name="Station number", value=str(data["Station number"]))
- if "Hol" in data and return_value_if_not_none(data["Hol"]) is not None:
- event.add_property(name="Hol", value=str(data["Hol"]))
- return event
-
-
-def _get_positions(data):
- # TODO: Refactor
- if "Latitude start" in data:
- latitude_start = return_value_if_not_none(data["Latitude start"])
- else:
- latitude_start = None
- if "Latitude stop" in data:
- latitude_stop = return_value_if_not_none(data["Latitude stop"])
- else:
- latitude_stop = None
- if "Longitude start" in data:
- longitude_start = return_value_if_not_none(data["Longitude start"])
- else:
- longitude_start = None
- if "Longitude stop" in data:
- longitude_stop = return_value_if_not_none(data["Longitude stop"])
- else:
- longitude_stop = None
- if "Sampling depth start" in data:
- sampling_depth_start = return_value_if_not_none(data["Sampling depth start"])
- else:
- sampling_depth_start = None
- if "Sampling depth stop" in data:
- sampling_depth_stop = return_value_if_not_none(data["Sampling depth stop"])
- else:
- sampling_depth_stop = None
- if "Water depth start" in data:
- water_depth_start = return_value_if_not_none(data["Water depth start"])
- else:
- water_depth_start = None
- if "Water depth stop" in data:
- water_depth_stop = return_value_if_not_none(data["Water depth stop"])
- else:
- water_depth_stop = None
- # insert start position
- position_start = db.Record()
- position_start.add_parent("StartPosition")
- position_start.add_property(name="Latitude", value=latitude_start)
- position_start.add_property(name="Longitude", value=longitude_start)
- if not pd.isna(sampling_depth_start):
- if sampling_depth_start < 0.0:
- sampling_depth_start *= -1.0
- # identifiable, so add even if it is None
- position_start.add_property(name="Sampling depth", value=sampling_depth_start)
- if not pd.isna(water_depth_start):
- if water_depth_start < 0:
- water_depth_start *= -1
- # identifiable, so add even if it is None
- position_start.add_property(name="Water depth", value=water_depth_start)
-
- # A stop position may be specified by depth stop alone:
- if not (pd.isna(sampling_depth_stop) and pd.isna(water_depth_stop)):
- # Copy all empty info from start position
- if pd.isna(latitude_stop) and pd.isna(longitude_stop):
- latitude_stop = latitude_start
- longitude_stop = longitude_start
- if pd.isna(sampling_depth_stop):
- sampling_depth_stop = sampling_depth_start
- if pd.isna(water_depth_stop):
- water_depth_stop = water_depth_start
- # If there is an endposition: insert endposition
- if not (pd.isna(latitude_stop) or pd.isna(longitude_stop)):
-
- position_end = db.Record()
- # position_end = db.Record("({}, {})".format(latitude_stop, longitude_stop))
- position_end.add_parent("StopPosition")
- position_end.add_property(name="Latitude", value=latitude_stop)
- position_end.add_property(name="Longitude", value=longitude_stop)
- if not pd.isna(sampling_depth_stop):
- if sampling_depth_stop < 0:
- sampling_depth_stop *= -1
- # position_end.name = position_end.name + " at -{}m".format(sampling_depth_stop)
- # identifiable, so add even if it is None
- position_end.add_property(name="Sampling depth", value=sampling_depth_stop)
- if not pd.isna(water_depth_stop):
- if water_depth_stop < 0:
- water_depth_stop *= -1
- # identifiable, so add even if it is None
- position_end.add_property(name="Water depth", value=water_depth_stop)
- # position_end.insert(unique=False)
- return [position_start, position_end]
- else:
- return [position_start]
-
-
-def get_gear(data):
- """
- Return the BIS ID of the Gear that is specified by 'Gear' and 'Gear configuration' in data.
-
- If no Such Gear Record exists, a new Gear Record is created.
- """
-
- qtext = f"FIND RECORD '{data['Gear']}'"
- if "Gear configuration" in data and pd.notnull(data["Gear configuration"]):
- qtext += f" WITH 'Configuration'='{data['Gear configuration']}'"
- try:
- res = db.execute_query(qtext, unique=True)
- except db.exceptions.EmptyUniqueQueryError:
- raise DataInconsistencyError(f"The query\n{qtext}\nreturned no results.")
- except db.exceptions.QueryNotUniqueError:
- raise DataInconsistencyError(f"The query\n{qtext}\nreturned more than one result.")
- return res
-
-
-def get_nagoya_case(data):
- """Create and retrun a NagoyaCase Record."""
- nagoya_case_number = return_value_if_not_none(data["Nagoya case number"])
-
- nagoya_case = db.Record(nagoya_case_number)
- nagoya_case.add_parent(name="NagoyaCase")
- nagoya_case.add_property(name="Nagoya Case Number", value=nagoya_case_number)
-
- return nagoya_case
-
-
-def get_person(text) -> db.Record:
- """
- Return the BIS ID of the person that is specifed as 'Main User' or 'Sampling Person' in data.
-
- If the Person is not present in the database, an Exception is raised. Creating new Person Reconrds can only be done by a priviledged user.
- """
- # Check in which format the person is identified:
- person_identifier = text.split(", ")
- if len(person_identifier) == 1:
- person = _get_person_by_abbreviation(person_identifier[0])
- else:
- person = _get_person_by_fullname(person_identifier[1], person_identifier[0])
-
- return person
-
-
-def _get_person_by_fullname(first_name, last_name):
- # seach for person in db
- res = db.execute_query(
- "FIND RECORD Person WITH 'First name' = '{}' AND 'Last name' = '{}'".format(first_name, last_name))
- # if person doesn't exist in database...
- if len(res) == 0:
- # There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
- error_msg = "There is no person Record with 'First name' = '{}' AND 'Last name' = '{}' in the database. ".format(
- first_name, last_name)
- raise DataInconsistencyError(error_msg)
- else:
- return res[0]
-
-
-def _get_person_by_abbreviation(abbreviation):
- # seach for person in db
- res = db.execute_query("FIND RECORD Person WITH 'Abbreviation' = '{}'".format(abbreviation))
- # if person doesn't exist in database...
- if len(res) == 0:
- # There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
- error_msg = "There is no Person Record with Abbreviation = '{}'".format(abbreviation)
- raise DataInconsistencyError(error_msg)
- else:
- return res[0]
-
-
def synchroize(records, additional_property_ents, htmluserlog_public):
crawler = Crawler(securityMode=SecurityMode.UPDATE)
identifiables_definition_file = os.path.expanduser("~/identifiables.yml")
@@ -468,15 +106,6 @@ def update_sample_records(data, htmluserlog_public):
# TODO Check data first and if there are Errors in the data: Provide the user with a download
# link to a template with Error descriptions.
- # Get property ids:
- person_property_id = db.get_entity_by_name("Main User").id
- sampling_person_property_id = db.get_entity_by_name("Sampling Person").id
- nagoya_case_property_id = get_id_of_datatype("NagoyaCase")
- container_property_id = get_id_of_datatype("Container")
- event_property_id = get_id_of_datatype("SourceEvent")
- pdfreport_property_id = get_id_of_datatype("PDFReport")
- parent_sample_property_id = db.get_entity_by_name("Parent Sample").id
-
additional_properties = data.keys().to_list()
additional_property_ids = {} # name-> id
additional_property_ents = {} # name-> Entity
@@ -502,65 +131,21 @@ def update_sample_records(data, htmluserlog_public):
for index, row in data.iterrows():
- sample_id_exists = not pd.isnull(row["BIS ID"])
+ sample_id_exists = not pd.isnull(row[get_column_header_name("entity_id")])
if not sample_id_exists:
raise DataInconsistencyError(f"Missing sample ID in row {index}")
try:
sample = db.execute_query(
- "FIND RECORD Sample WITH id = {}".format(row["BIS ID"]), unique=True)
+ "FIND RECORD Sample WITH id = {}".format(
+ row[get_column_header_name("entity_id")]),
+ unique=True)
except db.exceptions.EmptyUniqueQueryError:
- msg = "There is no Sample with ID = {} in the system.".format(row["BIS ID"])
+ msg = "There is no Sample with ID = {} in the system.".format(
+ row[get_column_header_name("entity_id")])
raise DataInconsistencyError(msg)
- sample = _update_property(entity=sample, property_id=person_property_id,
- property_name="Main User",
- value=get_person(row["Main User"]))
- if "Parent BIS ID" in row and return_value_if_not_none(row["Parent BIS ID"]) is not None:
- sample = _update_property(entity=sample, property_id=parent_sample_property_id,
- value=row["Parent BIS ID"])
- if ("Sampling Person" in row
- and return_value_if_not_none(row["Sampling Person"]) is not None):
- sample = _update_property(entity=sample, property_id=sampling_person_property_id,
- property_name="Sampling Person",
- value=get_person(row["Sampling Person"]))
- if "PI" in row and return_value_if_not_none(row["PI"]) is not None:
- sample = _update_property(entity=sample, property_id=db.get_entity_by_name("PI").id,
- property_name="PI",
- value=get_person(row["PI"]))
- if "Nagoya case number" in row and return_value_if_not_none(row["Nagoya case number"]) is not None:
- sample = _update_property(entity=sample, property_id=nagoya_case_property_id,
- property_name="NagoyaCase",
- value=get_nagoya_case(row))
- if "Storage ID" in row and return_value_if_not_none(row["Storage ID"]) is not None:
- sample = _update_property(entity=sample, property_id=container_property_id,
- property_name="Container",
- value=get_container(row))
- if "Collection" in row and return_value_if_not_none(row["Collection"]) is not None:
- sample = _update_property(entity=sample,
- property_id=db.get_entity_by_name("Collection").id,
- property_name="Collection",
- datatype=db.LIST("Collection"),
- value=[db.Record(name=el)
- .add_parent(name="Collection")
- for el in row["Collection"]])
- if "Sphere" in row and return_value_if_not_none(row["Sphere"]) is not None:
- sample = _update_property(entity=sample,
- property_id=db.get_entity_by_name("Sphere").id,
- property_name="Sphere",
- datatype=db.LIST("Sphere"),
- value=[db.Record(name=el)
- .add_parent(name="Sphere")
- for el in row["Sphere"]])
-
- if "Date collected start" in row and return_value_if_not_none(row["Date collected start"]) is not None:
- sample = _update_property(entity=sample, property_id=event_property_id, property_name='SourceEvent', value=get_event(
- row, get_gear(row)))
- if "PDFReport" in data.columns:
- sample = _update_property(
- entity=sample, property_id=pdfreport_property_id, property_name="PDFReport", value=row["PDFReport"])
- if "Date sampled start" in data.columns:
- sample = _append_times_to_entity(ent=sample, data=row, propname_prefix="Time sampled",
- colname_time_prefix="Time sampled", colname_date_prefix="Date sampled")
+ # All special properties are added here
+ sample = add_special_properties(sample, row)
# Add additional properties
for property_name in additional_property_ids.keys():
@@ -581,12 +166,16 @@ def update_sample_records(data, htmluserlog_public):
name=ent.properties[0].name, value=return_value_if_not_none(row[property_name]))
else:
value = return_value_if_not_none(row[property_name])
- sample = _update_property(
+ sample = update_property(
entity=sample, property_id=additional_property_ids[property_name],
value=value, property_name=property_name)
+ # Now, treat events and event data
+ sample = add_event_to_sample(sample, row)
samples.append(sample)
+ # Samples might need additional post processing
+ samples = post_process_samples(samples, data)
synchroize(samples, additional_property_ents, htmluserlog_public)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
index a23c47a849941e089d81f1b8afccf26e4ef02b98..13a2a1b3f77b0b35573e1c6c3246fab2ac1ff668 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_container_csv.py
@@ -36,18 +36,18 @@ from linkahead.exceptions import (EmptyUniqueQueryError,
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
- send_mail_with_defaults)
+ get_options_row, send_mail_with_defaults)
+from sample_helpers.utils import (CONSTANTS, get_column_header_name,
+ get_entity_name)
# suppress warning of diff function
-apilogger = logging.getLogger("caosdb.apiutils")
+apilogger = logging.getLogger("linkahead.apiutils")
apilogger.setLevel(logging.ERROR)
logger = logging.getLogger("caosadvancedtools")
-CACHE = {}
-
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
def cached_query(query, unique=False):
@@ -66,18 +66,20 @@ def reverse_semicolon_separated_list(value):
def generate_label_text(entity):
- if entity.get_property("Custom label") is not None and entity.get_property("Custom label").value:
- label = entity.get_property("Custom label").value
+ custom_label_prop_name = get_entity_name("custom_label_prop")
+ if entity.get_property(custom_label_prop_name) is not None and entity.get_property(custom_label_prop_name).value:
+ label = entity.get_property(custom_label_prop_name).value
else:
- label = entity.get_property("BIS label").value if entity.get_property(
- "BIS label") is not None else None
+ container_label_prop_name = get_entity_name("container_label_prop")
+ label = entity.get_property(container_label_prop_name).value if entity.get_property(
+ container_label_prop_name) is not None else None
if not label:
if not entity.name:
return entity.id
return f"{entity.id} {entity.name}"
if f"{label}" == f"{entity.id}":
- # prevent special case of BisLabel = BisID resulting in a preview
+ # prevent special case of Label = ID resulting in a preview
# that looks like "id, id".
return entity.id
return f"{entity.id} {label}"
@@ -85,7 +87,9 @@ def generate_label_text(entity):
def extract_parent_container(record, key):
- possible_parents = cached_query(f"FIND Container WHICH REFERENCES {record.id}")
+ possible_parents = cached_query(
+ f"FIND {get_entity_name('container_rt')} WHICH REFERENCES {record.id}"
+ )
values = []
for par in possible_parents:
@@ -96,16 +100,18 @@ def extract_parent_container(record, key):
return reverse_semicolon_separated_list(values)
-def extract_bis_id(record, key):
+def extract_eid(record, key):
return record.id
def extract_custom_label(record, key):
- if record.get_property("Custom label") is not None:
+ custom_label_prop_name = get_entity_name("custom_label_prop")
+
+ if record.get_property(custom_label_prop_name) is not None:
- return record.get_property("Custom label").value
+ return record.get_property(custom_label_prop_name).value
return None
@@ -117,8 +123,9 @@ def extract_pi(record, key):
pi_id = record.get_property("PI").value
pi_rec = cached_query(f"FIND RECORD Person WITH ID={pi_id}", unique=True)
- if pi_rec.get_property("Abbreviation") is not None and pi_rec.get_property("Abbreviation").value is not None:
- return pi_rec.get_property("Abbreviation").value
+ abbr_prop_name = get_entity_name("abbreviation_prop")
+ if pi_rec.get_property(abbr_prop_name) is not None and pi_rec.get_property(abbr_prop_name).value is not None:
+ return pi_rec.get_property(abbr_prop_name).value
return pi_id
return None
@@ -145,11 +152,14 @@ def extract_collection(record, key):
def extract_container_type(record, key):
- if record.get_property("ContainerType") is not None and record.get_property("ContainerType").value is not None:
- ct_id = record.get_property("ContainerType").value
- ctr = cached_query(f"FIND ContainerType WITH ID={ct_id}", unique=True)
- if ctr.get_property("Abbreviation") is not None and ctr.get_property("Abbreviation").value is not None:
- return ctr.get_property("Abbreviation").value
+ abbr_prop_name = get_entity_name("abbreviation_prop")
+ containertype_rt_name = get_entity_name("containertype_rt")
+
+ if record.get_property(containertype_rt_name) is not None and record.get_property(containertype_rt_name).value is not None:
+ ct_id = record.get_property(containertype_rt_name).value
+ ctr = cached_query(f"FIND {containertype_rt_name} WITH ID={ct_id}", unique=True)
+ if ctr.get_property(abbr_prop_name) is not None and ctr.get_property(abbr_prop_name).value is not None:
+ return ctr.get_property(abbr_prop_name).value
return ct_id
return None
@@ -159,7 +169,7 @@ def extract_storage_chain(record, key):
def find_referencing_containers(eid):
containing_containers = []
- candidates = cached_query(f"FIND CONTAINER WHICH REFERENCES {eid}")
+ candidates = cached_query(f"FIND {get_entity_name('container_rt')} WHICH REFERENCES {eid}")
if len(candidates) > 1:
logger.debug(f"Entity {eid} is referenced by more than one container.")
return []
@@ -183,25 +193,25 @@ def default_extractor(record, key):
EXTRACTORS = {
- "BIS ID": extract_bis_id,
- "BIS label": default_extractor,
- "Collection": extract_collection,
- "Container Contents": default_extractor,
- "Container size": default_extractor,
- "Container type": extract_container_type,
- "Custom label": extract_custom_label,
- "PDFReport": default_extractor,
- "PI": extract_pi,
- "Parent container": extract_parent_container,
- "Storage chain": extract_storage_chain,
+ get_column_header_name("entity_id"): extract_eid,
+ get_column_header_name("container_label_prop"): default_extractor,
+ get_column_header_name("Collection"): extract_collection,
+ get_column_header_name("container_size_prop"): default_extractor,
+ get_column_header_name("containertype_rt"): extract_container_type,
+ get_column_header_name("custom_label_prop"): extract_custom_label,
+ get_column_header_name("PDFReport"): default_extractor,
+ get_column_header_name("PI"): extract_pi,
+ get_column_header_name("Parent container"): extract_parent_container,
+ get_column_header_name("Storage chain"): extract_storage_chain,
}
# List of sample properties to be ignored because they are treated
# otherwise. Similar, but not identical to SPECIAL TREATMENT.
IGNORE_KEYS = [
- "Child container", # To be changed by updating the child, not the parent.
- "ContainerType", # handled separately above
- "Responsible", # Not to be changed via upload
+ # To be changed by updating the child, not the parent.
+ get_column_header_name("child_container_prop"),
+ get_column_header_name("containertype_rt"), # handled separately above
+ get_column_header_name("Responsible"), # Not to be changed via upload
]
@@ -225,29 +235,29 @@ def retrieve_containers(data):
container = []
not_found = []
- for bis_id in data:
- if isinstance(bis_id, int):
+ for eid in data:
+ if isinstance(eid, int):
try:
container.append(
cached_query(
- f"FIND RECORD Container WITH id = '{bis_id}'",
+ f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{eid}'",
unique=True))
except EmptyUniqueQueryError as e:
# we want to warn about these
- not_found.append(bis_id)
+ not_found.append(eid)
else:
found_at_least_one_in_range = False
- for next_bis_id in bis_id:
+ for next_eid in eid:
try:
container.append(
cached_query(
- f"FIND RECORD Container WITH id = '{next_bis_id}'",
+ f"FIND RECORD {get_entity_name('container_rt')} WITH id = '{next_eid}'",
unique=True))
found_at_least_one_in_range = True
except EmptyUniqueQueryError as e:
pass
if not found_at_least_one_in_range:
- not_found.append(f"{bis_id.start}-{bis_id.stop-1}")
+ not_found.append(f"{eid.start}-{eid.stop-1}")
return container, not_found
@@ -315,7 +325,7 @@ def main():
with open(args.filename) as form_json:
form_data = json.load(form_json)
- tmp = form_data["bis_ids"].split(",")
+ tmp = form_data["container_ids"].split(",")
data = []
for d in tmp:
if "-" in d:
@@ -355,7 +365,7 @@ def main():
f"{ke}\n\nPlease contact your admin."
)
else:
- msg = "{}export_sample_csv.py was called without the JSON file in args.{}".format(
+ msg = "{} export_container_csv.py was called without the JSON file in args. {}".format(
ERROR_PREFIX, ERROR_SUFFIX)
logger.error(msg)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
index 4f47b48eb46557cc49e5e77d9dcef25a7ac15445..7311fc101929f2012269d4001904c1c34edf3f09 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/export_sample_csv.py
@@ -25,33 +25,30 @@ import logging
import os
import sys
import urllib
-from datetime import date, datetime
-from typing import List
import linkahead as db
import pandas as pd
-from caosadvancedtools.datainconsistency import DataInconsistencyError
from caosadvancedtools.serverside import helper
from caosadvancedtools.table_export import BaseTableExporter
-from caosadvancedtools.table_importer import CSVImporter
-from caoscrawler import Crawler, SecurityMode
-from caoscrawler.crawl import ForbiddenTransaction
-from caoscrawler.identifiable_adapters import CaosDBIdentifiableAdapter
+from caoscrawler.config import get_config_setting
from caoscrawler.logging import configure_server_side_logging
from linkahead.cached import cached_get_entity_by, cached_query as cquery
from linkahead.common.datatype import get_id_of_datatype
from linkahead.exceptions import (EmptyUniqueQueryError, QueryNotUniqueError,
TransactionError)
-from dateutil import parser as dateparser
-from dateutil.parser import isoparse
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
- get_options_row, send_mail_with_defaults,
- SPECIAL_TREATMENT_SAMPLE as SPECIAL_TREATMENT)
+ get_options_row, send_mail_with_defaults)
from export_container_csv import (generate_label_text,
extract_storage_chain as container_storage_chain)
-from upload_sample_template import DATATYPE_DEFINITIONS
+from sample_helpers.sample_registration_get_person_identifier import get_person_identifier_from_rec
+from sample_helpers.sample_upload_column_definitions import (
+ DATATYPE_DEFINITIONS, SPECIAL_TREATMENT_SAMPLE as
+ SPECIAL_TREATMENT, use_custom_names)
+from sample_helpers.utils import (CONSTANTS, get_column_header_name,
+ get_entity_name)
+
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
@@ -59,21 +56,8 @@ apilogger.setLevel(logging.ERROR)
logger = logging.getLogger("caosadvancedtools")
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
-
-
-# Declare mapping of different time/date column names to property names
-TIME_NAME_MAPPINGS = {
- "date collected start": "time start",
- "time collected start": "time start",
- "date collected stop": "time stop",
- "time collected stop": "time stop",
- "date sampled start": "time sampled start",
- "time sampled start": "time sampled start",
- "date sampled stop": "time sampled stop",
- "time sampled stop": "time sampled stop",
-}
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
def cached_record(i):
@@ -91,7 +75,10 @@ def cached_query(query, unique=False):
def reverse_semicolon_separated_list(value):
if isinstance(value, list):
- return ";".join([str(val) for val in value if val is not None])
+ ret_str = ";".join([str(val) for val in value if val is not None])
+ if ',' in ret_str:
+ ret_str = f"\"{ret_str}\""
+ return ret_str
else:
return value
@@ -144,7 +131,7 @@ def extract_value_as_list(record, key):
def extract_storage_id(record, key):
- return extract_value_as_list(record, "Container")
+ return extract_value_as_list(record, get_entity_name("container_rt"))
def extract_pdf_id(record, key):
@@ -152,19 +139,20 @@ def extract_pdf_id(record, key):
return prop.value if prop is not None else None
-def extract_storage_container_label(record, key):
- ids = extract_value_as_list(record, "Container")
- return retrieve_values(ids, 'BIS Label')
-
-
-def extract_nagoya_case_number(record, key):
- ids = extract_value_as_list(record, "NagoyaCase")
- return retrieve_values(ids, key)
-
-
def extract_person(record, key):
ids = extract_value_as_list(record, key)
- return retrieve_values(ids, 'Abbreviation')
+ person_recs = [cached_record(i) for i in ids]
+ return [get_person_identifier_from_rec(r) for r in person_recs]
+
+
+def extract_event_responsible(record_key):
+ evt = retrieve_event(record)
+ if len(evt) == 0:
+ return None
+ elif len(evt) > 1:
+ logger.debug(f"Sample {record.id} references more than one event.")
+ return None
+ return extract_person(evt[0], get_entity_name("responsible_person_event"))
def extract_parent_sample(record, key):
@@ -179,74 +167,14 @@ def extract_reference_name(record, key):
for i in ids if i is not None]
-def retrieve_source_event(record):
- ids = extract_value_as_list(record, 'SourceEvent')
- if record.get_property("SourceEvent") is None:
+def retrieve_event(record):
+ ids = extract_value_as_list(record, get_entity_name("event_rt"))
+ if record.get_property(get_entity_name("event_rt")) is None:
# there are cases where this property is named "Event"
- ids = extract_value_as_list(record, 'Event')
+ ids = extract_value_as_list(record, get_entity_name("event_rt"))
return [cached_record(i) for i in ids]
-def retrieve_gear(record):
- ids = [e.get_property("Gear").value for e in retrieve_source_event(record)
- if e.get_property("Gear") is not None]
- return [cached_query(f"SELECT 'parent', 'Configuration' FROM ENTITY WITH id = '{i}'", unique=True) for i in ids]
-
-
-def extract_gear(record, key):
- return [e.get_parents()[0].name for e in retrieve_gear(record)]
-
-
-def extract_gear_configuration(record, key):
- return [e.get_property("Configuration").value for e in
- retrieve_gear(record)
- if e.get_property("Configuration") is not None]
-
-
-def extract_date_time(record, p):
- if p.lower() == "time start" or p.lower() == "time stop":
- # these are attached to the source event directly
- return [e.get_property(p).value for e in retrieve_source_event(record) if
- e.get_property(p) is not None and e.get_property(p).value is not None]
- else:
- return extract_value_as_list(record, p)
-
-
-def extract_date(record, key):
- if key.lower() in TIME_NAME_MAPPINGS.keys():
- time_key = TIME_NAME_MAPPINGS[key.lower()]
- else:
- time_key = key
- date_times = extract_date_time(record, time_key)
- return [isoparse(t).date().isoformat() for t in date_times]
-
-
-def extract_time(record, key):
- if key.lower() in TIME_NAME_MAPPINGS.keys():
- time_key = TIME_NAME_MAPPINGS[key.lower()]
- else:
- time_key = key
- date_times = extract_date_time(record, time_key)
- return [isoparse(t).time().isoformat() for t in date_times]
-
-
-def extract_time_zone(record, key):
- date_times = extract_date_time(record, "Time start")
- return [isoparse(t).tzname() for t in date_times]
-
-
-def extract_station_number(record, key):
- source_ev = retrieve_source_event(record)
- return [e.get_property(key).value for e in source_ev if
- e.get_property(key) is not None]
-
-
-def extract_station_id(record, key):
- source_ev = retrieve_source_event(record)
- return [e.get_property(key).value for e in source_ev if
- e.get_property(key) is not None]
-
-
def retrieve_positions(source_ev):
pos_ids = extract_value_as_list(source_ev, "Position")
return [cached_record(i) for i in pos_ids]
@@ -258,7 +186,7 @@ def has_parent(r, par):
def extract_position(record, position, component):
- source_evs = retrieve_source_event(record)
+ source_evs = retrieve_event(record)
result = []
for ev in source_evs:
_pos = [pos for pos in retrieve_positions(ev)]
@@ -275,83 +203,113 @@ def extract_position(record, position, component):
return [pos.get_property(component).value for pos in result if pos.get_property(component) is not None]
+def extract_ele_start(record, key):
+ return extract_position(record, get_entity_name("StartPosition"), get_entity_name("elevation"))
+
+
+def extract_ele_stop(record, key):
+ return extract_position(record, get_entity_name("StopPosition"), get_entity_name("elevation"))
+
+
def extract_lat_start(record, key):
- return extract_position(record, "StartPosition", "Latitude")
+ return extract_position(record, get_entity_name("StartPosition"), get_entity_name("latitude"))
def extract_lat_stop(record, key):
- return extract_position(record, "StopPosition", "Latitude")
+ return extract_position(record, get_entity_name("StopPosition"), get_entity_name("latitude"))
def extract_lng_start(record, key):
- return extract_position(record, "StartPosition", "Longitude")
+ return extract_position(record, get_entity_name("StartPosition"), get_entity_name("longitude"))
def extract_lng_stop(record, key):
- return extract_position(record, "StopPosition", "Longitude")
+ return extract_position(record, get_entity_name("StopPosition"), get_entity_name("longitude"))
-def extract_sampling_depth_start(record, key):
- return extract_position(record, "StartPosition", "Sampling depth")
+def extract_linkahead_url(record, key):
+ # base_uri = db.get_config().get("Connection", "url")
+ base_uri = get_config_setting("public_host_url")
+ return urllib.parse.urljoin(base_uri, f"Entity/{record.id}")
-def extract_sampling_depth_stop(record, key):
- return extract_position(record, "StopPosition", "Sampling depth")
+def extract_doi(record, key):
+ source_evs = retrieve_event(record)
+ if len(source_evs) > 1:
+ logger.error(
+ f"Sample {record.id} references more than one event so no unique DOI can be exported.")
+ return None
+ elif len(source_evs) == 0:
+ return None
+ ev = source_evs[0]
+ return ev.get_property(get_entity_name("igsn_doi_prop")).value if ev.get_property("igsn_doi_prop") is not None else None
-def extract_water_depth_start(record, key):
- return extract_position(record, "StartPosition", "Water depth")
+def _extract_event_prop(record, key, ref=False):
+ evt = retrieve_event(record)
+ if len(evt) == 0:
+ return None
+ elif len(evt) > 1:
+ logger.debug(f"Sample {record.id} references more than one event.")
+ return None
-def extract_water_depth_stop(record, key):
- return extract_position(record, "StopPosition", "Water depth")
+ if ref:
+ return extract_reference_name(evt[0], key)
+ return extract_value_as_list(evt[0], key)
-def extract_source_event_name(record, key):
- return [e.name for e in retrieve_source_event(record)]
+def extract_biome(record, key):
-def extract_hol(record, key):
- source_ev = retrieve_source_event(record)
- return [e.get_property(key).value for e in source_ev if
- e.get_property(key) is not None]
+ return _extract_event_prop(record, get_entity_name("Biome"), ref=True)
-def extract_bis_url(record, key):
- # base_uri = db.get_config().get("Connection", "url")
- base_uri = "https://biosamples.geomar.de/"
- return urllib.parse.urljoin(base_uri, f"Entity/{record.id}")
+def extract_campaign(record, key):
+ return _extract_event_prop(record, get_entity_name("Campaign"), ref=True)
-def extract_igsn(record, key):
- source_evs = retrieve_source_event(record)
- if len(source_evs) > 1:
- logger.error(
- f"Sample {record.id} references more than one SourceEvent so no unique IGSN can be exported.")
- return None
- elif len(source_evs) == 0:
- return None
- ev = source_evs[0]
- return ev.get_property(key).value if ev.get_property(key) is not None else None
+def extract_device(record, key):
-def extract_doi(record, key):
- source_evs = retrieve_source_event(record)
- if len(source_evs) > 1:
- logger.error(
- f"Sample {record.id} references more than one SourceEvent so no unique DOI can be exported.")
- return None
- elif len(source_evs) == 0:
- return None
- ev = source_evs[0]
- return ev.get_property("DOI").value if ev.get_property("DOI") is not None else None
+ return _extract_event_prop(record, get_entity_name("Device"), ref=True)
+
+
+def extract_end_date(record, key):
+
+ return _extract_event_prop(record, get_entity_name("end_date_prop"))
+
+
+def extract_start_date(record, key):
+
+ return _extract_event_prop(record, get_entity_name("start_date_prop"))
+
+
+def extract_level(record, key):
+
+ return _extract_event_prop(record, get_entity_name("level"))
+
+
+def extract_sphere(record, key):
+
+ return _extract_event_prop(record, get_entity_name("Sphere"), ref=True)
+
+
+def extract_locality_descr(record, key):
+
+ return _extract_event_prop(record, get_entity_name("locality_description_prop"))
+
+
+def extract_locality_name(record, key):
+
+ return _extract_event_prop(record, get_entity_name("locality_name_prop"))
def extract_storage_chain(record, key):
- if record.get_property("Container") is not None and record.get_property("Container").value:
+ if record.get_property(get_entity_name("container_rt")) is not None and record.get_property(get_entity_name("container_rt")).value:
- cont_id = record.get_property("Container").value
+ cont_id = record.get_property(get_entity_name("container_rt")).value
if isinstance(cont_id, list):
if len(cont_id) > 1:
logger.debug(f"Sample {record.id} has multiple containers.")
@@ -368,103 +326,71 @@ def extract_storage_chain(record, key):
def extract_event_url(record, key):
- events = retrieve_source_event(record)
+ events = retrieve_event(record)
if not events:
return None
if len(events) == 1:
- return urllib.parse.urljoin("https://biosamples.geomar.de", f"Entity/{events[0].id}")
+ return urllib.parse.urljoin(get_config_setting("public_host_url"), f"Entity/{events[0].id}")
logger.debug(f"Sample {record.id} has multiple events.")
return None
-# must be same keys as SPECIAL_TREATMENT
-EXTRACTORS = {
- "BIS ID": lambda record, key: record.id,
- "Parent BIS ID": extract_parent_sample,
- "AphiaID": default_find,
- "Collection": extract_reference_name,
- "Date collected start": extract_date,
- "Date collected stop": extract_date,
- "Date sampled start": extract_date,
- "Date sampled stop": extract_date,
+# must include all keys from SPECIAL_TREATMENT
+EXTRACTORS = use_custom_names({
+ "entity_id": lambda record, key: record.id,
"Main User": extract_person,
- "Sampling Person": extract_person,
- "PI": extract_person,
- "Person": extract_person,
- "Gear": extract_gear,
- "Gear configuration": extract_gear_configuration,
+ "Biome": extract_biome,
+ "Campaign": extract_campaign,
+ "Collector": extract_person,
+ "Curator": extract_person,
+ "Device": extract_device,
+ "Elevation start": extract_ele_start,
+ "Elevation stop": extract_ele_stop,
+ "Embargo": default_find,
+ "End date": extract_end_date,
"Latitude start": extract_lat_start,
- "Longitude start": extract_lng_start,
- "Storage ID": extract_storage_id,
- "Nagoya case number": extract_nagoya_case_number,
- "PDFReport": extract_pdf_id,
- "Subevent": extract_source_event_name,
- "Time collected start": extract_time,
- "Time collected stop": extract_time,
- "Time sampled start": extract_time,
- "Time sampled stop": extract_time,
- "Timezone": extract_time_zone,
- "Station ID": extract_station_id,
- "Station number": extract_station_number,
- "Sampling depth start": extract_sampling_depth_start,
- "Sampling depth stop": extract_sampling_depth_stop,
- "Water depth start": extract_water_depth_start,
- "Water depth stop": extract_water_depth_stop,
"Latitude stop": extract_lat_stop,
+ "Level": extract_level,
+ "LinkAhead URL": extract_linkahead_url,
+ "Longitude start": extract_lng_start,
"Longitude stop": extract_lng_stop,
- "Storage chain": extract_storage_chain,
- "Storage Container Label": extract_storage_container_label,
- "Hol": extract_hol,
+ "PDFReport": extract_pdf_id,
"Sampling method": default_find,
- # "Publications": TODO never used
- # "NCBI BioProject": TODO never used
- # "NCBI BioSample": TODO never used
- # "NCBI Accession": TODO never used
- "BIS URL": extract_bis_url,
- "IGSN": extract_igsn,
- "IGSN URL": extract_doi,
- "Sphere": default_find,
- "URL SourceEvent": extract_event_url,
-}
-
-REVERSE_COLUMN_CONVERTER = {
- "Collection": collection_value,
- "PI": person_value,
- "Person": person_value,
-}
+ "Sphere": extract_sphere,
+ "Start date": extract_start_date,
+ "Storage ID": extract_storage_id,
+ "Storage chain": extract_storage_chain,
+ "URL Event": extract_event_url,
+ "igsn_doi_prop": extract_doi,
+ "locality_description_prop": extract_locality_descr,
+ "locality_name_prop": extract_locality_name,
+ "parent_sample_prop": extract_parent_sample,
+ "responsible_person_event": extract_event_responsible
+})
+
+REVERSE_COLUMN_CONVERTER = use_custom_names({
+})
# List of sample properties to be ignored because they are treated
# otherwise. Similar, but not identical to SPECIAL TREATMENT.
-IGNORE_KEYS = [
- "NagoyaCase",
- "Parent Sample",
- "Container",
- "SourceEvent",
- "Event",
- "Date",
- "Sampling depth",
- "Water depth"
-]
+IGNORE_KEYS = use_custom_names([
+ "parent_sample_prop",
+ "container_rt",
+ "event_rt",
+])
# Additional list of keys to be ignored when extracting parent sample information
-IGNORE_KEYS_PARENT = IGNORE_KEYS + [
- "BIS ID",
-]
+IGNORE_KEYS_PARENT = IGNORE_KEYS + use_custom_names([
+ "entity_id",
+])
# List of columns to be exported although they are not known to or ignored by
# the import.
-ADDITIONAL_EXPORTS = [
- "BIS URL",
- "Date sampled start",
- "Date sampled stop",
- "IGSN URL",
- "IGSN",
- "Parent BIS ID",
+ADDITIONAL_EXPORTS = use_custom_names([
+ "LinkAhead URL",
+ "parent_sample_prop",
"Storage chain",
- "Time sampled start",
- "Time sampled stop",
- "URL SourceEvent"
-]
+])
def extract_value(r, e):
@@ -593,25 +519,25 @@ def to_csv(samples):
def retrieve_samples(data):
container = []
not_found = []
- for bis_id in data:
- if isinstance(bis_id, int):
+ for eid in data:
+ if isinstance(eid, int):
try:
container.append(
- cached_get_entity_by(query=f"FIND RECORD SAMPLE WITH id='{bis_id}'"))
+ cached_get_entity_by(query=f"FIND RECORD SAMPLE WITH id='{eid}'"))
except EmptyUniqueQueryError as e:
# we want to warn about these
- not_found.append(bis_id)
+ not_found.append(eid)
else:
found_at_least_one_in_range = False
- for next_bis_id in bis_id:
+ for next_eid in eid:
try:
container.append(
- cached_get_entity_by(query=f"FIND RECORD Sample WITH id='{next_bis_id}'"))
+ cached_get_entity_by(query=f"FIND RECORD Sample WITH id='{next_eid}'"))
found_at_least_one_in_range = True
except EmptyUniqueQueryError as e:
pass
if not found_at_least_one_in_range:
- not_found.append(f"{bis_id.start}-{bis_id.stop-1}")
+ not_found.append(f"{eid.start}-{eid.stop-1}")
return container, not_found
@@ -679,19 +605,6 @@ def main():
logger.info("Removing empty columns from export")
no_empty_columns = True
- if "from_date" in form_data:
- # Inserted after ...
- data = [el.id for el in db.execute_query(
- "SELECT id FROM sample WHICH REFERENCES A SourceEvent "
- "WHICH HAS AN IGSN AND "
- f"(WHICH WAS INSERTED SINCE {form_data['from_date']})")
- ]
- # ... + update after
- data += [el.id for el in db.execute_query(
- "SELECT id FROM sample WHICH REFERENCES A SourceEvent "
- "WHICH HAS AN IGSN AND "
- f"(WHICH WAS UPDATED SINCE {form_data['from_date']})")
- ]
elif "query_string" in form_data and form_data["query_string"]:
query_string = form_data["query_string"]
if not query_string.lower().startswith("find ") and not query_string.lower().startswith("select "):
@@ -710,11 +623,11 @@ def main():
)
return
else:
- if not form_data["bis_ids"]:
+ if not form_data["ids"]:
logger.error(
"Please specify the samples to be exported either by query or by id(s).")
return
- tmp = form_data["bis_ids"].split(",")
+ tmp = form_data["ids"].split(",")
data = []
for d in tmp:
if "-" in d:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
index f64e9341540ccc81506f1878c4f1c3048f21da43..fb6bd65d6f784188eff9330dc8367d7415cf8e00 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_containers.py
@@ -23,23 +23,26 @@
#
import csv
-import datetime
import json
import logging
import sys
-import caosdb as db
+import linkahead as db
from caosadvancedtools.serverside import helper
from caosadvancedtools.serverside.logging import configure_server_side_logging
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
get_options_row, send_mail_with_defaults)
+from sample_helpers.container_name import get_container_name_prefix
+from sample_helpers.container_registration_identifier import get_container_identifier
+from sample_helpers.container_registration_post_processing import (
+ post_process_containers, post_process_parent_container)
+from sample_helpers.utils import CONSTANTS, get_column_header_name, get_entity_name
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
-BIS_URL = 'https://biosamples.geomar.de/Entity/'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
logger = logging.getLogger("caosadvancedtools")
@@ -50,125 +53,95 @@ def get_parser():
return par
-def get_current_year():
- currentDateTime = datetime.datetime.now()
- date = currentDateTime.date()
- year = date.strftime("%Y")
- return year
-
-
-def get_abbreviation(id):
- try:
- rd = db.execute_query("FIND {}".format(id))[0]
- return rd.get_property("Abbreviation").value
- except:
- entity_url = BIS_URL + str(id)
- logger.error('{}There was a problem while querying for the abbreviation of <a href="{}">this BIS Entity</a>.{}'.format(
- ERROR_PREFIX, entity_url, ERROR_SUFFIX))
-
-
def create_new_label_counter(container_type_id, value=1):
counter = db.Record()
- counter.add_parent(name="LabelCounter")
- counter.add_property(name="Counter", value=value)
- counter.add_property(name="ContainerType", value=container_type_id)
+ counter.add_parent(name=get_entity_name("labelcounter_rt"))
+ counter.add_property(name=get_entity_name("labelcounter_prop"), value=value)
+ counter.add_property(name=get_entity_name("containertype_rt"), value=container_type_id)
counter.insert()
def get_label_counter(container_type_id):
counter = db.execute_query(
- "FIND LabelCounter WITH ContainerType = {}".format(container_type_id))
+ f"FIND '{get_entity_name('labelcounter_rt')}' WITH "
+ f"'{get_entity_name('containertype_rt')}' = {container_type_id}"
+ )
if len(counter) == 0:
create_new_label_counter(container_type_id)
return 1
else:
- return counter[0].get_property("Counter").value
+ return counter[0].get_property(get_entity_name("labelcounter_prop")).value
def set_label_counter(container_type_id, value):
counter = db.execute_query(
- "FIND LabelCounter WITH ContainerType = {}".format(container_type_id))
+ f"FIND '{get_entity_name('labelcounter_rt')}' WITH "
+ f"'{get_entity_name('containertype_rt')}' = {container_type_id}"
+ )
if len(counter) == 0:
create_new_label_counter(container_type_id, value)
else:
try:
- counter[0].get_property("Counter").value = value
+ counter[0].get_property(get_entity_name("labelcounter_prop")).value = value
counter.update()
except:
logger.error('{}There was an error when updating the internal label counter {}.{}'.format(
ERROR_PREFIX, counter[0], ERROR_SUFFIX))
-def get_bis_label_prefix(responsible_entity):
- """
- @return The prefix for the BIS Label, i.e. the BIS lable without the container number.
- """
- try:
- if responsible_entity.get_parent("Person") is not None:
- research_unit = db.execute_query("FIND ResearchUnit WITH id = {}".format(
- responsible_entity.get_property("ResearchUnit").value))[0]
- return "{}_{}_{}".format(get_bis_label_prefix(research_unit), get_abbreviation(responsible_entity.id), get_current_year())
- elif responsible_entity.get_parent("ResearchUnit") is not None:
- research_division = db.execute_query("FIND ResearchDivision WITH id = {}".format(
- responsible_entity.get_property("ResearchDivision").value))[0]
- return "{}_{}".format(get_bis_label_prefix(research_division), get_abbreviation(responsible_entity.id))
- else:
- return "{}".format(get_abbreviation(responsible_entity.id))
- except:
- logger.error('{}The system could not auto-generate the BIS Label for {}.{}'.format(
- ERROR_PREFIX, responsible_entity, ERROR_SUFFIX))
+def create_container_entities(responsible_id, container_type_id, container_size, number_of_containers, parent_container):
+ """Create the container entities specified via the "Register
+ Containers" form in the web interface.
+ Returns
+ -------
+ conts : db.Container
+ A container of the newly registered container entities.
-def create_container_entities(responsible_id, container_type_id, container_size, number_of_containers, parent_container):
"""
- Create the BIS Entities specified via the "Register Containers" Form in
- ext_bis_stockmanagement.js.
- @return A list of the newly registered entities."""
# Create Batch for insert
batch = db.Container()
# Get BIS Label for responsible person
responsible_entity = db.execute_query("FIND {}".format(responsible_id))[0]
- container_type_abbreviation = get_abbreviation(container_type_id)
- bis_label_prefix = get_bis_label_prefix(responsible_entity)
+ bis_label_prefix = get_container_name_prefix(responsible_id, container_type_id)
bis_label_counter = get_label_counter(container_type_id)
for i in range(number_of_containers):
- bis_label = "{}_{}_{}".format(
- bis_label_prefix, container_type_abbreviation, bis_label_counter + i)
+ bis_label = f"{bis_label_prefix}_{bis_label_counter+i}"
container = db.Record(bis_label)
- container.add_parent(name="Container")
- container.add_property(name="Responsible", value=responsible_id)
- container.add_property(name="ContainerType", value=container_type_id)
- container.add_property(name="Container size", value=container_size)
- container.add_property(name="BIS label", value=bis_label)
- container.add_property(name="Child container", value=[])
+ container.add_parent(name=get_entity_name("container_rt"))
+ container.add_property(name=get_entity_name("responsible_rt"), value=responsible_id)
+ container.add_property(name=get_entity_name("containertype_rt"), value=container_type_id)
+ container.add_property(name=get_entity_name("container_size_prop"), value=container_size)
+ container.add_property(name=get_entity_name("child_container_prop"), value=[])
batch += [container]
+
+ # Post process child containers
+ batch = post_process_containers(batch)
try:
batch.insert()
- for ent in batch:
- ent.retrieve_acl()
- ent.grant(role='Stock Manager', priority=False, permission="EDIT:ACL")
- ent.update_acl()
- except:
- logger.error("{}The registered containers could not be imported to the system.{}".format(
+ except Exception as e:
+ logger.error("{} The registered containers could not be imported to the system. {}".format(
ERROR_PREFIX, ERROR_SUFFIX))
+ logger.error(e)
return None
# TODO: Reset the internal_container_label_counter of person to its previous value if nothing has be inserted
# Add to parent container
if parent_container is not None:
+ child_cont_prop = db.Property(name=get_entity_name("child_container_prop")).retrieve()
new_childs = []
for entity in batch:
new_childs += [entity.id]
# Check if property Child container exists:
- if parent_container.get_property("Child container") is None:
- child_cont_prop = db.Property(name="Child container").retrieve()
+ if parent_container.get_property(child_cont_prop.name) is None:
parent_container.add_property(id=child_cont_prop.id, value=new_childs)
else:
# Check if the container allready has childs
- if parent_container.get_property("Child container").value is None:
- parent_container.get_property("Child container").value = new_childs
+ if parent_container.get_property(child_cont_prop.name).value is None:
+ parent_container.get_property(child_cont_prop.name).value = new_childs
else:
- parent_container.get_property("Child container").value += new_childs
+ parent_container.get_property(child_cont_prop.name).value += new_childs
+ parent_container = post_process_parent_container(parent_container)
parent_container.update()
set_label_counter(container_type_id=container_type_id,
@@ -187,7 +160,10 @@ def get_parent_container(id):
parent = db.execute_query("FIND {}".format(id))[0]
return parent
except:
- logger.info("No parent container specified. The BIS ID or BIS label of the parent container has to be entered in the template before it is uploaded.")
+ logger.info(
+ "No parent container specified. The Contianer ID or label of the "
+ "parent container has to be entered in the template before it is uploaded."
+ )
return None
@@ -204,21 +180,23 @@ def create_csv_template(template_internal_path, container_entities, container_ty
if parent_container is None:
parent_container_label = ""
else:
- parent_container_label = parent_container.get_property("BIS label").value
+ parent_container_label = get_container_identifier(parent_container)
with open(template_internal_path, 'w') as template_csv:
writer = csv.writer(template_csv)
# Write header
headers = [
- "BIS ID",
- "Container type",
- "Container size",
- "BIS label",
+ "entity_id",
+ "container_type_rt",
+ "container_size_prop",
+ "container_label",
"PI",
"Collection",
"Parent container",
"Custom label",
"Container Contents",
- "PDFReport"]
+ "PDFReport"
+ ]
+ headers = [get_column_header_name(header) for header in headers]
writer.writerow(headers)
# Write description with leading '#'
descriptions = get_description_row(headers)
@@ -233,7 +211,7 @@ def create_csv_template(template_internal_path, container_entities, container_ty
entity.id,
container_type.name,
container_size,
- entity.get_property("BIS label").value,
+ get_container_identifier(entity),
"",
"",
parent_container_label,
@@ -287,8 +265,6 @@ def main():
template_name = get_template_name(container_entities, file_format_extension)
template_display_path, template_internal_path = helper.get_shared_filename(
template_name)
- logger.info("Internal path: {}, Display path: {}".format(
- template_internal_path, template_display_path))
if (file_format_extension == "csv"):
create_csv_template(
template_internal_path=template_internal_path,
diff --git a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
index 7724b577012ee3592a8de12a987b3f16054f6559..15e22bd9c17a67098519e38f6fc8f9c976f09718 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/register_new_samples.py
@@ -11,10 +11,13 @@ from caosadvancedtools.serverside.logging import configure_server_side_logging
from bis_utils import (create_email_with_link_text,
get_description_row, get_email_from_username,
get_options_row, send_mail_with_defaults)
+from sample_helpers.sample_registration_get_person_identifier import get_person_identifier
+from sample_helpers.sample_registration_post_processing import post_process_samples
+from sample_helpers.utils import CONSTANTS, get_column_header_name, get_entity_name
+
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
-BIS_URL = 'https://localhost:10443/Entity/'
logger = logging.getLogger("caosadvancedtools")
@@ -23,58 +26,28 @@ def get_parser():
return par
-def get_responsible_person_id(data):
- return int(data["responsible_person"])
-
-
-def get_responsible_person_abbreviation(data):
- person = db.execute_query("FIND {}".format(get_responsible_person_id(data)))[0]
- return person.get_property("Abbreviation").value
-
-
-def get_number_of_samples(data):
- return int(data["number_of_samples"])
-# def is_samples_from_cruise(data):
-# return ("samples_from_cruise" in data and data["samples_from_cruise"] == "on")
-# def has_start_and_end_time(data):
-# return ("start_and_end_time" in data and data["start_and_end_time"] == "on")
-# def get_number_of_locations(data):
-# number_of_locations = int(data["number_of_locations"])
-# if number_of_locations < 1:
-# number_of_locations = 1 # At least one location is OBLIGATORY
-# return number_of_locations
-
-
-def get_reference_properties(data):
- return data["reference_properties"]
-
-
def get_column_names(data):
# Make sure each header starts with BIS ID and Main User
- starting_names = ["BIS ID", "Main User"]
+ starting_names = [get_column_header_name(name) for name in ["entity_id", "Main User"]]
# required_column_names is just a string of column names separated by
# commas.
other_names = data["required_column_names"].split(',') + data["column_names"]
starting_names.extend([name.strip()
for name in other_names if name.strip() not in starting_names])
- return starting_names
+ return [get_column_header_name(name) for name in starting_names]
def create_sample_entities(data):
- responsible_person_id = get_responsible_person_id(data)
- number_of_samples = get_number_of_samples(data)
- add_state = len(db.execute_query("FIND 'Sample life-cycle'"))
+ responsible_person_id = int(data["responsible_person"])
+ number_of_samples = int(data["number_of_samples"])
batch = db.Container()
for index in range(number_of_samples):
sample = db.Record()
- sample.add_parent(name="Sample")
- sample.add_property(name="Main User", value=responsible_person_id)
- sample.add_property("Container")
- sample.add_property("NagoyaCase")
- if add_state:
- sample.state = db.State(name="Registered", model="Sample life-cycle")
+ sample.add_parent(name=get_entity_name("Sample"))
+ sample.add_property(name=get_entity_name("Main User"), value=responsible_person_id)
batch += [sample]
+ batch = post_process_samples(batch)
batch.insert()
return batch
@@ -119,12 +92,8 @@ def read_input(args, log=False):
def create_csv_template(template_name, samples, form_input):
template_display_path, template_internal_path = helper.get_shared_filename(template_name)
# Read form_input
- responsible_person_abbreviation = get_responsible_person_abbreviation(form_input)
- number_of_samples = get_number_of_samples(form_input)
- # samples_from_cruise = is_samples_from_cruise(form_input)
- # start_and_end_time = has_start_and_end_time(form_input)
- # number_of_locations = get_number_of_locations(form_input)
- # reference_properties = get_reference_properties(form_input)
+ responsible_person_abbreviation = get_person_identifier(form_input)
+ number_of_samples = int(form_input["number_of_samples"])
header = get_column_names(form_input)
with open(template_internal_path, 'w') as csv_template:
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
new file mode 100644
index 0000000000000000000000000000000000000000..efcab85761fe841ff23dec3be219d62fcee3f3e7
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_name.py
@@ -0,0 +1,67 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+"""This module serves a function that generates a human-readable
+container name or label.
+
+"""
+
+import linkahead as db
+
+from .utils import get_entity_name
+
+
+def get_record_string(rec: db.Record) -> str:
+
+ if rec.get_property(get_entity_name("abbreviation_prop")) is not None and rec.get_property(get_entity_name("abbreviation_prop")).value:
+ return rec.get_property(get_entity_name("abbreviation_prop")).value
+
+ if rec.name:
+ return rec.name
+
+ return ""
+
+
+def get_container_name_prefix(responsible_id: int, container_type_id: int) -> str:
+ """Generate a container name prefix from the container type and
+ the responsible entity.
+
+ Parameters
+ ----------
+ responsible_id : int
+ LinkAhead id of the responsible entity (person, research
+ institution, ...)
+ container_type_id: int
+ LinkAhead id of the ContainerType Record corresponding to the
+ type of the given container.
+
+ Returns
+ -------
+ container_name_prefix : str
+ Name in the format `<responsible>_<container_type_name>`
+
+ """
+ resp = db.cached.cached_get_entity_by(eid=responsible_id)
+ ct = db.cached.cached_get_entity_by(eid=container_type_id)
+
+ resp_str = get_record_string(resp)
+ ct_str = get_record_string(ct)
+
+ if resp_str:
+ return f"{resp_str}_{ct_str}"
+
+ return ct_str
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_identifier.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_identifier.py
new file mode 100644
index 0000000000000000000000000000000000000000..52943d77a2ac4189120a8161d0f61cb81a090add
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_identifier.py
@@ -0,0 +1,43 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from .utils import get_entity_name
+
+
+def get_container_identifier(cont: db.Record) -> str:
+ """Return an identifier string that uniquely identifies the given
+ container entity in a registration/upload/export table file.
+
+ Parameters
+ ----------
+ cont : db.Record
+ The container record to be identified.
+
+ Returns
+ -------
+ identifier : str
+ The identifying string that uniquly identifies the given
+ container.
+ """
+ if (cont.get_property(get_entity_name("container_label_prop")) is not None and
+ cont.get_property(get_entity_name("container_label_prop")).value):
+ return cont.get_property(get_entity_name("container_label_prop")).value
+ elif cont.name:
+ return cont.name
+ return cont.id
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_post_processing.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_post_processing.py
new file mode 100644
index 0000000000000000000000000000000000000000..8ab70ba108910651decd80d7a5b34a9b60e95edd
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_registration_post_processing.py
@@ -0,0 +1,53 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+
+def post_process_containers(conts: db.Container):
+ """Dummy function to be overwritten by custom code if desired.
+
+ Parameters
+ ----------
+ conts : db.Container
+ Container of container entities to be post-processed.
+
+ Returns
+ -------
+ conts : db.Container
+ Container of post-processed container entities to be inserted.
+ """
+
+ return conts
+
+
+def post_process_parent_container(parent: db.Record):
+ """Dummy function to be overwritten by custom code if desired.
+
+ Parameters
+ ----------
+ parent : db.Record
+ parent container entitiy to be post-processed.
+
+ Returns
+ -------
+ parent : db.Record
+ Post-processed parent container entity to be
+ updated.
+ """
+
+ return parent
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_get_parent.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_get_parent.py
new file mode 100644
index 0000000000000000000000000000000000000000..4d11a3b74453298e13b2185ac4fbcf5650f2bb0f
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_get_parent.py
@@ -0,0 +1,35 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from .utils import get_entity_name
+
+
+def get_container_by_identifier(identifier: str) -> db.Record:
+ """Return a container identified by the given string identifier."""
+ # First try (integer) ID
+ try:
+ identifier = int(identifier)
+ query = f"FIND '{get_entity_name('container_rt')}' WITH ID={identifier}"
+ except ValueError:
+ # Then fall back to name or label
+ query = (f"FIND '{get_entity_name('container_rt')}' WITH "
+ f"name='{identifier}' OR WITH "
+ f"'{get_entity_name('container_label_prop')}'='{identifier}'")
+
+ return db.cached.cached_query(query)
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_post_processing.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_post_processing.py
new file mode 100644
index 0000000000000000000000000000000000000000..e8f696b7c6fbe6352fe618d37a138ac796614cd3
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/container_update_post_processing.py
@@ -0,0 +1,33 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+
+def post_process_containers_before_sync(child_containers):
+
+ return child_containers
+
+
+def post_process_parent_containers_before_sync(parent_containers):
+
+ return parent_containers
+
+
+def post_process_inserts_and_updates(inserts, updates):
+
+ return inserts, updates
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
new file mode 100644
index 0000000000000000000000000000000000000000..c575cb61f4cbd50676d8b944f7af7631963907bf
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/default_constants.yml
@@ -0,0 +1,79 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+csv_column_names:
+ entity_id: "LinkAhead ID"
+ custom_label_prop: "Custom Label"
+ start_date_prop: "Start date"
+ end_date_prop: "End date"
+ igsn_doi_prop: "IGSN DOI"
+ locality_description_prop: "Locality description"
+ locality_name_prop: "Locality name"
+ responsible_person_event: "Event responsible"
+ parent_sample_prop: "Parent LinkAhead ID"
+
+csv_column_descriptions:
+ LinkAhead ID: "An ID generated by LinkAhead (either integer or URL to this entity). Do not change this column!"
+ container_label: "The label automatically assigned by LinkAhead sample management. Do not change this column."
+ Collection: "Collection(s) to which this container or samples belongs (separated by ';')"
+ Container Contents: "Notes concerning the contents of this container"
+ Container size: "The size of the container (e.g 81 spaces)"
+ Container type: "The type of container. Do not change this column."
+ Custom label: "Any additional custom label you put on the container"
+ Date start: "The start date or datetime in ISO format"
+ Date stop: "The end date or datetime in ISO format"
+ Gear configuration: "How gear is configured, meshsize of the net, filter pore size, what kind of trawl"
+ Latitude start: "Latitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for S"
+ Latitude stop: "Latitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for S"
+ Longitude start: "Longitude where sampling started; in decimal degrees,use \".\" as decimal sign, use - for W"
+ Longitude stop: "Longitude where sampling ended; in decimal degrees,use \".\" as decimal sign, use - for W"
+ Notes / remarks: "Field for notes"
+ PDFReport: "A PDF containing additional information on the container or sampe contents"
+ PI: "The PI (by abbreviation) of the container or sample"
+ Parent container: "The LinkAhead ID (integer or URL) or name or BIS label of the container where this container is stored."
+ Sampling depth start: "The depth in meters where the sampling started as a positive value, not bottom depth"
+ Sampling depth stop: "The depth in meters where the sampling ended as a positive value,not bottom depth"
+ Storage ID: "LinkAhead ID of the Container that holds this sample"
+ Subevent: "Subevent given by D-Ship in Stationlog. Expl. AL123_14-4"
+ Timezone: "Timezone: Either UTC, CET, .... or in the form +hh[:mm], -hh:[mm]."
+ Water depth start: "The bottom depth in meters where the sampling started as a positive value"
+ Water depth stop: "The bottom depth in meters where the sampling ended as a positive value"
+
+entity_names:
+ abbreviation_prop: abbreviation
+ child_container_prop: "Child_Container"
+ container_label_prop: container_label
+ container_rt: Container
+ container_size_prop: "Container size"
+ containertype_rt: ContainerType
+ custom_label_prop: custom_label
+ end_date_prop: end_date
+ event_rt: Event
+ first_name_prop: first_name
+ igsn_doi_prop: igsn_doi
+ labelcounter_prop: counter
+ labelcounter_rt: LabelCounter
+ last_name_prop: last_name
+ parent_sample_prop: Parent_sample
+ responsible_rt: Responsible
+ start_date_prop: start_date
+ locality_description_prop: locality_description
+ locality_name_prop: locality_name
+ responsible_person_event: Responsible_Person
+
+error_prefix: "Something went wrong:"
+error_suffix: "Please contact your administrator(s)."
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py
new file mode 100644
index 0000000000000000000000000000000000000000..396bf0ef054275f901fb6fa6056dc95e6a624516
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_get_person_identifier.py
@@ -0,0 +1,49 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from .utils import get_entity_name
+
+
+def get_person_identifier(form_data: dict) -> str:
+ """Retrieve a person record from the given id, and replace by
+ abbreviation if present, else "last name, first name".
+
+ """
+ person_rec = db.cached.cached_get_entity_by(eid=form_data["responsible_person"])
+
+ return get_person_identifier_from_rec(person_rec)
+
+
+def get_person_identifier_from_rec(person_rec: db.Record) -> str:
+ # Use abbreviation if present
+ if (person_rec.get_property(get_entity_name("abbreviation_prop")) is not None and
+ person_rec.get_property(get_entity_name("abbreviation_prop")).value):
+ return person_rec.get_property(get_entity_name("abbreviation_prop")).value
+ first_name = person_rec.get_property(get_entity_name("first_name_prop")).value if person_rec.get_property(
+ get_entity_name("first_name_prop")) is not None else ""
+ last_name = person_rec.get_property(get_entity_name("last_name_prop")).value if person_rec.get_property(
+ get_entity_name("last_name_prop")) is not None else ""
+ # Else use first and last name ...
+ if first_name and last_name:
+ return f"{last_name}, {first_name}"
+ # ... or just last name if no first name
+ if last_name:
+ return last_name
+ # Last fallback id
+ return person_rec.id
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_post_processing.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_post_processing.py
new file mode 100644
index 0000000000000000000000000000000000000000..6d8fe9d623dc644423006b00a1b271330ffb5871
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_registration_post_processing.py
@@ -0,0 +1,26 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+
+def post_process_samples(samples: db.Container) -> db.Container:
+ """Post process the container of samples to be registerd before
+ they are inserted. Dummy function to be overwritten.
+
+ """
+ return samples
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
new file mode 100644
index 0000000000000000000000000000000000000000..9ec2fffef113f842440b1907f153b0e01cbe5050
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_add_special_properties.py
@@ -0,0 +1,78 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+import pandas as pd
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .sample_upload_get_container import get_container
+from .sample_upload_get_device import get_device
+from .sample_upload_get_person import get_person
+from .utils import get_column_header_name, get_entity_name, update_property, return_value_if_not_none
+
+
+def add_special_properties(sample: db.Record, data: pd.Series) -> db.Record:
+ """This function adds all the properties that can not be added
+ trivially from the given data row to the sample.
+
+ """
+
+ main_user_prop = db.get_entity_by_name(get_entity_name("Main User"))
+ pi_prop = db.get_entity_by_name(get_entity_name("PI"))
+ container_rt = db.get_entity_by_name(get_entity_name("container_rt"))
+ device_rt = db.get_entity_by_name(get_entity_name("Device"))
+ parent_sample_prop = db.get_entity_by_name(get_entity_name("parent_sample_prop"))
+
+ if (get_column_header_name("PI") in data and
+ return_value_if_not_none(data[get_column_header_name("PI")]) is not None):
+ pi_user = get_person(return_value_if_not_none(data[get_column_header_name("PI")]))
+ sample = update_property(sample, pi_prop.id, pi_user, property_name=pi_prop.name)
+
+ if (get_column_header_name("Main User") in data and
+ return_value_if_not_none(data[get_column_header_name("Main User")]) is not None):
+ main_user = get_person(return_value_if_not_none(data[get_column_header_name("Main User")]))
+ sample = update_property(sample, main_user_prop.id, main_user, property_name=main_user_prop.name)
+
+ if (get_column_header_name("Storage ID") in data and
+ return_value_if_not_none(data[get_column_header_name("Storage ID")]) is not None):
+ container = get_container(return_value_if_not_none(
+ data[get_column_header_name("Storage ID")]))
+ sample = update_property(sample, container_rt.id, container, property_name=container_rt.name)
+
+ if (get_column_header_name("Device") in data and
+ return_value_if_not_none(data[get_column_header_name("Device")]) is not None):
+ device = get_device(return_value_if_not_none(
+ data[get_column_header_name("Device")]))
+ sample = update_property(sample, device_rt.id, device, property_name=device_rt.name)
+
+ if (get_column_header_name("Parent LinkAhead ID") in data and
+ return_value_if_not_none(data[get_column_header_name("Parent LinkAhead ID")]) is not None):
+ parent = return_value_if_not_none(
+ data[get_column_header_name("Parent LinkAhead ID")])
+ sample = update_property(sample, parent_sample_prop.id, parent, property_name=parent_sample_prop.name)
+
+ for name in ["Curator", "Collector"]:
+ prop = db.get_entity_by_name(get_entity_name(name))
+ if (get_column_header_name(name) in data and
+ return_value_if_not_none(data[get_column_header_name(name)]) is not None):
+ persons = [get_person(id_str) for id_str in return_value_if_not_none(
+ data[get_column_header_name(name)])]
+ sample = update_property(sample, prop.id, persons,
+ datatype=db.LIST(get_entity_name("Person")), property_name=prop.name)
+
+ return sample
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
new file mode 100644
index 0000000000000000000000000000000000000000..058452266722257db5023f076031d2cc570a54dd
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_column_definitions.py
@@ -0,0 +1,131 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import re
+
+from datetime import date
+from dateutil.relativedelta import relativedelta
+from typing import Union
+
+from .utils import get_column_header_name
+
+
+def semicolon_separated_list(text):
+ return [el.strip() for el in text.split(";") if el != ""]
+
+
+def _embargo_converter(text: str):
+
+ datepattern = r"^(?P<year>\d{4,4})-(?P<month>\d{2,2})-(?P<day>\d{2,2})"
+ matches = re.match(datepattern, str(text))
+ if matches:
+ return date(int(matches.groupdict()["year"]), int(matches.groupdict()["month"]), int(matches.groupdict()["day"]))
+ if f"{text}".lower() in ["true", "yes"]:
+ # yes means embargo until today in one year
+ return date.today() + relativedelta(years=1)
+ if f"{text}".lower() in ["false", "no"]:
+ return ""
+ raise ValueError(
+ f"The embargo should be either a date in YYYY-MM-DD format, or 'true'/'yes' or 'false'/'no', but is {text}.")
+
+
+def use_custom_names(definition: Union[list, dict]):
+ """Replace names in list or dict keys by custom names with
+ `utils.get_column_header_name`.
+
+ """
+ if isinstance(definition, list):
+ return [get_column_header_name(name) for name in definition]
+ elif isinstance(definition, dict):
+ return {get_column_header_name(key): value for key, value in definition.items()}
+
+ raise ValueError(f"Expected dict or list, but got {type(definition)}.")
+
+
+DATATYPE_DEFINITIONS = use_custom_names({
+ "entity_id": str,
+ "Main User": str,
+ "Campaign": str,
+ "Elevation start": float,
+ "Elevation stop": float,
+ "End date": str,
+ "Latitude start": float,
+ "Latitude stop": float,
+ "Longitude start": float,
+ "Longitude stop": float,
+ "PI": str,
+ "Parent LinkAhead ID": str,
+ "SampleMethod": str,
+ "SampleType": str,
+ "Start date": str,
+ "Storage ID": str,
+})
+
+# Obligatory columns: Must exist and must not be empty
+# Must exist
+OBLIGATORY_COLUMNS = use_custom_names([
+ "entity_id",
+ "Start date",
+])
+
+OBLIGATORY_COLUMNS_CHILD = use_custom_names([
+ "entity_id",
+ "Parent LinkAhead ID",
+])
+
+COLUMN_CONVERTER = use_custom_names({
+ "Collector": semicolon_separated_list,
+ "Curator": semicolon_separated_list,
+ "Embargo": _embargo_converter,
+ "Event responsible": semicolon_separated_list,
+ "Sphere": semicolon_separated_list,
+})
+
+SPECIAL_TREATMENT_SAMPLE = use_custom_names([
+ "Biome",
+ "Campaign",
+ "Collector",
+ "Curator",
+ "Device",
+ "Elevation start",
+ "Elevation stop",
+ "Embargo",
+ "End date",
+ "responsible_person_event",
+ "igsn_doi_prop",
+ "Latitude start",
+ "Latitude stop",
+ "Level",
+ "locality_description_prop",
+ "locality_name_prop",
+ "Longitude start",
+ "Longitude stop",
+ "Main User",
+ "PI",
+ "PDFReport",
+ "parent_sample_prop",
+ "Sphere",
+ "Start date",
+ "Storage ID",
+ "entity_id",
+])
+
+IGNORED_COLUMN_NAMES_SAMPLE = use_custom_names([
+ "LinkAhead URL",
+ "Parent_sample",
+ "Storage chain",
+])
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_container.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_container.py
new file mode 100644
index 0000000000000000000000000000000000000000..40e2e735fa97fafced6410403c19b57decd19ebb
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_container.py
@@ -0,0 +1,43 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import get_entity_name
+
+
+def get_container(identifier: str) -> db.Record:
+ """Return the container record for a given identifier string. By
+ default, that's simply the id but may be overwritten for
+ customization.
+
+ """
+ try:
+ return db.cached.cached_get_entity_by(
+ query=f"FIND '{get_entity_name('container_rt')}' WITH ID='{identifier}'"
+ )
+ except db.EmptyUniqueQueryError:
+ try:
+ return db.cached.cached_get_entity_by(
+ query=f"FIND '{get_entity_name('container_rt')}' WITH name='{identifier}'"
+ )
+ except db.EmptyUniqueQueryError:
+ raise DataInconsistencyError(
+ f"Couldn't find a {get_entity_name('container_rt')} with name or id {identifier}."
+ )
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_device.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_device.py
new file mode 100644
index 0000000000000000000000000000000000000000..08cf3f0ac5b3148361fc8517cdbcbabf6f48e63e
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_device.py
@@ -0,0 +1,42 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import get_entity_name
+
+def get_device(identifier: str) -> db.Record:
+ """Return the container record for a given identifier string. By
+ default, that's simply the id but may be overwritten for
+ customization.
+
+ """
+ try:
+ return db.cached.cached_get_entity_by(
+ query=f"FIND '{get_entity_name('Device')}' WITH ID='{identifier}'"
+ )
+ except db.EmptyUniqueQueryError:
+ try:
+ return db.cached.cached_get_entity_by(
+ query=f"FIND '{get_entity_name('Device')}' WITH name='{identifier}'"
+ )
+ except db.EmptyUniqueQueryError:
+ raise DataInconsistencyError(
+ f"Couldn't find a {get_entity_name('Device')} with name or id {identifier}."
+ )
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
new file mode 100644
index 0000000000000000000000000000000000000000..c15df79805965ec982012775a113704979ecdf1b
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_event.py
@@ -0,0 +1,148 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+import pandas as pd
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .sample_upload_get_person import get_person
+from .utils import get_column_header_name, get_entity_name, update_property, return_value_if_not_none
+
+
+def add_event_to_sample(sample: db.Record, data: pd.Series) -> db.Record:
+ """Take a given sample and attach an event Record from the
+ data. Then, return the sample.
+
+ """
+
+ _perform_sanity_checks(sample, data)
+ event_rt = db.get_entity_by_name(get_entity_name("event_rt"), role="RECORDTYPE")
+ event = db.Record().add_parent(event_rt)
+
+ # We performed the sanity checks so we can assume that if the
+ # Start/Stop Latitude exists, all start/stop data exist.
+ positions = []
+ position_prop = db.get_entity_by_name(get_entity_name("Position"))
+
+ # Take care of positions
+ for mode in ["start", "stop"]:
+ if (get_column_header_name(f"Latitude {mode}") in data and
+ return_value_if_not_none(data[get_column_header_name(f"Latitude {mode}")]) is not None):
+ positions.append(
+ _create_position(
+ mode=mode,
+ lat=return_value_if_not_none(data[get_column_header_name(f"Latitude {mode}")]),
+ lng=return_value_if_not_none(data[get_column_header_name(f"Longitude {mode}")]),
+ ele=return_value_if_not_none(data[get_column_header_name(f"Elevation {mode}")]),
+ )
+ )
+ if positions:
+ event = update_property(event, position_prop.id, positions,
+ datatype=db.LIST(get_entity_name("Position")), property_name=position_prop.name)
+
+ # Further event properties
+ for event_p in ["Biome", "Campaign", "Device", "EventType",
+ "igsn_doi_prop", "level", "locality_description_prop",
+ "locality_name_prop", "Sphere"]:
+ prop = db.get_entity_by_name(get_entity_name(event_p))
+ if (get_column_header_name(event_p) in data and
+ return_value_if_not_none(data[get_column_header_name(event_p)]) is not None):
+ event = update_property(event, prop.id, return_value_if_not_none(
+ data[get_column_header_name(event_p)]), property_name=prop.name)
+
+ # Special treatment for (list of) persons
+ resp_prop = db.get_entity_by_name(get_entity_name("responsible_person_event"))
+ if (get_column_header_name("responsible_person_event") in data and
+ return_value_if_not_none(data[get_column_header_name("responsible_person_event")]) is not None):
+ resps = return_value_if_not_none(data[get_column_header_name("responsible_person_event")])
+ if not isinstance(resps, list):
+ resps = [resps]
+ recs = [get_person(resp) for resp in resps]
+ event = update_property(event, resp_prop.id, recs, datatype=db.LIST(
+ "Person"), property_name=resp_prop.name)
+
+ for time_p in ["start_date_prop", "end_date_prop"]:
+ prop = db.get_entity_by_name(get_entity_name(time_p))
+ if (get_column_header_name(time_p) in data and
+ return_value_if_not_none(data[get_column_header_name(time_p)]) is not None):
+ event = update_property(event, prop.id, return_value_if_not_none(
+ data[get_column_header_name(time_p)]), property_name=prop.name)
+
+ # only add if there was any event data at all:
+ if len(event.properties) > 0:
+ sample = update_property(sample, event_rt.id, event, property_name=event_rt.name)
+
+ return sample
+
+
+def _create_position(mode: str, lat: float, lng: float, ele: float):
+ pos = db.Record()
+ if mode.lower() == "start":
+ pos.add_parent(get_entity_name("StartPosition"))
+ elif mode.lower() == "stop":
+ pos.add_parent(get_entity_name("StopPosition"))
+ else:
+ pos.add_parent(get_entity_name("Position"))
+
+ pos.add_property(name=get_entity_name("latitude"), value=lat)
+ pos.add_property(name=get_entity_name("longitude"), value=lng)
+ pos.add_property(name=get_entity_name("elevation"), value=ele)
+
+ return pos
+
+
+def _perform_sanity_checks(sample, data):
+
+ if (get_column_header_name("end_date") in data and
+ return_value_if_not_none(data[get_column_header_name("end_date")]) is not None):
+ if (get_column_header_name("start_date") not in data or
+ return_value_if_not_none(data[get_column_header_name("start_date")]) is None):
+ raise DataInconsistencyError(
+ f"Sample with {get_entity_name('entity_id')} {sample.id} has a "
+ f"{get_column_header_name('end_date')} but no valid "
+ f"{get_column_header_name('start_date')}."
+ )
+
+ for name in ["start", "stop"]:
+ bool_list = [get_column_header_name(f"{val}_{name}") in data for val in [
+ "latitude", "longitude", "elevation"]]
+ raise_error = False
+ if any(bool_list):
+ if not all(bool_list):
+ raise_error = True
+ elif any([return_value_if_not_none(data[get_column_header_name(f"{val}_{name}")]) is None for val in ["latitude", "longitude", "elevation"]]):
+ raise_error = True
+
+ if raise_error:
+ raise DataInconsistencyError(
+ f"Sample with {get_entity_name('entity_id')} {sample.id} has an "
+ f"invalid {name} position. Please make sure that latitude, longitude, "
+ "and elevation are provided."
+ )
+
+ # only need to check lat since we already checked that if lat is
+ # present, lng and ele are present, too
+ if (get_column_header_name("latitude_stop") in data and
+ return_value_if_not_none(data[get_column_header_name("latitude_stop")]) is not None):
+ if (get_column_header_name("latitude_start") not in data or
+ return_value_if_not_none(data[get_column_header_name("latitude_start")]) is not None):
+ raise DataInconsistencyError(
+ f"Sample with {get_entity_name('entity_id')} {sample.id} has a "
+ f"{get_entity_name('StopPosition')} but no valid "
+ f"{get_entity_name('StartPosition')}."
+ )
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
new file mode 100644
index 0000000000000000000000000000000000000000..3e947804d60d10e20a6cd05219c02861b0c067a0
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_get_person.py
@@ -0,0 +1,79 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+
+from caosadvancedtools.datainconsistency import DataInconsistencyError
+
+from .utils import get_entity_name
+
+from linkahead.cached import cached_get_entity_by, cached_query as cquery
+
+def get_person(text: str) -> db.Record:
+ """Return the Person Record that is specifed as 'Main User' or
+ 'Sampling Person' in data.
+
+ If the Person is not present in the database, an Exception is
+ raised. Creating new Person Reconrds can only be done by a
+ priviledged user.
+
+ """
+ # Check in which format the person is identified:
+ person_identifier = text.split(", ")
+ if len(person_identifier) == 1:
+ person = _get_person_by_id(person_identifier[0])
+ else:
+ person = _get_person_by_fullname(person_identifier[1], person_identifier[0])
+
+ return person
+
+
+def _get_person_by_fullname(first_name: str, last_name: str) -> db.Record:
+ # seach for person in db
+ res = db.execute_query(
+ f"FIND '{get_entity_name('Person')}' WITH "
+ f"'{get_entity_name('first_name_prop')}'='{first_name}' "
+ f"AND '{get_entity_name('last_name_prop')}'='{last_name}'"
+ )
+ # if person doesn't exist in database...
+ if len(res) == 0:
+ # There is not enought data in the template to create a new Person record. Hence, we have to raise an Exception
+ error_msg = (
+ f"There is no person Record with '{get_entity_name('first_name_prop')}' "
+ f"= '{first_name}' "
+ f"AND '{get_entity_name('last_name_prop')}' = '{last_name}' in the database. ")
+ raise DataInconsistencyError(error_msg)
+ else:
+ return res[0]
+
+
+def _get_person_by_id(ident: str) -> db.Record:
+ options = cquery(f"FIND '{get_entity_name('Person')}' WITH ID='{ident}' ")
+ if len(options)==1:
+ return options[0]
+ options = cquery(f"FIND '{get_entity_name('Person')}' WITH "
+ f"'{get_entity_name('abbreviation_prop')}'='{ident}' ")
+ if len(options) == 1:
+ return options[0]
+ elif len(options) == 0:
+ raise DataInconsistencyError(
+ f"Could not find a {get_entity_name('Person')} with ID {ident}."
+ )
+ else:
+ raise DataInconsistencyError(
+ f"Found multiple {get_entity_name('Person')} with {get_entity_name('abbreviation_prop')}={ident}."
+ )
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
new file mode 100644
index 0000000000000000000000000000000000000000..54a034775389a16d5dc0d02d57195b37dcd94ca8
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/sample_upload_post_processing.py
@@ -0,0 +1,23 @@
+#
+# Copyright (C) 2025 Indiscale GmbH <info@indiscale.com>
+# Copyright (C) 2025 Florian Spreckelsen <f.spreckelsen@indiscale.com>
+#
+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU Affero General Public License as
+# published by the Free Software Foundation, either version 3 of the
+# License, or (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU Affero General Public License for more details.
+#
+# You should have received a copy of the GNU Affero General Public License
+# along with this program. If not, see <https://www.gnu.org/licenses/>.
+#
+import linkahead as db
+import pandas as pd
+
+def post_process_samples(samples: db.Container, data: pd.DataFrame) -> db.Container:
+
+ return samples
diff --git a/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
new file mode 100644
index 0000000000000000000000000000000000000000..d047e6bbfd6a39cae610526d17238d3675533447
--- /dev/null
+++ b/sample-management-custom/caosdb-server/scripting/bin/sample_helpers/utils.py
@@ -0,0 +1,79 @@
+import os
+import yaml
+
+from pathlib import Path
+
+import linkahead as db
+import pandas as pd
+
+with open(os.path.join(Path(__file__).parent, "default_constants.yml")) as yaml_file:
+ CONSTANTS = yaml.safe_load(yaml_file)
+
+if os.path.isfile(os.path.join(Path(__file__).parent, "constants.yml")):
+ with open(os.path.join(Path(__file__).parent, "constants.yml")) as custom_yaml_file:
+ CONSTANTS.update(yaml.safe_load(custom_yaml_file))
+
+
+def get_entity_name(name: str):
+
+ if name in CONSTANTS["entity_names"]:
+
+ return CONSTANTS["entity_names"][name]
+
+ return name
+
+
+def get_column_header_name(name: str):
+
+ if name in CONSTANTS["csv_column_names"]:
+ return CONSTANTS["csv_column_names"][name]
+
+ return get_entity_name(name)
+
+
+def update_property(entity: db.Record, property_id: int, value, property_name="", datatype=None):
+ """
+ Set the property of an entity.
+
+ If the entity already has the property, just the value is set.
+ Else, the property is added to the entity
+ """
+ # TODO: Replace by assure_property_is etc.
+
+ # If the value in the spreadsheet is empty (nan)
+ if ((isinstance(value, list) and len(value) == 0)
+ or (not isinstance(value, list) and pd.isna(value))):
+ # Remove the property from te Entity if it has it
+ try:
+ entity.get_properties().get_by_name(property_name)
+ entity.remove_property(property_name)
+ except KeyError:
+ pass
+ return entity
+ if entity.get_property(property_id) is None:
+ if datatype:
+ entity.add_property(id=property_id, value=value, name=property_name, datatype=datatype)
+ else:
+ entity.add_property(id=property_id, value=value, name=property_name)
+ else:
+ if isinstance(value, list) and not entity.get_property(property_id).datatype.startswith("LIST"):
+ entity.get_property(property_id).datatype = db.LIST(
+ entity.get_property(property_id).datatype)
+ entity.get_property(property_id).value = value
+ return entity
+
+
+def return_value_if_not_none(val):
+ """Workaround for somewhat weird pandas behavior. Return value if actual
+ value, otherwise, return None.
+
+ """
+ if isinstance(val, list):
+ if len(val) == 0:
+ return None
+ if len(val) == 1:
+ if pd.isnull(val[0]) or val[0] is None or f"{val[0]}".lower() == "nan" or f"{val[0]}" == "":
+ return None
+ elif pd.isnull(val) or val is None or f"{val}".lower() == "nan" or f"{val}" == "":
+ return None
+ return val
diff --git a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
index 6334551716ec80205b3765d81907f71e69a7026d..4a03f1d5bec3207a17d971d98fd96a42722e2070 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/update_containers.py
@@ -36,13 +36,17 @@ from linkahead.cached import cached_query, cached_get_entity_by
from bis_utils import (get_do_not_insert_type_names,
replace_entity_urls_by_ids, whitespace_cleanup_in_df)
+from sample_helpers.container_update_get_parent import get_container_by_identifier
+from sample_helpers.container_update_post_processing import (
+ post_process_containers_before_sync, post_process_parent_containers_before_sync, post_process_inserts_and_updates)
+from sample_helpers.utils import (CONSTANTS, get_column_header_name, get_entity_name)
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
apilogger.setLevel(logging.ERROR)
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
logger = logging.getLogger("caosadvancedtools")
@@ -55,17 +59,6 @@ def _value_in_row(key, row):
return True
-def _get_parent_by_identifier(parent_identifier):
- """Get parent specified either by BIS ID, name, or BIS label."""
- try:
- parent_identifier = int(parent_identifier)
- query = f"FIND Container WITH ID={parent_identifier}"
- except ValueError:
- query = (f"FIND Container WITH name='{parent_identifier}' "
- f"OR WITH 'BIS label'='{parent_identifier}'")
- return cached_query(query)
-
-
def get_parser():
par = helper.get_argument_parser()
return par
@@ -96,29 +89,35 @@ def main():
# Get referenced container entities
child_containers = db.Container()
parent_containers = db.Container()
+ id_column_name = get_column_header_name("entity_id")
+ parent_column_name = get_column_header_name("Parent container")
for index, row in data.iterrows():
- if not _value_in_row("BIS ID", row):
- logger.error(f"BIS ID is missing in row {index+1}. Nothing was updated.")
+ if not _value_in_row(id_column_name, row):
+ logger.error(f"{id_column_name} is missing in row {index+1}. Nothing was updated.")
return 1
try:
- child = db.Record(id=int(row["BIS ID"]))
+ child = db.Record(id=int(row[id_column_name]))
except ValueError:
logger.error(
- f"Invalid BIS ID {row['BIS ID']} in row {index + 1}. Nothing was updated.")
+ f"Invalid {id_column_name} {row[id_column_name]} in row {index + 1}. Nothing was updated.")
return 1
- child.add_parent("Container")
+ child.add_parent(get_entity_name("container_rt"))
child_containers.append(child)
- if _value_in_row("Parent container", row):
- parent_identifier = row["Parent container"]
- parent = _get_parent_by_identifier(parent_identifier)
+ if _value_in_row(parent_column_name, row):
+ parent_identifier = row[parent_column_name]
+ parent = get_container_by_identifier(parent_identifier)
if len(parent) == 0:
logger.error(
- f"Couldn't find parent with identifier '{parent_identifier}' in row {index+1}.")
+ f"Couldn't find parent with identifier '{parent_identifier}' "
+ f"in row {index+1}."
+ )
return 1
elif len(parent) > 1:
- logger.error(f"Parent with identifier '{parent_identifier}' in row {index+1} was not unique. "
- "Please specify with BIS ID instead.")
+ logger.error(
+ f"Parent with identifier '{parent_identifier}' in row "
+ f"{index+1} was not unique. Please specify with "
+ f"{id_column_name} instead.")
return 1
parent = parent[0]
try:
@@ -132,34 +131,44 @@ def main():
return 1
# Get IDs of proerperties
- child_container_prop = cached_get_entity_by(query="FIND Property WITH name = 'Child container'")
- custom_label_prop = cached_get_entity_by(query="FIND Property WITH name = 'Custom label'")
- pdf_rt = cached_get_entity_by(query="FIND RECORDTYPE WITH name=PDFReport")
+ child_container_prop = cached_get_entity_by(
+ query=f"FIND Property WITH name = '{get_entity_name('child_container_prop')}'"
+ )
+ custom_label_prop = cached_get_entity_by(
+ query=f"FIND Property WITH name = '{get_entity_name('custom_label_prop')}'"
+ )
+ pdf_rt = cached_get_entity_by(
+ query=f"FIND RECORDTYPE WITH name='{get_entity_name('PDFReport')}'"
+ )
# Update (/create) container entities
for index, row in data.iterrows():
# Add child to parent
parent = None
- if _value_in_row("Parent container", row):
- parent_identifier = row["Parent container"]
+ if _value_in_row(parent_column_name, row):
+ parent_identifier = row[parent_column_name]
# This has already been checked above for uniqueness
- candidate = _get_parent_by_identifier(parent_identifier)[0]
+ candidate = get_container_by_identifier(parent_identifier)[0]
# A bit redundant, but we need the exact Python object here that is in the parent_containers list.
parent = parent_containers.get_entity_by_id(candidate.id)
if parent.get_property(child_container_prop.id) is None:
parent.add_property(id=child_container_prop.id,
- name=child_container_prop.name, value=[int(row["BIS ID"])])
+ name=child_container_prop.name, value=[int(row[id_column_name])])
else:
if parent.get_property(child_container_prop.id).value is None:
- parent.get_property(child_container_prop.id).value = [int(row["BIS ID"])]
+ parent.get_property(child_container_prop.id).value = [int(row[id_column_name])]
else:
- if int(row["BIS ID"]) not in parent.get_property(child_container_prop.id).value:
+ if int(row[id_column_name]) not in parent.get_property(child_container_prop.id).value:
parent.get_property(child_container_prop.id).value.append(
- int(row["BIS ID"]))
-
- # remove the current child from all other parents (don't do anything if the parent didn't change)
- old_parents = cached_query(f"FIND Container WHICH REFERENCES {int(row['BIS ID'])}")
+ int(row[id_column_name]))
+
+ # remove the current child from all other parents (don't
+ # do anything if the parent didn't change)
+ old_parents = cached_query(
+ f"FIND {get_entity_name('container_rt')} WHICH REFERENCES "
+ f"{int(row[id_column_name])}"
+ )
for old_parent in old_parents:
if parent is not None and old_parent.id == parent.id:
# old parent also is new parent
@@ -169,29 +178,30 @@ def main():
old_parent = parent_containers.get_entity_by_id(old_parent.id)
except KeyError:
parent_containers.append(old_parent)
- old_parent.remove_value_from_property("Child container", int(
- row["BIS ID"]), remove_if_empty_afterwards=False)
- if old_parent.get_property("Child container").value is None:
- old_parent.get_property("Child container").value = []
+ old_parent.remove_value_from_property(child_container_prop.name, int(
+ row[id_column_name]), remove_if_empty_afterwards=False)
+ if old_parent.get_property(child_container_prop.name).value is None:
+ old_parent.get_property(child_container_prop.name).value = []
# Add custom label o child
- child = child_containers.get_entity_by_id(id=int(row["BIS ID"]))
- if _value_in_row("Custom label", row):
- child.name = row["Custom label"]
+ child = child_containers.get_entity_by_id(id=int(row[id_column_name]))
+ if _value_in_row(get_column_header_name("custom_label_prop"), row):
+ child.name = row[get_column_header_name("custom_label_prop")]
if child.get_property(custom_label_prop.id) is None:
child.add_property(id=custom_label_prop.id,
- name=custom_label_prop.name, value=row["Custom label"])
+ name=custom_label_prop.name, value=row[get_column_header_name("custom_label_prop")])
else:
- child.get_property(custom_label_prop.id).value = row["Custom label"]
+ child.get_property(
+ custom_label_prop.id).value = row[get_column_header_name("custom_label_prop")]
# Treat PI
- if _value_in_row("PI", row):
- pi = row["PI"]
- pi_prop = cached_get_entity_by(query="FIND PROPERTY Pi")
+ if _value_in_row(get_column_header_name("PI"), row):
+ pi = row[get_column_header_name("PI")]
+ pi_prop = cached_get_entity_by(query=f"FIND PROPERTY {get_entity_name('PI')}")
try:
query = f"FIND RECORD Person WITH ID={int(pi)}"
except ValueError:
- query = f"FIND RECORD Person WITH AN Abbreviation='{pi}'"
+ query = f"FIND RECORD Person WITH AN '{get_entity_name('abbreviation_prop')}'='{pi}'"
try:
pi_rec = cached_get_entity_by(query=query)
if child.get_property(pi_prop.name) is not None:
@@ -199,67 +209,63 @@ def main():
else:
child.add_property(id=pi_prop.id, name=pi_prop.name, value=pi_rec.id)
except db.EmptyUniqueQueryError:
- logger.warning(f"There is no PI with BIS ID or abbreviation {pi}. Skipping.")
+ logger.warning(f"There is no PI with ID or {get_entity_name('abbreviation_prop')} {pi}. Skipping.")
# Collection(s)
- if _value_in_row("Collection", row):
- collection_rt = cached_get_entity_by(query="FIND RECORDTYPE Collection")
- if not ";" in str(row["Collection"]):
- collections = [row["Collection"]]
+ if _value_in_row(get_column_header_name("Collection"), row):
+ collection_rt = cached_get_entity_by(query=f"FIND RECORDTYPE '{get_entity_name('Collection')}'")
+ if not ";" in str(row[get_column_header_name("Collection")]):
+ collections = [row[get_column_header_name("Collection")]]
else:
- collections = [coll.strip() for coll in str(row["Collection"]).split(';')]
+ collections = [coll.strip() for coll in str(row[get_column_header_name("Collection")]).split(';')]
prop_val = []
for coll in collections:
try:
- query = f"FIND RECORD Collection WITH ID={int(coll)}"
+ query = f"FIND '{collection_rt.name}' WITH ID={int(coll)}"
except ValueError:
- query = f"FIND RECORD Collection WITH name='{coll}'"
+ query = f"FIND RECORD '{collection_rt.name}' WITH name='{coll}'"
try:
coll_rec = cached_get_entity_by(query=query)
prop_val.append(coll_rec.id)
except db.EmptyUniqueQueryError:
- logger.warning(f"There is no collection with name or BIS ID {coll}. Skipping.")
+ logger.warning(f"There is no {collection_rt.name} with name or ID {coll}. Skipping.")
continue
if prop_val:
- if child.get_property("Collection") is not None:
- child.get_property("Collection").datatype = db.LIST("Collection")
- child.get_property("Collection").value = prop_val
+ if child.get_property(collection_rt.name) is not None:
+ child.get_property(collection_rt.name).datatype = db.LIST(collection_rt.name)
+ child.get_property(collection_rt.name).value = prop_val
else:
child.add_property(id=collection_rt.id, name=collection_rt.name, datatype=db.LIST(
- "Collection"), value=prop_val)
+ collection_rt.name), value=prop_val)
# Treat Container Contents
- if _value_in_row("Container Contents", row):
- if not (_value_in_row("PI", row) and _value_in_row("Collection", row)):
- logger.error(
- f"Container Contents are given for container {child.id} but it "
- "is missing PI and/or Collection info. No updates have been performed."
- )
- return 1
- contents_prop = cached_get_entity_by(query="FIND PROPERTY 'Container Contents'")
+ if _value_in_row(get_column_header_name("Container Contents"), row):
+ contents_prop = cached_get_entity_by(
+ query=f"FIND PROPERTY '{get_entity_name('Container Contents')}'"
+ )
if child.get_property(contents_prop.name) is not None:
- child.get_property(contents_prop.name).value = row["Container Contents"]
+ child.get_property(contents_prop.name).value = row[get_column_header_name("Container Contents")]
else:
child.add_property(id=contents_prop.id, name=contents_prop.name,
- value=row["Container Contents"])
+ value=row[get_column_header_name("Container Contents")])
# Treat PDF Report
- if _value_in_row("PDFReport", row):
- pdf_id = row["PDFReport"]
+ if _value_in_row(get_column_header_name("PDFReport"), row):
+ pdf_id = row[get_column_header_name("PDFReport")]
try:
pdf_id = int(pdf_id)
- pdf_rec = cached_query(f"FIND FILE PDFReport WITH ID={pdf_id}")
+ pdf_rec = cached_query(f"FIND FILE {get_entity_name('PDFReport')} WITH ID={pdf_id}")
if not pdf_rec:
logger.warning(
- f"There is no PDFReport with Bis ID {pdf_id}, so no PDF is attached to container {child.id}.")
+ f"There is no PDFReport with ID {pdf_id}, so no PDF is attached to container {child.id}.")
else:
- if child.get_property("PDFReport") is not None:
- child.get_property("PDFReport").value = pdf_id
+ if child.get_property(get_entity_name("PDFReport")) is not None:
+ child.get_property(get_property("PDFReport")).value = pdf_id
else:
child.add_property(id=pdf_rt.id, name=pdf_rt.name, value=pdf_id)
except ValueError:
logger.warning(
- f"There is no valid Bis ID provided for container {child.id}."
+ f"There is no valid ID provided for container {child.id}."
f"Provided was {pdf_id}. Skipping")
# This is a workaround for weird merging errors in the
@@ -267,13 +273,13 @@ def main():
# following release.
merged = []
for par in parent_containers:
- if (data['BIS ID'] == par.id).any():
+ if (data[id_column_name] == par.id).any():
# A container to be updated is used as another containers parent:
child = child_containers.get_entity_by_id(par.id)
# All parents have a child sample property with a value (which may
# be empty). No child sample has this property, so the following is
# okay without checks:
- prop = par.get_property("Child container")
+ prop = par.get_property(child_container_prop.name)
child.add_property(name=prop.name, id=prop.id, value=prop.value)
merged.append(par)
for par in merged:
@@ -282,6 +288,8 @@ def main():
parent_containers.remove(par)
# TODO Add notes as CommentAnnotation
crawler = Crawler(securityMode=SecurityMode.UPDATE)
+ child_containers = post_process_containers_before_sync(child_containers)
+ parent_containers = post_process_parent_containers_before_sync(parent_containers)
to_be_synchronized = child_containers + parent_containers
inserts, updates = crawler.synchronize(
@@ -291,10 +299,8 @@ def main():
if "SHARED_DIR" in os.environ:
_notify_about_inserts_and_updates(len(inserts), len(updates), htmluserlog_public,
crawler.run_id)
- for ent in inserts + updates:
- ent.retrieve_acl()
- ent.grant(role='Stock Manager', priority=False, permission="EDIT:ACL")
- ent.update_acl()
+ inserts, updates = post_process_inserts_and_updates(inserts, updates)
+
logger.info(f"Successfully processed {len(child_containers)} containers and "
f"{len(parent_containers)} parent containers.")
diff --git a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
index f66744a9b118f90311718f802741f8e546e98e5c..716000720b5a8595dd0add4a31e870c9dac7b275 100755
--- a/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
+++ b/sample-management-custom/caosdb-server/scripting/bin/upload_sample_template.py
@@ -27,12 +27,9 @@ import json
import logging
import os
import pandas as pd
-import re
import subprocess
import sys
-from datetime import date, datetime
-from dateutil.relativedelta import relativedelta
from pathlib import Path
from tempfile import NamedTemporaryFile
@@ -45,128 +42,21 @@ from caoscrawler.logging import configure_server_side_logging
from bis_utils import (replace_entity_urls_by_ids,
SPECIAL_TREATMENT_SAMPLE, whitespace_cleanup_in_df)
+from sample_helpers.sample_upload_column_definitions import (
+ COLUMN_CONVERTER, DATATYPE_DEFINITIONS,
+ OBLIGATORY_COLUMNS, OBLIGATORY_COLUMNS_CHILD, SPECIAL_TREATMENT_SAMPLE)
+from sample_helpers.utils import CONSTANTS, get_column_header_name
# suppress warning of diff function
apilogger = logging.getLogger("linkahead.apiutils")
apilogger.setLevel(logging.ERROR)
-def semicolon_separated_list(text):
- return [el.strip() for el in text.split(";") if el != ""]
-
-
-def _embargo_converter(text: str):
-
- datepattern = r"^(?P<year>\d{4,4})-(?P<month>\d{2,2})-(?P<day>\d{2,2})"
- matches = re.match(datepattern, str(text))
- if matches:
- return date(int(matches.groupdict()["year"]), int(matches.groupdict()["month"]), int(matches.groupdict()["day"]))
- if f"{text}".lower() in ["true", "yes"]:
- # yes means embargo until today in one year
- return date.today() + relativedelta(years=1)
- if f"{text}".lower() in ["false", "no"]:
- return ""
- raise ValueError(
- f"The embargo should be either a date in YYYY-MM-DD format, or 'true'/'yes' or 'false'/'no', but is {text}.")
-
-
-ERROR_PREFIX = 'Something went wrong: '
-ERROR_SUFFIX = ' Please conatct <a href="mailto:biosamples@geomar.de">biosamples@geomar.de</a> if you encounter this issue.'
+ERROR_PREFIX = CONSTANTS["error_prefix"]
+ERROR_SUFFIX = CONSTANTS["error_suffix"]
# Column datatypes
-DATATYPE_DEFINITIONS = {
- "AphiaID": int,
- "BIS ID": str,
- "Campaign": str,
- "Date collected start": str,
- "Date collected stop": str,
- "Date sampled start": str,
- "Date sampled stop": str,
- "Fixation": str,
- "Gear configuration": str,
- "Gear": str,
- "Hol": int,
- "Latitude start": float,
- "Latitude stop": float,
- "Longitude start": float,
- "Longitude stop": float,
- "Main User": str,
- "Nagoya case number": str,
- "PI": str,
- "Parent BIS ID": str,
- "Platform": str,
- "Sample Context": str,
- "Sample container": str,
- "SampleType": str,
- "SampleTypeSpecific": str,
- "Sampling Person": str,
- "Sampling depth start": float,
- "Sampling depth stop": float,
- "Sampling method": str,
- "Station ID": str,
- "Station number": str,
- "Storage Container Label": str,
- "Storage ID": str,
- "StorageTemperature": str,
- "Subevent": str,
- "Time collected start": str,
- "Time collected stop": str,
- "Time sampled start": str,
- "Time sampled stop": str,
- "Timezone": str,
- "Water depth start": float,
- "Water depth stop": float,
-}
-
-# Obligatory columns: Must exist and must not be empty
-# Must exist
-OBLIGATORY_COLUMNS = [
- "BIS ID",
- "Collection",
- "Date collected start",
- "Fixation",
- "Gear",
- "Latitude start",
- "Longitude start",
- "Main User",
- "Nagoya case number",
- "PI",
- "Sample Context",
- "Sample container",
- "SampleType",
- "SampleTypeSpecific",
- "Sphere",
- "Storage ID",
- "StorageTemperature",
-]
-
-OBLIGATORY_COLUMNS_CHILD = [
- "BIS ID",
- "Date sampled start",
- "Fixation",
- "Main User",
- "Parent BIS ID",
- "Sample Context",
- "Sample container",
- "SampleType",
- "SampleTypeSpecific",
- "Sphere",
- "Storage ID",
- "StorageTemperature",
-]
-
-COLUMN_CONVERTER = {
- "Collection": semicolon_separated_list,
- "Ecotaxa URL": semicolon_separated_list,
- "NCBI Accession": semicolon_separated_list,
- "NCBI BioProject": semicolon_separated_list,
- "NCBI BioSample": semicolon_separated_list,
- "OSIS URL": semicolon_separated_list,
- "Embargo": _embargo_converter,
- "Publications": semicolon_separated_list,
- "Sphere": semicolon_separated_list,
-}
logger = logging.getLogger("caosadvancedtools")
@@ -179,7 +69,7 @@ def get_parser():
def _is_child_sample_table(filename):
tmp_data = pd.read_csv(filename, sep=',')
if 'Parent BIS ID' in tmp_data.columns:
- return not tmp_data["Parent BIS ID"].isnull().all()
+ return not tmp_data[get_column_header_name("Parent LinkAhead ID")].isnull().all()
return False
@@ -266,25 +156,27 @@ def main():
property_name = eprop.name
if property_name in SPECIAL_TREATMENT_SAMPLE:
continue
- if db.apiutils.is_reference(eprop):
- rt = db.get_entity_by_id(eprop.id)
- if len(rt.properties) == 1:
- converter = _get_converter_from_property_datatype(rt.properties[0].datatype)
- elif len(rt.properties) == 1:
- converter = str
+ if property_name not in DATATYPE_DEFINITIONS:
+ if db.apiutils.is_reference(eprop):
+ rt = db.get_entity_by_id(eprop.id)
+ if len(rt.properties) == 1:
+ converter = _get_converter_from_property_datatype(rt.properties[0].datatype)
+ elif len(rt.properties) < 1:
+ converter = str
+ else:
+ converter = None
else:
- converter = None
- else:
- converter = _get_converter_from_property_datatype(eprop.datatype)
- if converter is None:
- continue
- DATATYPE_DEFINITIONS[property_name] = converter
+ converter = _get_converter_from_property_datatype(eprop.datatype)
+ if converter is None:
+ continue
+ DATATYPE_DEFINITIONS[property_name] = converter
if sample.get_importance(property_name) == db.OBLIGATORY:
# This is only needed if the sample is not a child sample
OBLIGATORY_COLUMNS.append(property_name)
try:
data = read_data_from_file(path)
- data = replace_entity_urls_by_ids(data, ["BIS ID", "Storage ID", "Parent BIS ID"])
+ data = replace_entity_urls_by_ids(data, [get_column_header_name(name) for name in [
+ "entity_id", "Storage ID", "Parent LinkAhead ID"]])
pickle_out = NamedTemporaryFile(delete=False, suffix=".pkl")
data.to_pickle(pickle_out.name)
except DataInconsistencyError as err:
diff --git a/sample-management-custom/caosdb-server/scripting/home/identifiables.yml b/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
index f37c5c380ca38a583d74a8f09314f3850b810e47..c3df242f791a8224fadd31da7c0ffe75889ef775 100644
--- a/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
+++ b/sample-management-custom/caosdb-server/scripting/home/identifiables.yml
@@ -1,40 +1,24 @@
-NagoyaCase:
- - 'Nagoya case number'
-Device:
+Campaign:
- name
-SourceEvent:
- - Gear
- - Time start
- - Position
-Gear:
- # TODO?
- - name
-Fixation:
- # TODO?
- - enumValue
-Platform:
- # TODO?
- - name
-FunctionalGroup:
- # TODO?
+ControlledRecordType:
- name
+Event:
+ - start_date
+ - Position
SampleType:
- # TODO?
- - name
-Collection:
- name
-SampleTypeSpecific:
- # TODO?
+SampleMethod:
- name
Sphere:
- name
StartPosition:
- - Latitude
- - Longitude
- - Water depth
- - Sampling depth
+ - latitude
+ - longitude
+ - elevation
StopPosition:
- - Latitude
- - Longitude
- - Water depth
- - Sampling depth
+ - latitude
+ - longitude
+ - elevation
+Person:
+ - first_name
+ - last_name
diff --git a/test-profile/custom/other/restore/caosdb.sql b/test-profile/custom/other/restore/caosdb.2025-03-11T15:15:22.815622880+00:00.dump.sql
similarity index 81%
rename from test-profile/custom/other/restore/caosdb.sql
rename to test-profile/custom/other/restore/caosdb.2025-03-11T15:15:22.815622880+00:00.dump.sql
index 1182c12275a990e9755ec2c415a23eae0ca27a65..de206c453444440da48c8688c07420d83707ea0f 100644
--- a/test-profile/custom/other/restore/caosdb.sql
+++ b/test-profile/custom/other/restore/caosdb.2025-03-11T15:15:22.815622880+00:00.dump.sql
@@ -2,7 +2,7 @@
--
-- Host: sqldb Database: caosdb
-- ------------------------------------------------------
--- Server version 10.11.9-MariaDB-ubu2204
+-- Server version 11.4.5-MariaDB-ubu2404
/*!40101 SET @OLD_CHARACTER_SET_CLIENT=@@CHARACTER_SET_CLIENT */;
/*!40101 SET @OLD_CHARACTER_SET_RESULTS=@@CHARACTER_SET_RESULTS */;
@@ -36,7 +36,7 @@ CREATE TABLE `archive_collection_type` (
CONSTRAINT `archive_collection_type_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_collection_type_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_collection_type_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -45,6 +45,11 @@ CREATE TABLE `archive_collection_type` (
LOCK TABLES `archive_collection_type` WRITE;
/*!40000 ALTER TABLE `archive_collection_type` DISABLE KEYS */;
+INSERT INTO `archive_collection_type` VALUES
+(0,0,113,'LIST',1),
+(0,192,162,'LIST',1),
+(0,194,162,'LIST',1),
+(0,196,162,'LIST',1);
/*!40000 ALTER TABLE `archive_collection_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -71,7 +76,7 @@ CREATE TABLE `archive_data_type` (
CONSTRAINT `archive_data_type_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_data_type_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_data_type_ibfk_4` FOREIGN KEY (`datatype`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -81,7 +86,14 @@ CREATE TABLE `archive_data_type` (
LOCK TABLES `archive_data_type` WRITE;
/*!40000 ALTER TABLE `archive_data_type` DISABLE KEYS */;
INSERT INTO `archive_data_type` VALUES
-(0,188,177,105,1);
+(0,0,113,111,1),
+(0,0,120,118,1),
+(0,192,163,124,1),
+(0,194,163,124,1),
+(0,196,163,124,1),
+(0,192,162,139,1),
+(0,194,162,139,1),
+(0,196,162,139,1);
/*!40000 ALTER TABLE `archive_data_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -107,7 +119,7 @@ CREATE TABLE `archive_date_data` (
CONSTRAINT `archive_date_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_date_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_date_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -116,6 +128,13 @@ CREATE TABLE `archive_date_data` (
LOCK TABLES `archive_date_data` WRITE;
/*!40000 ALTER TABLE `archive_date_data` DISABLE KEYS */;
+INSERT INTO `archive_date_data` VALUES
+(0,196,147,20231220,'FIX',2,1),
+(0,196,148,20231220,'FIX',3,1),
+(0,194,147,20231220,'FIX',2,1),
+(0,194,148,20231220,'FIX',3,1),
+(0,192,147,20231220,'FIX',2,1),
+(0,192,148,20231220,'FIX',3,1);
/*!40000 ALTER TABLE `archive_date_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -142,7 +161,7 @@ CREATE TABLE `archive_datetime_data` (
CONSTRAINT `archive_datetime_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_datetime_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_datetime_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -165,7 +184,7 @@ CREATE TABLE `archive_desc_overrides` (
`domain_id` int(10) unsigned NOT NULL,
`entity_id` int(10) unsigned NOT NULL,
`property_id` int(10) unsigned NOT NULL,
- `description` text NOT NULL,
+ `description` mediumtext NOT NULL,
`_iversion` int(10) unsigned NOT NULL,
UNIQUE KEY `archive_desc_overrides-d-e-p-v` (`domain_id`,`entity_id`,`property_id`,`_iversion`),
KEY `domain_id` (`domain_id`,`entity_id`,`_iversion`),
@@ -175,7 +194,7 @@ CREATE TABLE `archive_desc_overrides` (
CONSTRAINT `archive_desc_overrides_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_desc_overrides_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_desc_overrides_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -210,7 +229,7 @@ CREATE TABLE `archive_double_data` (
CONSTRAINT `archive_double_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_double_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_double_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -231,7 +250,7 @@ DROP TABLE IF EXISTS `archive_entities`;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `archive_entities` (
`id` int(10) unsigned NOT NULL,
- `description` text DEFAULT NULL,
+ `description` mediumtext DEFAULT NULL,
`role` enum('RECORDTYPE','RECORD','FILE','_REPLACEMENT','PROPERTY','DATATYPE','ROLE','QUERYTEMPLATE') NOT NULL,
`acl` int(10) unsigned DEFAULT NULL,
`_iversion` int(10) unsigned NOT NULL,
@@ -239,7 +258,7 @@ CREATE TABLE `archive_entities` (
KEY `acl` (`acl`),
CONSTRAINT `archive_entities_ibfk_1` FOREIGN KEY (`id`, `_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`) ON DELETE CASCADE,
CONSTRAINT `archive_entities_ibfk_2` FOREIGN KEY (`acl`) REFERENCES `entity_acl` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -249,16 +268,18 @@ CREATE TABLE `archive_entities` (
LOCK TABLES `archive_entities` WRITE;
/*!40000 ALTER TABLE `archive_entities` DISABLE KEYS */;
INSERT INTO `archive_entities` VALUES
-(188,NULL,'RECORD',2,1),
+(113,NULL,'PROPERTY',2,1),
+(120,NULL,'PROPERTY',2,1),
+(184,NULL,'RECORD',2,1),
+(185,NULL,'RECORD',2,1),
+(186,NULL,'RECORD',2,1),
+(187,NULL,'RECORD',2,1),
+(189,NULL,'RECORD',2,1),
+(190,NULL,'RECORD',2,1),
+(191,NULL,'RECORD',2,1),
(192,NULL,'RECORD',2,1),
-(193,NULL,'RECORD',2,1),
-(193,NULL,'RECORD',3,2),
(194,NULL,'RECORD',2,1),
-(195,NULL,'RECORD',2,1),
-(195,NULL,'RECORD',3,2),
-(196,NULL,'RECORD',2,1),
-(197,NULL,'RECORD',2,1),
-(198,NULL,'RECORD',2,1);
+(196,NULL,'RECORD',2,1);
/*!40000 ALTER TABLE `archive_entities` ENABLE KEYS */;
UNLOCK TABLES;
@@ -284,7 +305,7 @@ CREATE TABLE `archive_enum_data` (
CONSTRAINT `archive_enum_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_enum_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_enum_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -305,13 +326,13 @@ DROP TABLE IF EXISTS `archive_files`;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `archive_files` (
`file_id` int(10) unsigned NOT NULL,
- `path` text NOT NULL,
+ `path` mediumtext NOT NULL,
`size` bigint(20) unsigned NOT NULL,
`hash` binary(64) DEFAULT NULL,
`_iversion` int(10) unsigned NOT NULL,
PRIMARY KEY (`file_id`,`_iversion`),
CONSTRAINT `archive_files_ibfk_1` FOREIGN KEY (`file_id`, `_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -346,7 +367,7 @@ CREATE TABLE `archive_integer_data` (
CONSTRAINT `archive_integer_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_integer_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_integer_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -356,9 +377,7 @@ CREATE TABLE `archive_integer_data` (
LOCK TABLES `archive_integer_data` WRITE;
/*!40000 ALTER TABLE `archive_integer_data` DISABLE KEYS */;
INSERT INTO `archive_integer_data` VALUES
-(0,192,137,1,'FIX',0,1,NULL),
-(0,194,137,1,'FIX',0,1,NULL),
-(0,196,137,1,'FIX',0,1,NULL);
+(0,187,162,1,'FIX',0,1,NULL);
/*!40000 ALTER TABLE `archive_integer_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -378,7 +397,7 @@ CREATE TABLE `archive_isa` (
KEY `child` (`child`,`child_iversion`),
CONSTRAINT `archive_isa_ibfk_1` FOREIGN KEY (`parent`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_isa_ibfk_2` FOREIGN KEY (`child`, `child_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -388,18 +407,16 @@ CREATE TABLE `archive_isa` (
LOCK TABLES `archive_isa` WRITE;
/*!40000 ALTER TABLE `archive_isa` DISABLE KEYS */;
INSERT INTO `archive_isa` VALUES
-(188,1,100,0),
-(188,1,101,0),
-(188,1,106,1),
-(193,1,111,1),
-(192,1,136,1),
-(195,1,111,1),
-(193,2,111,1),
-(194,1,136,1),
-(197,1,111,1),
-(195,2,111,1),
-(196,1,136,1),
-(198,1,118,1);
+(187,1,131,1),
+(191,1,111,1),
+(190,1,111,1),
+(189,1,111,1),
+(186,1,118,1),
+(185,1,118,1),
+(184,1,118,1),
+(196,1,126,1),
+(194,1,126,1),
+(192,1,126,1);
/*!40000 ALTER TABLE `archive_isa` ENABLE KEYS */;
UNLOCK TABLES;
@@ -426,7 +443,7 @@ CREATE TABLE `archive_name_data` (
CONSTRAINT `archive_name_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_name_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_name_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -436,11 +453,11 @@ CREATE TABLE `archive_name_data` (
LOCK TABLES `archive_name_data` WRITE;
/*!40000 ALTER TABLE `archive_name_data` DISABLE KEYS */;
INSERT INTO `archive_name_data` VALUES
-(0,193,20,'fad_mru_myn_2025_bld_1','FIX',0,1),
-(0,195,20,'fad_mru_myn_2025_rom_1','FIX',0,1),
-(0,193,20,'fad_mru_myn_2025_bld_1','FIX',0,2),
-(0,197,20,'fad_mru_myn_2025_fri_1','FIX',0,1),
-(0,195,20,'fad_mru_myn_2025_rom_1','FIX',0,2);
+(0,113,20,'Child container','FIX',0,1),
+(0,191,20,'MM_sb_3','FIX',0,1),
+(0,190,20,'MM_sb_2','FIX',0,1),
+(0,189,20,'MM_sb_1','FIX',0,1),
+(0,120,20,'Parent sample','FIX',0,1);
/*!40000 ALTER TABLE `archive_name_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -465,7 +482,7 @@ CREATE TABLE `archive_name_overrides` (
CONSTRAINT `archive_name_overrides_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_name_overrides_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_name_overrides_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -475,11 +492,7 @@ CREATE TABLE `archive_name_overrides` (
LOCK TABLES `archive_name_overrides` WRITE;
/*!40000 ALTER TABLE `archive_name_overrides` DISABLE KEYS */;
INSERT INTO `archive_name_overrides` VALUES
-(0,193,177,'BIS label',1),
-(0,193,177,'BIS label',2),
-(0,195,177,'BIS label',1),
-(0,195,177,'BIS label',2),
-(0,197,177,'BIS label',1);
+(0,187,162,'counter',1);
/*!40000 ALTER TABLE `archive_name_overrides` ENABLE KEYS */;
UNLOCK TABLES;
@@ -504,7 +517,7 @@ CREATE TABLE `archive_null_data` (
CONSTRAINT `archive_null_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_null_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_null_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -514,13 +527,9 @@ CREATE TABLE `archive_null_data` (
LOCK TABLES `archive_null_data` WRITE;
/*!40000 ALTER TABLE `archive_null_data` DISABLE KEYS */;
INSERT INTO `archive_null_data` VALUES
-(0,193,178,'FIX',0,1),
-(0,195,178,'FIX',0,1),
-(0,193,178,'FIX',0,2),
-(0,197,178,'FIX',0,1),
-(0,195,178,'FIX',0,2),
-(0,198,111,'FIX',1,1),
-(0,198,119,'FIX',2,1);
+(0,191,162,'FIX',0,1),
+(0,190,162,'FIX',0,1),
+(0,189,162,'FIX',0,1);
/*!40000 ALTER TABLE `archive_null_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -533,11 +542,11 @@ DROP TABLE IF EXISTS `archive_query_template_def`;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `archive_query_template_def` (
`id` int(10) unsigned NOT NULL,
- `definition` mediumtext NOT NULL,
+ `definition` longtext NOT NULL,
`_iversion` int(10) unsigned NOT NULL,
PRIMARY KEY (`id`,`_iversion`),
CONSTRAINT `archive_query_template_def_ibfk_1` FOREIGN KEY (`id`, `_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -574,7 +583,7 @@ CREATE TABLE `archive_reference_data` (
CONSTRAINT `archive_reference_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_reference_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_reference_data_ibfk_4` FOREIGN KEY (`value`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -584,32 +593,32 @@ CREATE TABLE `archive_reference_data` (
LOCK TABLES `archive_reference_data` WRITE;
/*!40000 ALTER TABLE `archive_reference_data` DISABLE KEYS */;
INSERT INTO `archive_reference_data` VALUES
-(0,188,177,187,NULL,'FIX',0,1),
-(0,188,105,177,NULL,'REPLACEMENT',4,1),
-(0,193,101,188,NULL,'FIX',0,1),
-(0,193,110,189,NULL,'FIX',1,1),
-(0,193,117,177,NULL,'REPLACEMENT',3,1),
-(0,193,112,178,NULL,'REPLACEMENT',4,1),
-(0,192,110,189,NULL,'FIX',1,1),
-(0,195,101,188,NULL,'FIX',0,1),
-(0,195,110,190,NULL,'FIX',1,1),
-(0,195,117,177,NULL,'REPLACEMENT',3,1),
-(0,195,112,178,NULL,'REPLACEMENT',4,1),
-(0,193,101,188,NULL,'FIX',0,2),
-(0,193,110,189,NULL,'FIX',1,2),
-(0,193,117,177,NULL,'REPLACEMENT',3,2),
-(0,193,112,178,NULL,'REPLACEMENT',4,2),
-(0,194,110,190,NULL,'FIX',1,1),
-(0,197,101,188,NULL,'FIX',0,1),
-(0,197,110,191,NULL,'FIX',1,1),
-(0,197,117,177,NULL,'REPLACEMENT',3,1),
-(0,197,112,178,NULL,'REPLACEMENT',4,1),
-(0,195,101,188,NULL,'FIX',0,2),
-(0,195,110,190,NULL,'FIX',1,2),
-(0,195,117,177,NULL,'REPLACEMENT',3,2),
-(0,195,112,178,NULL,'REPLACEMENT',4,2),
-(0,196,110,191,NULL,'FIX',1,1),
-(0,198,124,188,NULL,'FIX',0,1);
+(0,187,132,162,NULL,'REPLACEMENT',0,1),
+(0,187,107,181,NULL,'FIX',1,1),
+(0,191,101,182,NULL,'FIX',0,1),
+(0,191,107,181,NULL,'FIX',1,1),
+(0,191,113,162,NULL,'REPLACEMENT',3,1),
+(0,190,101,182,NULL,'FIX',0,1),
+(0,190,107,181,NULL,'FIX',1,1),
+(0,190,113,162,NULL,'REPLACEMENT',3,1),
+(0,189,101,182,NULL,'FIX',0,1),
+(0,189,107,181,NULL,'FIX',1,1),
+(0,189,113,162,NULL,'REPLACEMENT',3,1),
+(0,186,121,182,NULL,'FIX',0,1),
+(0,185,121,182,NULL,'FIX',0,1),
+(0,184,121,182,NULL,'FIX',0,1),
+(0,196,162,197,NULL,'FIX',0,1),
+(0,196,139,162,NULL,'REPLACEMENT',0,1),
+(0,196,163,177,NULL,'FIX',0,1),
+(0,196,124,163,NULL,'REPLACEMENT',1,1),
+(0,194,162,195,NULL,'FIX',0,1),
+(0,194,139,162,NULL,'REPLACEMENT',0,1),
+(0,194,163,177,NULL,'FIX',0,1),
+(0,194,124,163,NULL,'REPLACEMENT',1,1),
+(0,192,162,193,NULL,'FIX',0,1),
+(0,192,139,162,NULL,'REPLACEMENT',0,1),
+(0,192,163,177,NULL,'FIX',0,1),
+(0,192,124,163,NULL,'REPLACEMENT',1,1);
/*!40000 ALTER TABLE `archive_reference_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -624,7 +633,7 @@ CREATE TABLE `archive_text_data` (
`domain_id` int(10) unsigned NOT NULL,
`entity_id` int(10) unsigned NOT NULL,
`property_id` int(10) unsigned NOT NULL,
- `value` text NOT NULL,
+ `value` mediumtext NOT NULL,
`status` enum('OBLIGATORY','RECOMMENDED','SUGGESTED','FIX') NOT NULL,
`pidx` int(10) unsigned NOT NULL,
`_iversion` int(10) unsigned NOT NULL,
@@ -635,7 +644,7 @@ CREATE TABLE `archive_text_data` (
CONSTRAINT `archive_text_data_ibfk_1` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_text_data_ibfk_2` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `archive_text_data_ibfk_3` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -645,20 +654,9 @@ CREATE TABLE `archive_text_data` (
LOCK TABLES `archive_text_data` WRITE;
/*!40000 ALTER TABLE `archive_text_data` DISABLE KEYS */;
INSERT INTO `archive_text_data` VALUES
-(0,188,107,'My','FIX',0,1),
-(0,188,102,'myn','FIX',1,1),
-(0,188,108,'Name','FIX',2,1),
-(0,188,109,'my.name@example.com','FIX',3,1),
-(0,193,113,'20 rooms','FIX',2,1),
-(0,193,177,'fad_mru_myn_2025_bld_1','FIX',0,1),
-(0,195,113,'30 m²','FIX',2,1),
-(0,195,177,'fad_mru_myn_2025_rom_1','FIX',0,1),
-(0,193,113,'20 rooms','FIX',2,2),
-(0,193,177,'fad_mru_myn_2025_bld_1','FIX',0,2),
-(0,197,113,'300 l','FIX',2,1),
-(0,197,177,'fad_mru_myn_2025_fri_1','FIX',0,1),
-(0,195,113,'30 m²','FIX',2,2),
-(0,195,177,'fad_mru_myn_2025_rom_1','FIX',0,2);
+(0,191,114,'32','FIX',2,1),
+(0,190,114,'32','FIX',2,1),
+(0,189,114,'32','FIX',2,1);
/*!40000 ALTER TABLE `archive_text_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -681,7 +679,7 @@ CREATE TABLE `collection_type` (
CONSTRAINT `collection_type_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `collection_type_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `collection_type_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -691,16 +689,19 @@ CREATE TABLE `collection_type` (
LOCK TABLES `collection_type` WRITE;
/*!40000 ALTER TABLE `collection_type` DISABLE KEYS */;
INSERT INTO `collection_type` VALUES
-(0,0,112,'LIST'),
-(0,0,125,'LIST'),
-(0,0,126,'LIST'),
-(0,0,127,'LIST'),
-(0,0,128,'LIST'),
-(0,0,129,'LIST'),
-(0,0,141,'LIST'),
-(0,0,164,'LIST'),
-(0,153,177,'LIST'),
-(0,210,178,'LIST');
+(0,0,113,'LIST'),
+(0,0,122,'LIST'),
+(0,0,123,'LIST'),
+(0,0,137,'LIST'),
+(0,0,154,'LIST'),
+(0,0,160,'LIST'),
+(0,126,165,'LIST'),
+(0,189,163,'LIST'),
+(0,190,163,'LIST'),
+(0,191,163,'LIST'),
+(0,192,162,'LIST'),
+(0,194,162,'LIST'),
+(0,196,162,'LIST');
/*!40000 ALTER TABLE `collection_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -725,7 +726,7 @@ CREATE TABLE `data_type` (
CONSTRAINT `datatype_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `datatype_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`),
CONSTRAINT `datatype_forkey_type` FOREIGN KEY (`datatype`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -735,72 +736,77 @@ CREATE TABLE `data_type` (
LOCK TABLES `data_type` WRITE;
/*!40000 ALTER TABLE `data_type` DISABLE KEYS */;
INSERT INTO `data_type` VALUES
-(0,0,134,12),
-(0,0,137,12),
-(0,0,144,13),
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-(0,0,146,13),
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(0,0,20,14),
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(0,0,104,14),
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(0,0,128,14),
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-(0,111,178,110),
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-(0,0,122,118),
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-(0,119,178,138),
-(0,153,177,143),
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-(0,150,177,148),
-(0,153,178,148),
-(0,210,177,148);
+(0,0,150,14),
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+(0,111,162,101),
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+(0,0,154,103),
+(0,184,162,103),
+(0,185,162,103),
+(0,186,162,103),
+(0,111,163,107),
+(0,131,162,107),
+(0,111,165,108),
+(0,108,162,109),
+(0,180,162,109),
+(0,0,113,111),
+(0,118,162,111),
+(0,0,120,118),
+(0,118,163,119),
+(0,118,166,124),
+(0,126,164,124),
+(0,192,163,124),
+(0,194,163,124),
+(0,196,163,124),
+(0,0,145,126),
+(0,118,167,126),
+(0,0,156,127),
+(0,118,168,127),
+(0,176,162,127),
+(0,189,163,130),
+(0,190,163,130),
+(0,191,163,130),
+(0,135,163,133),
+(0,174,163,133),
+(0,126,165,139),
+(0,192,162,139),
+(0,194,162,139),
+(0,196,162,139),
+(0,126,166,143),
+(0,126,162,144),
+(0,126,163,146),
+(0,126,167,153);
/*!40000 ALTER TABLE `data_type` ENABLE KEYS */;
UNLOCK TABLES;
@@ -824,7 +830,7 @@ CREATE TABLE `date_data` (
CONSTRAINT `date_ov_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `date_ov_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `date_ov_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -834,7 +840,12 @@ CREATE TABLE `date_data` (
LOCK TABLES `date_data` WRITE;
/*!40000 ALTER TABLE `date_data` DISABLE KEYS */;
INSERT INTO `date_data` VALUES
-(0,210,151,20250101,'FIX',0);
+(0,196,147,20231220,'FIX',2),
+(0,196,148,20231220,'FIX',3),
+(0,194,147,20231220,'FIX',2),
+(0,194,148,20231220,'FIX',3),
+(0,192,147,20231220,'FIX',2),
+(0,192,148,20231220,'FIX',3);
/*!40000 ALTER TABLE `date_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -859,7 +870,7 @@ CREATE TABLE `datetime_data` (
CONSTRAINT `dat_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `dat_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `dat_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -890,7 +901,7 @@ CREATE TABLE `desc_overrides` (
CONSTRAINT `desc_ov_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `desc_ov_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `desc_ov_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -923,7 +934,7 @@ CREATE TABLE `double_data` (
CONSTRAINT `dou_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `dou_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `dou_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -933,8 +944,13 @@ CREATE TABLE `double_data` (
LOCK TABLES `double_data` WRITE;
/*!40000 ALTER TABLE `double_data` DISABLE KEYS */;
INSERT INTO `double_data` VALUES
-(0,211,146,1.1,'FIX',0,-1941227323),
-(0,211,147,1.2,'FIX',1,-1941227323);
+(0,193,140,13.2,'FIX',0,-1941227323),
+(0,193,141,1,'FIX',1,-1941227323),
+(0,195,140,14,'FIX',0,-1941227323),
+(0,195,141,2,'FIX',1,-1941227323),
+(0,195,142,23,'FIX',2,NULL),
+(0,197,140,16.3,'FIX',0,-1941227323),
+(0,197,141,3,'FIX',1,-1941227323);
/*!40000 ALTER TABLE `double_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -953,7 +969,7 @@ CREATE TABLE `entities` (
PRIMARY KEY (`id`),
KEY `entity_entity_acl` (`acl`),
CONSTRAINT `entity_entity_acl` FOREIGN KEY (`acl`) REFERENCES `entity_acl` (`id`)
-) ENGINE=InnoDB AUTO_INCREMENT=212 DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB AUTO_INCREMENT=198 DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -983,116 +999,101 @@ INSERT INTO `entities` VALUES
(24,'Description of an entity.','PROPERTY',0),
(100,'Abstract type to denote that a RecordType is controlled, i.e.,\nthat no new Records of this type may be created during\nsample/container upload. Add this type as a parent to any\nRecordType you want to be controlled.\n','RECORDTYPE',2),
(101,NULL,'RECORDTYPE',2),
-(102,'An abbreviation for this entity that is used for creating BIS labels','PROPERTY',2),
+(102,'An abbreviation for this entity that is used for identification purposes','PROPERTY',2),
(103,NULL,'RECORDTYPE',2),
-(104,'A german name for an entitiy. This can be used in queries since it is an alias.','PROPERTY',2),
-(105,NULL,'RECORDTYPE',2),
-(106,NULL,'RECORDTYPE',2),
-(107,NULL,'PROPERTY',2),
-(108,NULL,'PROPERTY',2),
-(109,NULL,'PROPERTY',2),
-(110,NULL,'RECORDTYPE',2),
+(104,NULL,'PROPERTY',2),
+(105,NULL,'PROPERTY',2),
+(106,NULL,'PROPERTY',2),
+(107,NULL,'RECORDTYPE',2),
+(108,NULL,'RECORDTYPE',2),
+(109,NULL,'RECORDTYPE',2),
+(110,NULL,'PROPERTY',2),
(111,NULL,'RECORDTYPE',2),
-(112,NULL,'PROPERTY',2),
-(113,'The size of the container, e.g. number of spaces or dimension','PROPERTY',2),
-(114,'A custom label for a container that doesn\'t have to follow the BIS labeling guidelines.','PROPERTY',2),
-(115,NULL,'PROPERTY',2),
+(112,'A standardized label for a container','PROPERTY',2),
+(113,NULL,'PROPERTY',2),
+(114,'The size of the container, e.g. number of spaces or dimension','PROPERTY',2),
+(115,'A custom label for a container that doesn\'t have to follow the automatic labeling guidelines.','PROPERTY',2),
(116,NULL,'PROPERTY',2),
-(117,'A standardized label for a container in BIS.','PROPERTY',2),
+(117,NULL,'PROPERTY',2),
(118,NULL,'RECORDTYPE',2),
(119,NULL,'RECORDTYPE',2),
-(120,NULL,'RECORDTYPE',2),
-(121,NULL,'RECORDTYPE',2),
+(120,NULL,'PROPERTY',2),
+(121,NULL,'PROPERTY',2),
(122,NULL,'PROPERTY',2),
(123,NULL,'PROPERTY',2),
-(124,NULL,'PROPERTY',2),
+(124,NULL,'RECORDTYPE',2),
(125,NULL,'PROPERTY',2),
-(126,'DOIs of publications related to this sample.','PROPERTY',2),
-(127,NULL,'PROPERTY',2),
+(126,NULL,'RECORDTYPE',2),
+(127,NULL,'RECORDTYPE',2),
(128,NULL,'PROPERTY',2),
(129,NULL,'PROPERTY',2),
-(130,'A short description of the sampling methodology used for this sample.','PROPERTY',2),
-(131,NULL,'PROPERTY',2),
+(130,NULL,'RECORDTYPE',2),
+(131,NULL,'RECORDTYPE',2),
(132,NULL,'PROPERTY',2),
-(133,NULL,'PROPERTY',2),
-(134,'An ID for this taxon that allows to uniquely identify it on http://www.marinespecies.org.','PROPERTY',2),
+(133,NULL,'RECORDTYPE',2),
+(134,'The Marine Regions Geographic Identifier, i.e. a PID (Persistent Identifier) for a geographic region on https://www.marineregions.org','PROPERTY',2),
(135,NULL,'RECORDTYPE',2),
-(136,NULL,'RECORDTYPE',2),
+(136,'A link to the Nagoya documents (or an indication where to find the documents).','PROPERTY',2),
(137,NULL,'PROPERTY',2),
-(138,NULL,'RECORDTYPE',2),
-(139,'The Marine Regions Geographic Identifier, i.e. a PID (Persistent Identifier) for a geographic region on https://www.marineregions.org','PROPERTY',2),
-(140,'A link to the Nagoya documents (or an indication where to find the documents).','PROPERTY',2),
+(138,'An identifier for nagoya cases. This is managed by the Nagoya-Coordinator and should be taken care of before sampling.','PROPERTY',2),
+(139,NULL,'RECORDTYPE',2),
+(140,NULL,'PROPERTY',2),
(141,NULL,'PROPERTY',2),
-(142,'An identifier for nagoya cases. This is managed by the Nagoya-Coordinator and should be taken care of before sampling.','PROPERTY',2),
+(142,NULL,'PROPERTY',2),
(143,NULL,'RECORDTYPE',2),
-(144,'The depth of the water in meters as a positive value','PROPERTY',2),
-(145,'The depth in meters where the sampling took place as a positive value','PROPERTY',2),
-(146,NULL,'PROPERTY',2),
-(147,NULL,'PROPERTY',2),
-(148,NULL,'RECORDTYPE',2),
+(144,NULL,'RECORDTYPE',2),
+(145,NULL,'PROPERTY',2),
+(146,'Cruise name or leg description','RECORDTYPE',2),
+(147,'The date and time the event started.','PROPERTY',2),
+(148,'The date and time the event ended.','PROPERTY',2),
(149,NULL,'PROPERTY',2),
-(150,NULL,'RECORDTYPE',2),
-(151,'The date and time the event started.','PROPERTY',2),
-(152,'The date and time the event ended.','PROPERTY',2),
+(150,NULL,'PROPERTY',2),
+(151,NULL,'PROPERTY',2),
+(152,NULL,'PROPERTY',2),
(153,NULL,'RECORDTYPE',2),
(154,NULL,'PROPERTY',2),
-(155,NULL,'PROPERTY',2),
+(155,NULL,'RECORDTYPE',2),
(156,NULL,'PROPERTY',2),
-(157,NULL,'PROPERTY',2),
-(158,'The name/identifier of a station where regular sampling activity takes place.','PROPERTY',2),
+(157,NULL,'RECORDTYPE',2),
+(158,NULL,'RECORDTYPE',2),
(159,NULL,'RECORDTYPE',2),
-(160,NULL,'RECORDTYPE',2),
-(161,NULL,'RECORDTYPE',2),
-(162,NULL,'RECORDTYPE',2),
-(163,NULL,'RECORDTYPE',2),
-(164,NULL,'PROPERTY',2),
-(165,NULL,'RECORDTYPE',2),
-(166,NULL,'PROPERTY',2),
-(167,NULL,'RECORDTYPE',2),
-(168,NULL,'RECORDTYPE',2),
-(169,'Cruise name or leg description','RECORDTYPE',2),
-(170,NULL,'RECORDTYPE',2),
-(171,NULL,'RECORDTYPE',2),
-(172,'PDF files which contain reports and additional information about samples, collections, or containers','RECORDTYPE',2),
-(173,NULL,'RECORDTYPE',2),
-(174,NULL,'RECORDTYPE',2),
-(175,NULL,'RECORDTYPE',2),
-(176,NULL,'RECORDTYPE',2),
-(177,NULL,'_REPLACEMENT',0),
-(178,NULL,'_REPLACEMENT',0),
-(179,NULL,'_REPLACEMENT',0),
-(180,NULL,'_REPLACEMENT',0),
-(181,NULL,'_REPLACEMENT',0),
-(182,NULL,'_REPLACEMENT',0),
-(183,NULL,'_REPLACEMENT',0),
-(184,NULL,'_REPLACEMENT',0),
-(185,NULL,'_REPLACEMENT',0),
+(160,NULL,'PROPERTY',2),
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UNLOCK TABLES;
@@ -1108,7 +1109,7 @@ CREATE TABLE `entity_acl` (
`acl` varbinary(65525) NOT NULL,
PRIMARY KEY (`id`),
KEY `entity_acl_acl` (`acl`(3072))
-) ENGINE=InnoDB AUTO_INCREMENT=4 DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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@@ -1119,8 +1120,7 @@ LOCK TABLES `entity_acl` WRITE;
/*!40000 ALTER TABLE `entity_acl` DISABLE KEYS */;
INSERT INTO `entity_acl` VALUES
(0,''),
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/*!40000 ALTER TABLE `entity_acl` ENABLE KEYS */;
UNLOCK TABLES;
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('162',160),
('163',161),
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/*!40000 ALTER TABLE `entity_ids` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1289,7 +1276,7 @@ CREATE TABLE `entity_version` (
KEY `srid` (`srid`),
CONSTRAINT `entity_version_ibfk_1` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`) ON DELETE CASCADE,
CONSTRAINT `entity_version_ibfk_2` FOREIGN KEY (`srid`) REFERENCES `transactions` (`srid`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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/*!40000 ALTER TABLE `entity_version` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1453,7 +1429,7 @@ CREATE TABLE `enum_data` (
CONSTRAINT `enum_ov_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `enum_ov_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `enum_ov_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1476,7 +1452,7 @@ CREATE TABLE `feature_config` (
`_key` varchar(255) NOT NULL,
`_value` varchar(255) DEFAULT NULL,
PRIMARY KEY (`_key`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1505,7 +1481,7 @@ CREATE TABLE `files` (
`checked_timestamp` bigint(20) NOT NULL DEFAULT 0,
PRIMARY KEY (`file_id`),
CONSTRAINT `fil_file_id_entity` FOREIGN KEY (`file_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1538,7 +1514,7 @@ CREATE TABLE `integer_data` (
CONSTRAINT `int_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `int_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `int_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
--
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LOCK TABLES `integer_data` WRITE;
/*!40000 ALTER TABLE `integer_data` DISABLE KEYS */;
INSERT INTO `integer_data` VALUES
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UNLOCK TABLES;
@@ -1569,7 +1543,7 @@ CREATE TABLE `isa_cache` (
KEY `isa_cache_parent_entity` (`parent`),
CONSTRAINT `isa_cache_child_entity` FOREIGN KEY (`child`) REFERENCES `entities` (`id`),
CONSTRAINT `isa_cache_parent_entity` FOREIGN KEY (`parent`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1581,81 +1555,64 @@ LOCK TABLES `isa_cache` WRITE;
INSERT INTO `isa_cache` VALUES
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/*!40000 ALTER TABLE `isa_cache` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1681,7 +1638,7 @@ CREATE TABLE `name_data` (
CONSTRAINT `name_data_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `name_data_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `name_data_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1712,97 +1669,80 @@ INSERT INTO `name_data` VALUES
(0,100,20,'ControlledRecordType','FIX',0),
(0,101,20,'Responsible','FIX',0),
(0,102,20,'Abbreviation','FIX',0),
-(0,103,20,'ResearchDivision','FIX',0),
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(0,111,20,'Container','FIX',0),
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-(0,115,20,'Container Contents','FIX',0),
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-(0,117,20,'BIS Label','FIX',0),
+(0,112,20,'container_label','FIX',0),
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/*!40000 ALTER TABLE `name_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1825,7 +1765,7 @@ CREATE TABLE `name_overrides` (
CONSTRAINT `name_ov_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `name_ov_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `name_ov_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1835,10 +1775,7 @@ CREATE TABLE `name_overrides` (
LOCK TABLES `name_overrides` WRITE;
/*!40000 ALTER TABLE `name_overrides` DISABLE KEYS */;
INSERT INTO `name_overrides` VALUES
-(0,193,177,'BIS label'),
-(0,197,177,'BIS label'),
-(0,195,177,'BIS label'),
-(0,198,180,'Sample Context');
+(0,187,162,'counter');
/*!40000 ALTER TABLE `name_overrides` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1861,7 +1798,7 @@ CREATE TABLE `null_data` (
CONSTRAINT `null_forkey_dom` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `null_forkey_ent` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `null_forkey_pro` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1871,79 +1808,74 @@ CREATE TABLE `null_data` (
LOCK TABLES `null_data` WRITE;
/*!40000 ALTER TABLE `null_data` DISABLE KEYS */;
INSERT INTO `null_data` VALUES
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+(0,174,163,'FIX',0),
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+(0,193,142,'FIX',2),
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/*!40000 ALTER TABLE `null_data` ENABLE KEYS */;
UNLOCK TABLES;
@@ -1961,7 +1893,7 @@ CREATE TABLE `passwd` (
`it` int(10) unsigned DEFAULT 5000,
`salt` varbinary(255) NOT NULL,
PRIMARY KEY (`principal`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -1985,7 +1917,7 @@ CREATE TABLE `permissions` (
`permissions` mediumtext NOT NULL,
PRIMARY KEY (`role`),
CONSTRAINT `perm_name_roles` FOREIGN KEY (`role`) REFERENCES `roles` (`name`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -2011,7 +1943,7 @@ CREATE TABLE `query_template_def` (
`definition` mediumtext NOT NULL,
PRIMARY KEY (`id`),
CONSTRAINT `query_template_def_ibfk_1` FOREIGN KEY (`id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -2048,7 +1980,7 @@ CREATE TABLE `reference_data` (
CONSTRAINT `ref_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`),
CONSTRAINT `ref_value_entity` FOREIGN KEY (`value`) REFERENCES `entities` (`id`),
CONSTRAINT `reference_data_ibfk_1` FOREIGN KEY (`value`, `value_iversion`) REFERENCES `entity_version` (`entity_id`, `_iversion`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
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@@ -2133,7 +2083,7 @@ CREATE TABLE `roles` (
`name` varbinary(255) NOT NULL,
`description` mediumtext DEFAULT NULL,
PRIMARY KEY (`name`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
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`name` varchar(255) NOT NULL,
`value` blob DEFAULT NULL,
PRIMARY KEY (`name`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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CONSTRAINT `str_domain_id_entity` FOREIGN KEY (`domain_id`) REFERENCES `entities` (`id`),
CONSTRAINT `str_entity_id_entity` FOREIGN KEY (`entity_id`) REFERENCES `entities` (`id`),
CONSTRAINT `str_property_id_entity` FOREIGN KEY (`property_id`) REFERENCES `entities` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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`realm` varbinary(255) NOT NULL,
KEY `entity_id` (`entity_id`)
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/*!40101 SET character_set_client = @saved_cs_client */;
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/*!40000 ALTER TABLE `transaction_log` DISABLE KEYS */;
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-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
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/*!40101 SET character_set_client = @saved_cs_client */;
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+('a7994338-93c3-4cb7-9eaa-e0ea57de0069','admin','PAM',1741702289,139000000),
+('b9286cef-88c4-4e3d-90e1-ee09a76feae8','admin','PAM',1741702954,287000000),
+('bb848008-57b3-427d-876a-c5ff774d3d88','admin','PAM',1741704540,640000000),
+('bdf470b8-c562-4e4d-a2f2-1f2680822aed','admin','PAM',1741702512,658000000),
('cf83e1357eefb8bdf1542850d66d8007d620e4050b5715dc83f4a921d36ce9ce47d0d13c5d85f2b0ff8318d2877eec2f63b931bd47417a81a538327af927da3e','administration','CaosDB',0,0),
-('d0af8a57-7550-42b2-aba9-4b254897976b','admin','PAM',1736265392,704000000),
-('da56170f-ae54-4ecf-9aa4-342d7512384f','admin','PAM',1736265798,309000000),
-('daa492ef-1495-4123-9966-9951328211b3','admin','PAM',1736265204,580000000),
-('dbf1dd0f-405c-4952-b8b6-62e169c79397','admin','PAM',1736265204,802000000),
-('df3a0e97-6feb-42aa-8800-074ee5520428','admin','PAM',1736265392,321000000),
-('f284f0d8-aba2-44e9-bfc7-ae68fab970b9','admin','PAM',1736265770,375000000),
-('fe535f2d-6865-41b7-bab1-781f412454f6','admin','PAM',1736265441,988000000);
+('d66682c8-1138-4734-be3d-3e7f491899b2','admin','PAM',1741702380,899000000),
+('dcd7eccb-3e38-4c04-9a98-0159bda1e2c6','admin','PAM',1741704265,193000000),
+('df090b99-7e9b-43ba-a461-367778e17068','admin','PAM',1741702362,280000000),
+('f2003a25-cbfa-4513-ac3d-2cfc5ca7f2f4','admin','PAM',1741702565,386000000),
+('f4a55cb7-a8f1-407e-9254-9de3402cd960','admin','PAM',1741702796,807000000),
+('f8cff7ae-db88-47cd-9f9e-2877478a8856','admin','PAM',1741702183,776000000),
+('fa408261-eb8d-4da1-9ed6-026e344ec756','admin','PAM',1741702250,689000000),
+('fbab0a14-0ffb-4385-84c7-9d003b932757','admin','PAM',1741702528,907000000);
/*!40000 ALTER TABLE `transactions` ENABLE KEYS */;
UNLOCK TABLES;
@@ -2465,7 +2393,7 @@ CREATE TABLE `units_lin_con` (
`b_divisor` int(11) NOT NULL,
`c` decimal(65,30) NOT NULL,
PRIMARY KEY (`signature_from`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -2493,7 +2421,7 @@ CREATE TABLE `user_info` (
PRIMARY KEY (`realm`,`name`),
KEY `subject_entity` (`entity`),
CONSTRAINT `subjects_ibfk_2` FOREIGN KEY (`entity`) REFERENCES `entity_ids` (`id`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -2521,7 +2449,7 @@ CREATE TABLE `user_roles` (
PRIMARY KEY (`realm`,`user`,`role`),
KEY `user_roles_ibfk_1` (`role`),
CONSTRAINT `user_roles_ibfk_1` FOREIGN KEY (`role`) REFERENCES `roles` (`name`)
-) ENGINE=InnoDB DEFAULT CHARSET=utf8mb3 COLLATE=utf8mb3_unicode_ci;
+) ENGINE=InnoDB DEFAULT CHARSET=utf8mb4 COLLATE=utf8mb4_uca1400_as_ci;
/*!40101 SET character_set_client = @saved_cs_client */;
--
@@ -2544,13 +2472,13 @@ UNLOCK TABLES;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `CaosDBVersion`() RETURNS varchar(255) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `CaosDBVersion`() RETURNS varchar(255) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
-RETURN 'v8.0.0' ;;
+RETURN 'v8.1.0' ;;
DELIMITER ;
/*!50003 SET sql_mode = @saved_sql_mode */ ;
/*!50003 SET character_set_client = @saved_cs_client */ ;
@@ -2562,11 +2490,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `constructDateTimeWhereClauseForColumn`(seconds_col VARCHAR(255), nanos_col VARCHAR(255), vDateTimeSecLow VARCHAR(255), vDateTimeNSLow VARCHAR(255), vDateTimeSecUpp VARCHAR(255), vDateTimeNSUpp VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `constructDateTimeWhereClauseForColumn`(seconds_col VARCHAR(255), nanos_col VARCHAR(255), vDateTimeSecLow VARCHAR(255), vDateTimeNSLow VARCHAR(255), vDateTimeSecUpp VARCHAR(255), vDateTimeNSUpp VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
@@ -2631,9 +2559,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `convert_unit`(unit_sig BIGINT, value DECIMAL(65,30)) RETURNS decimal(65,30)
DETERMINISTIC
@@ -2654,11 +2582,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `getAggValueWhereClause`(entities VARCHAR(255), properties VARCHAR(255)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `getAggValueWhereClause`(entities VARCHAR(255), properties VARCHAR(255)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
RETURN CONCAT(" EXISTS (SELECT 1 FROM `", entities, "` AS ent WHERE ent.id = subdata.entity_id LIMIT 1)", IF(properties IS NOT NULL AND properties != '', CONCAT(" AND EXISTS (SELECT 1 FROM `", properties, "` as props WHERE props.id = subdata.property_id LIMIT 1)"),''));
@@ -2674,11 +2602,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `getDateTimeWhereClause`(vDateTime VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `getDateTimeWhereClause`(vDateTime VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
DECLARE sep_loc INTEGER DEFAULT LOCATE('--',vDateTime);
@@ -2705,11 +2633,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `getDateWhereClause`(vDateTimeDotNotation VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `getDateWhereClause`(vDateTimeDotNotation VARCHAR(255), operator CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
DECLARE isInterval INTEGER DEFAULT LOCATE('--',vDateTimeDotNotation);
@@ -2814,11 +2742,11 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
-CREATE DEFINER=`root`@`%` FUNCTION `getDoubleWhereClause`(value DOUBLE, unit_sig BIGINT, valueStdUnit DECIMAL(65,30), stdUnit_sig BIGINT, o CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+CREATE DEFINER=`root`@`%` FUNCTION `getDoubleWhereClause`(value DOUBLE, unit_sig BIGINT, valueStdUnit DECIMAL(65,30), stdUnit_sig BIGINT, o CHAR(4)) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
DETERMINISTIC
BEGIN
RETURN IF(unit_sig IS NULL AND value IS NOT NULL,
@@ -2839,9 +2767,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_head_relative`(EntityID VARCHAR(255),
HeadOffset INT UNSIGNED) RETURNS varbinary(255)
@@ -2874,9 +2802,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_head_version`(EntityID VARCHAR(255)) RETURNS varbinary(255)
READS SQL DATA
@@ -2894,9 +2822,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_iversion`(InternalEntityID INT UNSIGNED,
Version VARBINARY(255)) RETURNS int(10) unsigned
@@ -2920,9 +2848,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_primary_parent_version`(EntityID VARCHAR(255),
Version VARBINARY(255)) RETURNS varbinary(255)
@@ -2952,12 +2880,12 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `get_version_timestamp`(EntityID VARCHAR(255),
- Version VARBINARY(255)) RETURNS varchar(255) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+ Version VARBINARY(255)) RETURNS varchar(255) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
READS SQL DATA
BEGIN
DECLARE InternalEntityID INT UNSIGNED DEFAULT NULL;
@@ -2983,9 +2911,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `is_feature_config`(_Key VARCHAR(255),
Expected VARCHAR(255)) RETURNS tinyint(1)
@@ -3006,12 +2934,12 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `makeStmt`(sourceSet VARCHAR(255), targetSet VARCHAR(255), data VARCHAR(20000),
- properties VARCHAR(20000), versioned BOOLEAN) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_unicode_ci
+ properties VARCHAR(20000), versioned BOOLEAN) RETURNS varchar(20000) CHARSET utf8mb3 COLLATE utf8mb3_uca1400_as_ci
NO SQL
BEGIN
IF sourceSet = "entities" AND versioned THEN
@@ -3064,9 +2992,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `standard_unit`(unit_sig BIGINT) RETURNS bigint(20)
DETERMINISTIC
@@ -3087,9 +3015,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `_get_head_iversion`(InternalEntityID INT UNSIGNED) RETURNS int(10) unsigned
READS SQL DATA
@@ -3117,9 +3045,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` FUNCTION `_get_version`(InternalEntityID INT UNSIGNED,
IVersion INT UNSIGNED) RETURNS varbinary(255)
@@ -3142,9 +3070,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyBackReference`(in sourceSet VARCHAR(255), targetSet VARCHAR(255),
in propertiesTable VARCHAR(255), in entitiesTable VARCHAR(255), in subQuery BOOLEAN,
@@ -3323,9 +3251,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyIDFilter`(in sourceSet VARCHAR(255), in targetSet VARCHAR(255),
in o CHAR(2), in EntityID VARCHAR(255), in agg CHAR(3), in versioned BOOLEAN)
@@ -3460,9 +3388,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyPOV`(in sourceSet VARCHAR(255),
in targetSet VARCHAR(255),
@@ -3765,9 +3693,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyRefPOV`(in sourceSet VARCHAR(255), in targetSet VARCHAR(255),
in properties VARCHAR(255), in refs VARCHAR(255),
@@ -3805,9 +3733,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applySAT`(in sourceSet VARCHAR(255), in targetSet VARCHAR(255), in loc MEDIUMTEXT, in op CHAR(5))
BEGIN
@@ -3834,9 +3762,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `applyTransactionFilter`(in sourceSet VARCHAR(255), targetSet VARCHAR(255), in transaction VARCHAR(255), in operator_u CHAR(2), in realm VARCHAR(255), in userName VARCHAR(255), in ilb BIGINT, in ilb_nanos INT UNSIGNED, in eub BIGINT, in eub_nanos INT UNSIGNED, in operator_t CHAR(2))
BEGIN
@@ -3876,9 +3804,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `calcComplementUnion`(in targetSet VARCHAR(255), in subResultSet VARCHAR(255), in universe VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -3916,9 +3844,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `calcDifference`(in resultSetTable VARCHAR(255), in diff VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -3943,9 +3871,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `calcIntersection`(in resultSetTable VARCHAR(255), in intersectWith VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -3978,9 +3906,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `calcUnion`(in targetSet VARCHAR(255), in sourceSet VARCHAR(255))
BEGIN
@@ -4001,9 +3929,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `cleanUpLinCon`()
BEGIN
@@ -4022,9 +3950,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `cleanUpQuery`()
BEGIN
@@ -4049,9 +3977,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `copyTable`(in fromTable VARCHAR(255), in toTable VARCHAR(255))
BEGIN
@@ -4072,9 +4000,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `createTmpTable`(out newTableName VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -4102,9 +4030,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `createTmpTable2`(out newTableName VARCHAR(255))
BEGIN
@@ -4128,9 +4056,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `deleteEntity`(in EntityID VARCHAR(255))
BEGIN
@@ -4184,9 +4112,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `deleteEntityProperties`(in EntityID VARCHAR(255))
BEGIN
@@ -4357,9 +4285,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `deleteIsa`(IN InternalEntityID INT UNSIGNED)
BEGIN
@@ -4395,9 +4323,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `deleteLinCon`(in sig BIGINT)
BEGIN
@@ -4416,9 +4344,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `entityACL`(out ACLID INT UNSIGNED, in ACLSTR VARBINARY(65525))
BEGIN
@@ -4439,9 +4367,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `finishNegationFilter`(in resultSetTable VARCHAR(255), in diff VARCHAR(255))
BEGIN
@@ -4458,9 +4386,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `finishSubProperty`(in sourceSet VARCHAR(255),in targetSet VARCHAR(255),
in list VARCHAR(255), in versioned BOOLEAN)
@@ -4486,9 +4414,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `getChildren`(in tableName varchar(255), in versioned BOOLEAN)
BEGIN
@@ -4555,9 +4483,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `getDependentEntities`(in EntityID VARCHAR(255))
BEGIN
@@ -4659,9 +4587,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `getFileIdByPath`(in FilePath TEXT)
BEGIN
@@ -4680,9 +4608,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `getIdByName`(in Name VARCHAR(255), in Role VARCHAR(255), in Lmt INT UNSIGNED)
BEGIN
@@ -4743,9 +4671,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `get_version_history`(
in EntityID VARCHAR(255))
@@ -4796,9 +4724,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initBackReference`(in PropertyID VARCHAR(255), in PropertyName VARCHAR(255), in EntityID VARCHAR(255), in EntityName VARCHAR(255))
BEGIN
@@ -4854,9 +4782,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initDisjunctionFilter`(in versioned BOOLEAN)
BEGIN
@@ -4873,9 +4801,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initEmptyTargetSet`(in targetSet VARCHAR(255), in versioned BOOLEAN)
BEGIN
@@ -4905,9 +4833,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initEntity`(in eid VARCHAR(255), in ename VARCHAR(255),
in enameLike VARCHAR(255), in enameRegexp VARCHAR(255),
@@ -5041,9 +4969,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initPOVPropertiesTable`(in PropertyID VARCHAR(255), in PropertyName VARCHAR(255), in sourceSet VARCHAR(255))
BEGIN
@@ -5123,9 +5051,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initPOVRefidsTable`(in PropertyID VARCHAR(255), in PropertyName VARCHAR(255))
BEGIN
@@ -5152,9 +5080,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initQuery`(in versioned BOOLEAN)
BEGIN
@@ -5175,9 +5103,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initSubEntity`(in EntityID VARCHAR(255), in ename VARCHAR(255), in tableName VARCHAR(255))
BEGIN
@@ -5227,9 +5155,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `initSubProperty`(in sourceSet VARCHAR(255), in propertiesTable VARCHAR(255), in refIdsTable VARCHAR(255))
BEGIN
@@ -5278,9 +5206,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertEntity`(in EntityID VARCHAR(255), in EntityName VARCHAR(255), in EntityDesc TEXT, in EntityRole VARCHAR(255), in ACL VARBINARY(65525))
BEGIN
@@ -5332,9 +5260,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertEntityCollection`(in PropertyID VARCHAR(255), in Collection VARCHAR(255))
BEGIN
@@ -5356,9 +5284,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertEntityDataType`(in PropertyID VARCHAR(255), in DataTypeID VARCHAR(255))
BEGIN
@@ -5381,9 +5309,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertEntityProperty`(
in DomainID VARCHAR(255),
@@ -5523,9 +5451,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertIsa`(IN ChildID VARCHAR(255), IN ParentID VARCHAR(255))
insert_is_a_proc: BEGIN
@@ -5588,9 +5516,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insertLinCon`(in signature_from BIGINT, in signature_to BIGINT, in a DECIMAL(65,30), in b_dividend BIGINT, in b_divisor BIGINT, in c DECIMAL(65,30))
BEGIN
@@ -5609,9 +5537,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `insert_single_child_version`(
in InternalEntityID INT UNSIGNED,
@@ -5664,9 +5592,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `intersectTable`(in resultSetTable VARCHAR(255), in diff VARCHAR(255))
BEGIN
@@ -5687,9 +5615,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `isSubtype`(in ChildID VARCHAR(255), in ParentID VARCHAR(255))
BEGIN
@@ -5714,9 +5642,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `overrideDesc`(in InternalDomainID INT UNSIGNED, in InternalEntityID INT UNSIGNED, in InternalPropertyID INT UNSIGNED, in Description TEXT)
BEGIN
@@ -5733,9 +5661,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `overrideName`(in InternalDomainID INT UNSIGNED, in InternalEntityID INT UNSIGNED, in InternalPropertyID INT UNSIGNED, in Name VARCHAR(255))
BEGIN
@@ -5752,9 +5680,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `overrideType`(in InternalDomainID INT UNSIGNED, in InternalEntityID INT UNSIGNED, in InternalPropertyID INT UNSIGNED, in InternalDataTypeID INT UNSIGNED)
BEGIN
@@ -5771,9 +5699,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `raiseWarning`(in str VARCHAR(20000))
BEGIN
@@ -5790,9 +5718,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `registerReplacementIds`(in amount INT UNSIGNED)
BEGIN
@@ -5821,9 +5749,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `registerTempTableName`(out newTableName VARCHAR(255))
BEGIN
@@ -5869,9 +5797,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveEntity`(
in EntityID VARCHAR(255),
@@ -6027,9 +5955,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveEntityParents`(
in EntityID VARCHAR(255),
@@ -6108,9 +6036,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveEntityProperties`(
in DomainID VARCHAR(255),
@@ -6430,9 +6358,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveOverrides`(
in DomainID VARCHAR(255),
@@ -6625,9 +6553,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `retrieveQueryTemplateDef`(
in EntityID VARCHAR(255),
@@ -6680,9 +6608,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `setFileProperties`(
in EntityID VARCHAR(255),
@@ -6727,9 +6655,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `set_transaction`(
srid VARBINARY(255),
@@ -6754,9 +6682,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `showEntityAutoIncr`()
BEGIN
@@ -6778,9 +6706,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `updateEntity`(
in EntityID VARCHAR(255),
@@ -6892,9 +6820,9 @@ DELIMITER ;
/*!50003 SET @saved_cs_client = @@character_set_client */ ;
/*!50003 SET @saved_cs_results = @@character_set_results */ ;
/*!50003 SET @saved_col_connection = @@collation_connection */ ;
-/*!50003 SET character_set_client = utf8mb3 */ ;
-/*!50003 SET character_set_results = utf8mb3 */ ;
-/*!50003 SET collation_connection = utf8mb3_general_ci */ ;
+/*!50003 SET character_set_client = latin1 */ ;
+/*!50003 SET character_set_results = latin1 */ ;
+/*!50003 SET collation_connection = latin1_swedish_ci */ ;
DELIMITER ;;
CREATE DEFINER=`root`@`%` PROCEDURE `updateLinCon`(in sig_from BIGINT, in sig_to BIGINT, in new_a DECIMAL(65,30), in new_b_dividend BIGINT, in new_b_divisor BIGINT, in new_c DECIMAL(65,30))
BEGIN
@@ -6916,4 +6844,4 @@ DELIMITER ;
/*!40101 SET COLLATION_CONNECTION=@OLD_COLLATION_CONNECTION */;
/*!40111 SET SQL_NOTES=@OLD_SQL_NOTES */;
--- Dump completed on 2025-01-07 16:05:15
+-- Dump completed on 2025-03-11 15:15:22
diff --git a/test-profile/custom/other/restore/caosroot.2025-03-11T16151741706122.tar.gz b/test-profile/custom/other/restore/caosroot.2025-03-11T16151741706122.tar.gz
new file mode 100644
index 0000000000000000000000000000000000000000..3318963c255112ead04d39119581dc5972ab58a6
Binary files /dev/null and b/test-profile/custom/other/restore/caosroot.2025-03-11T16151741706122.tar.gz differ
diff --git a/test-profile/custom/other/restore/caosroot.tar.gz b/test-profile/custom/other/restore/caosroot.tar.gz
deleted file mode 100644
index 63e35ca3beaa34a5406928fc902d002cac087289..0000000000000000000000000000000000000000
Binary files a/test-profile/custom/other/restore/caosroot.tar.gz and /dev/null differ