From d2ce1ec9178d38e7838ee91445f7808b52858e2a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Thu, 5 May 2022 13:43:35 +0200
Subject: [PATCH] data and styling
---
integrationtests/data/35/.dataspace.json | 15 +++
.../03_raw_data/001_dataset1/demo-dataset.csv | 101 ++++++++++++++++++
.../35/03_raw_data/001_dataset1/metadata.json | 51 +++++++++
.../data/35/03_raw_data/README_RawData.md | 25 +++++
.../35/03_raw_data/metadata-template.json | 52 +++++++++
.../README_ProcessedData.md | 10 ++
.../04_data_processing/metadata-template.json | 52 +++++++++
.../data/35/05_results/README_Results.md | 7 ++
integrationtests/data/35/README.md | 5 +
integrationtests/test.py | 26 ++---
10 files changed, 331 insertions(+), 13 deletions(-)
create mode 100644 integrationtests/data/35/.dataspace.json
create mode 100644 integrationtests/data/35/03_raw_data/001_dataset1/demo-dataset.csv
create mode 100644 integrationtests/data/35/03_raw_data/001_dataset1/metadata.json
create mode 100644 integrationtests/data/35/03_raw_data/README_RawData.md
create mode 100644 integrationtests/data/35/03_raw_data/metadata-template.json
create mode 100644 integrationtests/data/35/04_data_processing/README_ProcessedData.md
create mode 100644 integrationtests/data/35/04_data_processing/metadata-template.json
create mode 100644 integrationtests/data/35/05_results/README_Results.md
create mode 100644 integrationtests/data/35/README.md
diff --git a/integrationtests/data/35/.dataspace.json b/integrationtests/data/35/.dataspace.json
new file mode 100644
index 00000000..7473a604
--- /dev/null
+++ b/integrationtests/data/35/.dataspace.json
@@ -0,0 +1,15 @@
+{
+ "name": "DEMO",
+ "dataspace_id": 20002,
+ "archived": false,
+ "coordinator": {
+ "full_name": "Max Schmitt",
+ "firstname": "Max",
+ "lastname": "Schmitt",
+ "email": "max.schmitt@email.de"
+ },
+ "start_date": "2022-03-01",
+ "end_date": "2032-02-28",
+ "comment": "Demonstration data space for DataCloud",
+ "url": "https://datacloud.de/index.php/f/7679"
+}
diff --git a/integrationtests/data/35/03_raw_data/001_dataset1/demo-dataset.csv b/integrationtests/data/35/03_raw_data/001_dataset1/demo-dataset.csv
new file mode 100644
index 00000000..7a4d684e
--- /dev/null
+++ b/integrationtests/data/35/03_raw_data/001_dataset1/demo-dataset.csv
@@ -0,0 +1,101 @@
+index,A[kg],B[s],pH,Temp.[C]
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diff --git a/integrationtests/data/35/03_raw_data/001_dataset1/metadata.json b/integrationtests/data/35/03_raw_data/001_dataset1/metadata.json
new file mode 100644
index 00000000..f263bc3c
--- /dev/null
+++ b/integrationtests/data/35/03_raw_data/001_dataset1/metadata.json
@@ -0,0 +1,51 @@
+{
+ "title": "Random numbers created on a random autumn day in a random office",
+ "abstract": "For demonstration purposes we created random numbers on a computer in an office of the CLOUD. This demonstration dataset is used in the DataCloud, a curated cloud storage for scientific data.",
+ "Event": [
+ {
+ "longitude": 18.445078548041533,
+ "datetime": "2022-02-10T16:36:48+01:00",
+ "start_date": "2021-10-01",
+ "latitude": 53.10833068997861,
+ "elevation": 2,
+ "location": "Bremen, Germany"
+ }
+ ],
+ "license": "CC-BY",
+ "authors": [
+ {
+ "firstname": "Max",
+ "lastname": "Schmitt",
+ "full_name": "Max Schmitt",
+ "affiliation": "CLOUD",
+ "ORCID": "0000-0001-6233-1866",
+ "email": "max.schmitt@email.de"
+ },
+ {
+ "firstname": "Alexa",
+ "lastname": "Nozone",
+ "full_name": "Alexa Nozone",
+ "affiliation": "CLOUD",
+ "email": "alexa.nozone@email.de"
+ }
+ ],
+ "comment": "For questions about the DataCloud or this demonstration dataset, contact research-data@email.de",
+ "project": {
+ "name": "Demonstration of Extremly important Metadata in Folders",
+ "full_name": "Project",
+ "project_acronym": "DEMO",
+ "project_type": "national",
+ "institute": "CLOUD",
+ "start_date": "2021-10-01",
+ "end_date": "2031-12-31",
+ "url": "https://www.cloud.de/de/forschung-infrastruktur/forschungsdaten-services.html",
+ "coordinator": {
+ "firstname": "Max",
+ "lastname": "Schmitt",
+ "email": "max.schmitt@email.de"
+ }
+ },
+ "method": {
+ "name": "Random Number Generator"
+ }
+}
diff --git a/integrationtests/data/35/03_raw_data/README_RawData.md b/integrationtests/data/35/03_raw_data/README_RawData.md
new file mode 100644
index 00000000..2317ff86
--- /dev/null
+++ b/integrationtests/data/35/03_raw_data/README_RawData.md
@@ -0,0 +1,25 @@
+# Raw Data
+
+The `03_raw_data` folder is here to store all raw data of each dataset
+associated with the project – the data that has not been edited by you yet but
+which you plan to use in your research. It can be e.g. your unprocessed field
+sampling records, or useful data from an online repository. Organize your data
+in this folder in the following way:
+
+- Each dataset should reside inside a subfolder. It is recommended to number and name these folders clearly, e.g. `03_raw_data/001_precipitationgermany2017`.
+
+- **IMPORTANT**: provide the folder with information about your raw data by
+ filling out a metadata form for each of your datasets! For this,
+
+ - either copy the `metadata-template.json` file and put it into your dataset
+ folder. Open the copy with a text editor and fill out the fields.
+ - or use the metadata editor in the DataCoud web client (press the "+" button
+ and use "New matadata.json" file)
+
+ If you can’t find information about your data to fill in here, you should
+ reconsider using it - it is important to be able to trace your data sources to
+ ensure a FAIR scientific process!
+
+- For processing any of the data, make a copy of the dataset and paste it into
+ the `04_data_processing` folder. This way, you make sure to keep your raw data
+ in its original state.
\ No newline at end of file
diff --git a/integrationtests/data/35/03_raw_data/metadata-template.json b/integrationtests/data/35/03_raw_data/metadata-template.json
new file mode 100644
index 00000000..7f457d23
--- /dev/null
+++ b/integrationtests/data/35/03_raw_data/metadata-template.json
@@ -0,0 +1,52 @@
+{
+ "dataset": {
+ "title": "",
+ "abstract": "See https://github.com/CLOUD/metadata-schema for schema specification",
+ "license": "CC-BY",
+ "authors": [
+ {
+ "firstname": "",
+ "lastname": "",
+ "affiliation": "",
+ "ORCID": "XXXX-XXXX-XXXX-XXXX",
+ "email": "name@domain.de"
+ },
+ {
+ "firstname": "",
+ "lastname": "",
+ "affiliation": "",
+ "email": "name@domain.de",
+ "ORCID": "XXXX-XXXX-XXXX-XXXX"
+ }
+ ],
+ "project": {
+ "name": "",
+ "acronym": "",
+ "type": "DFG/",
+ "institute": "CLOUD",
+ "start_date": "YYYY-MM-DD",
+ "end_date": "YYYY-MM-DD",
+ "url": "",
+ "coordinator": {
+ "lastname": "",
+ "email": "",
+ "firstname": ""
+ }
+ },
+ "events_in_data": false,
+ "events": [
+ {
+ "longitude": 0,
+ "latitude": 0,
+ "elevation": 0,
+ "location": "",
+ "datetime": "YYYY-MM-DDTHH:mm:ss"
+ }
+ ],
+ "method": {
+ "name": "",
+ "url": ""
+ },
+ "max_files": 100
+ }
+}
diff --git a/integrationtests/data/35/04_data_processing/README_ProcessedData.md b/integrationtests/data/35/04_data_processing/README_ProcessedData.md
new file mode 100644
index 00000000..ce1b002b
--- /dev/null
+++ b/integrationtests/data/35/04_data_processing/README_ProcessedData.md
@@ -0,0 +1,10 @@
+# Data Processing
+
+The actual work is done in this `04_data_processing` folder. Depending on your
+field and type and size of project, you can organize this folder in the way that
+fits your process best. Here, a bit of chaos can happen ;) Keep in mind to
+document your processing steps in the `02_materials_and_methods` folder and to
+put in your final results into the `05_results` folder. In the end of your
+project, it should be possible to delete everything in this folder and
+reconstruct the working process using the documentation and raw data from
+previous folders.
diff --git a/integrationtests/data/35/04_data_processing/metadata-template.json b/integrationtests/data/35/04_data_processing/metadata-template.json
new file mode 100644
index 00000000..05f9394d
--- /dev/null
+++ b/integrationtests/data/35/04_data_processing/metadata-template.json
@@ -0,0 +1,52 @@
+{
+ "dataset": {
+ "title": "",
+ "abstract": "See https://github.com/cloud/metadata-schema for schema specification",
+ "license": "CC-BY",
+ "authors": [
+ {
+ "firstname": "",
+ "lastname": "",
+ "affiliation": "",
+ "ORCID": "XXXX-XXXX-XXXX-XXXX",
+ "email": "name@domain.de"
+ },
+ {
+ "firstname": "",
+ "lastname": "",
+ "affiliation": "",
+ "email": "name@domain.de",
+ "ORCID": "XXXX-XXXX-XXXX-XXXX"
+ }
+ ],
+ "project": {
+ "name": "",
+ "acronym": "",
+ "type": "DFG/",
+ "institute": "CLOUD",
+ "start_date": "YYYY-MM-DD",
+ "end_date": "YYYY-MM-DD",
+ "url": "",
+ "coordinator": {
+ "lastname": "",
+ "email": "",
+ "firstname": ""
+ }
+ },
+ "events_in_data": false,
+ "events": [
+ {
+ "longitude": 0,
+ "latitude": 0,
+ "elevation": 0,
+ "location": "",
+ "datetime": "YYYY-MM-DDTHH:mm:ss"
+ }
+ ],
+ "method": {
+ "name": "",
+ "url": ""
+ },
+ "max_files": 100
+ }
+}
diff --git a/integrationtests/data/35/05_results/README_Results.md b/integrationtests/data/35/05_results/README_Results.md
new file mode 100644
index 00000000..ae0ab657
--- /dev/null
+++ b/integrationtests/data/35/05_results/README_Results.md
@@ -0,0 +1,7 @@
+# Results
+
+All the results that are final versions of your data analysis or processing,
+should be copied into this `05_results` folder. Organize your results folder in
+the way most fitting to your project.
+
+Provide metadata to your results files.
diff --git a/integrationtests/data/35/README.md b/integrationtests/data/35/README.md
new file mode 100644
index 00000000..809d699c
--- /dev/null
+++ b/integrationtests/data/35/README.md
@@ -0,0 +1,5 @@
+# Dataspace: DEMO
+
+This is a Dataspace in the CLOUD DataCloud providing safe, curated cloud storage
+for all of CLOUD's research data.
+
diff --git a/integrationtests/test.py b/integrationtests/test.py
index efff6430..2d881800 100755
--- a/integrationtests/test.py
+++ b/integrationtests/test.py
@@ -28,6 +28,7 @@
module description
"""
+import os
from caosdb import EmptyUniqueQueryError
import argparse
import sys
@@ -42,7 +43,6 @@ import yaml
from caosadvancedtools.testutils import clear_database, set_test_key
set_test_key("10b128cf8a1372f30aa3697466bb55e76974e0c16a599bb44ace88f19c8f61e2")
-import os
def rfp(*pathcomponents):
"""
@@ -52,14 +52,12 @@ def rfp(*pathcomponents):
return os.path.join(os.path.dirname(__file__), *pathcomponents)
-
-
@pytest.fixture
def usemodel():
model = parse_model_from_yaml(rfp("model.yml"))
model.sync_data_model(noquestion=True, verbose=False)
-
+
@pytest.fixture
def ident():
ident = CaosDBIdentifiableAdapter()
@@ -68,12 +66,12 @@ def ident():
ident.register_identifiable(
"Person", db.RecordType()
.add_parent(name="Person")
- #.add_property(name="first_name")
+ # .add_property(name="first_name")
.add_property(name="last_name"))
ident.register_identifiable(
"Measurement", db.RecordType()
.add_parent(name="Measurement")
- #.add_property(name="identifier")
+ # .add_property(name="identifier")
.add_property(name="date")
.add_property(name="project"))
ident.register_identifiable(
@@ -150,6 +148,7 @@ def test_multiple_insertions(clear_database, usemodel, ident, crawler):
assert len(ins) == 0
assert len(ups) == 0
+
def test_insertion(clear_database, usemodel, ident, crawler):
ins, ups = crawler.synchronize()
@@ -169,6 +168,7 @@ def test_insertion(clear_database, usemodel, ident, crawler):
assert len(ins) == 0
assert len(ups) == 0
+
def test_insertion_and_update(clear_database, usemodel, ident, crawler):
ins, ups = crawler.synchronize()
@@ -184,7 +184,8 @@ def test_insertion_and_update(clear_database, usemodel, ident, crawler):
ins, ups = cr.synchronize()
assert len(ins) == 0
assert len(ups) == 1
-
+
+
def test_identifiable_update(clear_database, usemodel, ident, crawler):
ins, ups = crawler.synchronize()
@@ -197,7 +198,7 @@ def test_identifiable_update(clear_database, usemodel, ident, crawler):
l = cr.updateList
for record in l:
if (record.parents[0].name == "Measurement" and
- record.get_property("date").value == "2020-01-03"):
+ record.get_property("date").value == "2020-01-03"):
# maybe a bit weird, but add an email address to a measurement
record.add_property(name="email", value="testperson@testaccount.test")
print("one change")
@@ -206,14 +207,13 @@ def test_identifiable_update(clear_database, usemodel, ident, crawler):
assert len(ins) == 0
assert len(ups) == 1
-
# Test the change within one property:
cr = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr)
l = cr.updateList
for record in l:
if (record.parents[0].name == "Measurement" and
- record.get_property("date").value == "2020-01-03"):
+ record.get_property("date").value == "2020-01-03"):
record.add_property(name="email", value="testperson@coolmail.test")
print("one change")
break
@@ -227,7 +227,7 @@ def test_identifiable_update(clear_database, usemodel, ident, crawler):
l = cr.updateList
for record in l:
if (record.parents[0].name == "Measurement" and
- record.get_property("date").value == "2020-01-03"):
+ record.get_property("date").value == "2020-01-03"):
record.add_property(name="email", value="testperson@coolmail.test")
record.get_property("date").value = "2012-01-02"
print("one change")
@@ -269,6 +269,7 @@ def test_file_insertion(clear_database, usemodel, ident, crawler_extended):
assert len(r) == 1
assert r[0].get_property("ReadmeFile").value == f.id
+
def test_file_update(clear_database, usemodel, ident, crawler_extended):
ins1, ups1 = crawler_extended.synchronize(commit_changes=True)
fileList_ins = [r for r in ins1 if r.role == "File"]
@@ -288,7 +289,7 @@ def test_file_update(clear_database, usemodel, ident, crawler_extended):
res = db.execute_query("Find File")
assert len(res) == 11
assert len(res[0].parents) == 0
-
+
cr2 = Crawler(debug=True, identifiableAdapter=ident)
crawl_standard_test_directory(cr2, cfood="scifolder_extended2.yml")
@@ -302,7 +303,6 @@ def test_file_update(clear_database, usemodel, ident, crawler_extended):
res = db.execute_query("Find File")
assert len(res) == 11
assert res[0].parents[0].name == "ProjectMarkdownReadme"
-
# TODO: Implement file update checks (based on checksum)
# Add test with actual file update:
--
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