diff --git a/CHANGELOG.md b/CHANGELOG.md
index 7df6439d5ee38b236a0731cf5ca09b82c7fcf002..95189b50054033f54054a21388a67ca47c8356ea 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -8,20 +8,35 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
## [Unreleased] ##
### Added ###
+
- DateElementConverter: allows to interpret text as a date object
- the restricted_path argument allows to crawl only a subtree
+- logging that provides a summary of what is inserted and updated
+- You can now access the file system path of a structure element (if it has one) using the variable
+ name ``<converter name>.path``
+- ``add_prefix`` and ``remove_prefix`` arguments for the command line interface
+ and the ``crawler_main`` function for the adding/removal of path prefixes when
+ creating file entities.
### Changed ###
- The definitions for the default converters were removed from crawl.py and placed into
a separate yaml file called `default_converters.yml`. There is a new test testing for
the correct loading behavior of that file.
+- JSONFileConverter, YAMLFileConverter and MarkdownFileConverter now inherit from
+ SimpleFileConverter. Behavior is unchanged, except that the MarkdownFileConverter now raises a
+ ConverterValidationError when the YAML header cannot be read instead of silently not matching.
### Deprecated ###
+- The ``prefix`` argument of `crawler_main` is deprecated. Use the new argument
+ ``remove_prefix`` instead.
+
### Removed ###
+- The command line argument ``--prefix``. Use the new argument ``--remove-prefix`` instead.
### Fixed ###
+
- an empty string as name is treated as no name (as does the server). This, fixes
queries for identifiables since it would contain "WITH name=''" otherwise
which is an impossible condition. If your cfoods contained this case, they are ill defined.
diff --git a/INSTALL.md b/INSTALL.md
new file mode 100644
index 0000000000000000000000000000000000000000..ba220626460c559aeded69d360c85917e0c78066
--- /dev/null
+++ b/INSTALL.md
@@ -0,0 +1,57 @@
+# Installation ##
+
+
+## Linux ####
+
+Make sure that Python (at least version 3.8) and pip is installed, using your system tools and
+documentation.
+
+Then open a terminal and continue in the [Generic installation](#generic-installation) section.
+
+## Windows ####
+
+If a Python distribution is not yet installed, we recommend Anaconda Python, which you can download
+for free from [https://www.anaconda.com](https://www.anaconda.com). The "Anaconda Individual Edition" provides most of all
+packages you will ever need out of the box. If you prefer, you may also install the leaner
+"Miniconda" installer, which allows you to install packages as you need them.
+
+After installation, open an Anaconda prompt from the Windows menu and continue in the [Generic
+installation](#generic-installation) section.
+
+## MacOS ####
+
+If there is no Python 3 installed yet, there are two main ways to
+obtain it: Either get the binary package from
+[python.org](https://www.python.org/downloads/) or, for advanced
+users, install via [Homebrew](https://brew.sh/). After installation
+from python.org, it is recommended to also update the TLS certificates
+for Python (this requires administrator rights for your user):
+
+```sh
+# Replace this with your Python version number:
+cd /Applications/Python\ 3.9/
+
+# This needs administrator rights:
+sudo ./Install\ Certificates.command
+```
+
+After these steps, you may continue with the [Generic
+installation](#generic-installation).
+
+## Generic installation ####
+
+The CaosDB crawler is available as [PyPi
+package](https://pypi.org/project/caoscrawler/) and can simply installed by
+
+```sh
+pip3 install caoscrawler
+```
+
+Alternatively, obtain the sources from GitLab and install from there (`git` must
+be installed for this option):
+
+```sh
+git clone https://gitlab.com/caosdb/caosdb-crawler
+cd caosdb-crawler
+pip3 install --user .
+```
diff --git a/integrationtests/test_data/extroot/realworld_example/dataset_cfoods.yml b/integrationtests/test_data/extroot/realworld_example/dataset_cfoods.yml
index 7a64d708667182b80b739812e5fdf3369fc5b462..37a34d125dcff1d121b1bded2fe959c4d30ff403 100644
--- a/integrationtests/test_data/extroot/realworld_example/dataset_cfoods.yml
+++ b/integrationtests/test_data/extroot/realworld_example/dataset_cfoods.yml
@@ -153,6 +153,13 @@ Data:
metadata_json: &metadata_json_template
type: JSONFile
match: metadata.json
+ records:
+ JSONFile:
+ parents:
+ - JSONFile
+ role: File
+ path: ${metadata_json.path}
+ file: ${metadata_json.path}
validate: schema/dataset.schema.json
subtree:
jsondict:
diff --git a/integrationtests/test_data/extroot/realworld_example/schema/dataspace.schema.json b/integrationtests/test_data/extroot/realworld_example/schema/dataspace.schema.json
index 01653bfa821e0a0acbb5a481bfd458e2ed784fb9..36233230ae05f9df58ae4e492ff1f709322f6e51 100644
--- a/integrationtests/test_data/extroot/realworld_example/schema/dataspace.schema.json
+++ b/integrationtests/test_data/extroot/realworld_example/schema/dataspace.schema.json
@@ -9,6 +9,7 @@
"minimum": 20000
},
"archived": { "type": "boolean" },
+ "JSONFile": { "type": "object" },
"url": {
"type": "string",
"description": "link to folder on file system (CaosDB or cloud folder)"
diff --git a/integrationtests/test_data/extroot/use_case_simple_presentation/cfood.yml b/integrationtests/test_data/extroot/use_case_simple_presentation/cfood.yml
index 6495e1828dc56e99459c162f7751951f880ea55c..c55be2157a1f079ecfb5809c3658586f9114fad1 100644
--- a/integrationtests/test_data/extroot/use_case_simple_presentation/cfood.yml
+++ b/integrationtests/test_data/extroot/use_case_simple_presentation/cfood.yml
@@ -25,8 +25,8 @@ extroot:
parents:
- mdfile
role: File
- path: $DataFile
- file: $DataFile
+ path: ${DataFile.path}
+ file: ${DataFile.path}
Experiment:
mdfile: $mdfile
@@ -68,8 +68,8 @@ extroot:
parents:
- mdfile
role: File
- path: $DataFile
- file: $DataFile
+ path: ${DataFile.path}
+ file: ${DataFile.path}
Experiment: {}
diff --git a/integrationtests/test_realworld_example.py b/integrationtests/test_realworld_example.py
index 4158ed22278ef5c871a22d45885e58fbfa84ea3b..cb5ed2c769945af033bc56a2d6af3bf1cec86de4 100644
--- a/integrationtests/test_realworld_example.py
+++ b/integrationtests/test_realworld_example.py
@@ -25,6 +25,7 @@
an integration test module that runs a test against a (close to) real world example
"""
from caosdb.utils.register_tests import clear_database, set_test_key
+import logging
import json
import os
@@ -35,6 +36,7 @@ from caoscrawler.identifiable_adapters import CaosDBIdentifiableAdapter
from caoscrawler.structure_elements import Directory
import pytest
from caosadvancedtools.models.parser import parse_model_from_json_schema, parse_model_from_yaml
+from caosadvancedtools.loadFiles import loadpath
import sys
@@ -52,6 +54,17 @@ def rfp(*pathcomponents):
DATADIR = rfp("test_data", "extroot", "realworld_example")
+@pytest.fixture
+def addfiles():
+ loadpath(path='/opt/caosdb/mnt/extroot/',
+ include=None,
+ exclude=None,
+ prefix="",
+ dryrun=False,
+ forceAllowSymlinks=True,
+ )
+
+
@pytest.fixture
def usemodel():
# First load dataspace data model
@@ -85,22 +98,21 @@ def create_identifiable_adapter():
return ident
-def test_dataset(clear_database, usemodel):
- ident = create_identifiable_adapter()
- crawler = Crawler(identifiableAdapter=ident)
- crawler_definition = crawler.load_definition(
- os.path.join(DATADIR, "dataset_cfoods.yml"))
- # print(json.dumps(crawler_definition, indent=3))
- # Load and register converter packages:
- converter_registry = crawler.load_converters(crawler_definition)
- # print("DictIntegerElement" in converter_registry)
-
- records = crawler.start_crawling(
- Directory("data", os.path.join(DATADIR, 'data')),
- crawler_definition,
- converter_registry
+def test_dataset(clear_database, usemodel, addfiles, caplog):
+ caplog.set_level(logging.DEBUG, logger="caoscrawler")
+ identifiable_path = os.path.join(DATADIR, "identifiables.yml")
+ crawler_definition_path = os.path.join(DATADIR, "dataset_cfoods.yml")
+ crawler_main(
+ os.path.join(DATADIR, 'data'),
+ crawler_definition_path,
+ identifiable_path,
+ True,
+ os.path.join(DATADIR, "provenance.yml"),
+ False,
+ remove_prefix=DATADIR,
+ # this test will fail without this prefix since the crawler would try to create new files
+ add_prefix="/extroot/realworld_example"
)
- crawler.synchronize()
dataspace = db.execute_query("FIND RECORD Dataspace WITH name=35 AND dataspace_id=20002 AND "
"archived=FALSE AND url='https://datacloud.de/index.php/f/7679'"
@@ -119,13 +131,17 @@ def test_dataset(clear_database, usemodel):
"start_datetime='2022-02-10T16:36:48+01:00'") == 1
assert db.execute_query(f"FIND Event WITH latitude=53", unique=True)
+ # test logging
+ assert "Executed inserts" in caplog.text
+ assert "Going to insert" in caplog.text
+ assert "Executed updates" in caplog.text
+
-def test_event_update(clear_database, usemodel):
+def test_event_update(clear_database, usemodel, addfiles):
identifiable_path = os.path.join(DATADIR, "identifiables.yml")
crawler_definition_path = os.path.join(DATADIR, "dataset_cfoods.yml")
- # TODO(fspreck): Use crawler_main
crawler_main(
os.path.join(DATADIR, 'data'),
crawler_definition_path,
@@ -133,7 +149,9 @@ def test_event_update(clear_database, usemodel):
True,
os.path.join(DATADIR, "provenance.yml"),
False,
- ""
+ remove_prefix=DATADIR,
+ # this test will fail without this prefix since the crawler would try to create new files
+ add_prefix="/extroot/realworld_example"
)
old_dataset_rec = db.execute_query(
diff --git a/integrationtests/test_use_case_simple_presentation.py b/integrationtests/test_use_case_simple_presentation.py
index 91c523be90a4d0117a7cc54217cae0b911511957..5fc0f6c7d85a0fce4490c72952e711fe241a0099 100644
--- a/integrationtests/test_use_case_simple_presentation.py
+++ b/integrationtests/test_use_case_simple_presentation.py
@@ -38,9 +38,7 @@ DATADIR = os.path.join(os.path.dirname(__file__), "test_data",
"extroot", "use_case_simple_presentation")
-def test_complete_crawler(
- clear_database
-):
+def test_complete_crawler(clear_database):
# Setup the data model:
model = parser.parse_model_from_yaml(os.path.join(DATADIR, "model.yml"))
model.sync_data_model(noquestion=True, verbose=False)
@@ -57,13 +55,24 @@ def test_complete_crawler(
dryrun=False,
forceAllowSymlinks=False)
+ # test that a bad value for "remove_prefix" leads to runtime error
+ with pytest.raises(RuntimeError) as re:
+ crawler_main(DATADIR,
+ os.path.join(DATADIR, "cfood.yml"),
+ os.path.join(DATADIR, "identifiables.yml"),
+ True,
+ os.path.join(DATADIR, "provenance.yml"),
+ False,
+ remove_prefix="sldkfjsldf")
+ assert "path does not start with the prefix" in str(re.value)
+
crawler_main(DATADIR,
os.path.join(DATADIR, "cfood.yml"),
os.path.join(DATADIR, "identifiables.yml"),
True,
os.path.join(DATADIR, "provenance.yml"),
False,
- "/use_case_simple_presentation")
+ remove_prefix=os.path.abspath(DATADIR))
res = db.execute_query("FIND Record Experiment")
assert len(res) == 1
diff --git a/src/caoscrawler/converters.py b/src/caoscrawler/converters.py
index 0d1c5d631e7ba4bea61e6c437f6c125b1a55125a..80a3728ce5b1f413d2bdd674b26a7dca1122eef5 100644
--- a/src/caoscrawler/converters.py
+++ b/src/caoscrawler/converters.py
@@ -56,6 +56,10 @@ SPECIAL_PROPERTIES = ("description", "name", "id", "path",
logger = logging.getLogger(__name__)
+class CrawlerTemplate(Template):
+ braceidpattern = r"(?a:[_a-z][_\.a-z0-9]*)"
+
+
def _only_max(children_with_keys):
return [max(children_with_keys, key=lambda x: x[1])[0]]
@@ -110,6 +114,19 @@ class ConverterValidationError(Exception):
self.message = msg
+def create_path_value(func):
+ """decorator for create_values functions that adds a value containing the path
+
+ should be used for StructureElement that are associated with file system objects that have a
+ path, like File or Directory.
+ """
+
+ def inner(self, values: GeneralStore, element: StructureElement):
+ func(self, values=values, element=element)
+ values.update({self.name + ".path": element.path})
+ return inner
+
+
def replace_variables(propvalue, values: GeneralStore):
"""
This function replaces variables in property values (and possibly other locations,
@@ -133,7 +150,7 @@ def replace_variables(propvalue, values: GeneralStore):
if isinstance(values[varname], db.Entity):
return values[varname]
- propvalue_template = Template(propvalue)
+ propvalue_template = CrawlerTemplate(propvalue)
return propvalue_template.safe_substitute(**values.get_storage())
@@ -241,7 +258,7 @@ def create_records(values: GeneralStore, records: RecordStore, def_records: dict
continue
# Allow replacing variables in keys / names of properties:
- key_template = Template(key)
+ key_template = CrawlerTemplate(key)
key = key_template.safe_substitute(**values.get_storage())
keys_modified.append((name, key))
@@ -477,6 +494,10 @@ class DirectoryConverter(Converter):
return children
+ @create_path_value
+ def create_values(self, values: GeneralStore, element: StructureElement):
+ super().create_values(values=values, element=element)
+
def typecheck(self, element: StructureElement):
return isinstance(element, Directory)
@@ -524,6 +545,10 @@ class SimpleFileConverter(Converter):
def create_children(self, generalStore: GeneralStore, element: StructureElement):
return list()
+ @create_path_value
+ def create_values(self, values: GeneralStore, element: StructureElement):
+ super().create_values(values=values, element=element)
+
@Converter.debug_matching("name")
def match(self, element: StructureElement):
# TODO: See comment on types and inheritance
@@ -542,7 +567,7 @@ class FileConverter(SimpleFileConverter):
super().__init__(*args, **kwargs)
-class MarkdownFileConverter(Converter):
+class MarkdownFileConverter(SimpleFileConverter):
"""
reads the yaml header of markdown files (if a such a header exists).
"""
@@ -552,8 +577,18 @@ class MarkdownFileConverter(Converter):
if not isinstance(element, File):
raise RuntimeError("A markdown file is needed to create children.")
- header = yaml_header_tools.get_header_from_file(
- element.path, clean=False)
+ try:
+ header = yaml_header_tools.get_header_from_file(
+ element.path, clean=False)
+ except yaml_header_tools.NoValidHeader:
+ if generalStore is not None and self.name in generalStore:
+ path = generalStore[self.name]
+ else:
+ path = "<path not set>"
+ raise ConverterValidationError(
+ "Error during the validation (yaml header cannot be read) of the markdown file "
+ "located at the following node in the data structure:\n"
+ f"{path}")
children: List[StructureElement] = []
for name, entry in header.items():
@@ -566,25 +601,6 @@ class MarkdownFileConverter(Converter):
"Header entry {} has incompatible type.".format(name))
return children
- def typecheck(self, element: StructureElement):
- return isinstance(element, File)
-
- @Converter.debug_matching("name")
- def match(self, element: StructureElement):
- # TODO: See comment on types and inheritance
- if not isinstance(element, File):
- raise RuntimeError("Element must be a file.")
- m = re.match(self.definition["match"], element.name)
- if m is None:
- return None
- try:
- yaml_header_tools.get_header_from_file(element.path)
- except yaml_header_tools.NoValidHeader:
- # TODO(salexan): Raise a validation error instead of just not
- # matching silently.
- return None
- return m.groupdict()
-
def convert_basic_element(element: Union[list, dict, bool, int, float, str, None], name=None,
msg_prefix=""):
@@ -691,20 +707,7 @@ class DictDictElementConverter(DictElementConverter):
super().__init__(*args, **kwargs)
-class JSONFileConverter(Converter):
- def typecheck(self, element: StructureElement):
- return isinstance(element, File)
-
- @Converter.debug_matching("name")
- def match(self, element: StructureElement):
- # TODO: See comment on types and inheritance
- if not self.typecheck(element):
- raise RuntimeError("Element must be a file")
- m = re.match(self.definition["match"], element.name)
- if m is None:
- return None
- return m.groupdict()
-
+class JSONFileConverter(SimpleFileConverter):
def create_children(self, generalStore: GeneralStore, element: StructureElement):
# TODO: See comment on types and inheritance
if not isinstance(element, File):
@@ -726,20 +729,7 @@ class JSONFileConverter(Converter):
return [structure_element]
-class YAMLFileConverter(Converter):
- def typecheck(self, element: StructureElement):
- return isinstance(element, File)
-
- @Converter.debug_matching("name")
- def match(self, element: StructureElement):
- # TODO: See comment on types and inheritance
- if not self.typecheck(element):
- raise RuntimeError("Element must be a file")
- m = re.match(self.definition["match"], element.name)
- if m is None:
- return None
- return m.groupdict()
-
+class YAMLFileConverter(SimpleFileConverter):
def create_children(self, generalStore: GeneralStore, element: StructureElement):
# TODO: See comment on types and inheritance
if not isinstance(element, File):
diff --git a/src/caoscrawler/crawl.py b/src/caoscrawler/crawl.py
index ef06ab15777be7405c924860d8d0ab0cc32ff3bc..c77dcee1f29eac69732ce353e0271761eca2df13 100644
--- a/src/caoscrawler/crawl.py
+++ b/src/caoscrawler/crawl.py
@@ -49,6 +49,7 @@ from typing import Any, Optional, Type, Union
import caosdb as db
+from caosadvancedtools.utils import create_entity_link
from caosadvancedtools.cache import UpdateCache, Cache
from caosadvancedtools.crawler import Crawler as OldCrawler
from caosdb.apiutils import (compare_entities, EntityMergeConflictError,
@@ -1016,20 +1017,25 @@ class Crawler(object):
referencing_entities)
for record in to_be_updated]
# Merge with existing data to prevent unwanted overwrites
- to_be_updated = self._merge_properties_from_remote(to_be_updated,
- identified_records)
+ to_be_updated = self._merge_properties_from_remote(to_be_updated, identified_records)
# remove unnecessary updates from list by comparing the target records
# to the existing ones
- to_be_updated = self.remove_unnecessary_updates(
- to_be_updated, identified_records)
+ to_be_updated = self.remove_unnecessary_updates(to_be_updated, identified_records)
+ logger.info(f"Going to insert {len(to_be_inserted)} Entities and update "
+ f"{len(to_be_inserted)} Entities.")
if commit_changes:
self.execute_parent_updates_in_list(to_be_updated, securityMode=self.securityMode,
run_id=self.run_id, unique_names=unique_names)
+ logger.info(f"Added parent RecordTypes where necessary.")
self.execute_inserts_in_list(
to_be_inserted, self.securityMode, self.run_id, unique_names=unique_names)
+ logger.info(f"Executed inserts:\n"
+ + self.create_entity_summary(to_be_inserted))
self.execute_updates_in_list(
to_be_updated, self.securityMode, self.run_id, unique_names=unique_names)
+ logger.info(f"Executed updates:\n"
+ + self.create_entity_summary(to_be_updated))
update_cache = UpdateCache()
pending_inserts = update_cache.get_inserts(self.run_id)
@@ -1044,6 +1050,25 @@ class Crawler(object):
return (to_be_inserted, to_be_updated)
+ @staticmethod
+ def create_entity_summary(entities: list[db.Entity]):
+ """ Creates a summary string reprensentation of a list of entities."""
+ parents = {}
+ for el in entities:
+ for pp in el.parents:
+ if pp.name not in parents:
+ parents[pp.name] = [el]
+ else:
+ parents[pp.name].append(el)
+ output = ""
+ for key, value in parents.items():
+ output += f"{key}:\n"
+ for el in value:
+ output += create_entity_link(el) + ", "
+
+ output = output[:-2] + "\n"
+ return output
+
@staticmethod
def inform_about_pending_changes(pending_changes, run_id, path, inserts=False):
# Sending an Email with a link to a form to authorize updates is
@@ -1228,7 +1253,9 @@ def crawler_main(crawled_directory_path: str,
prefix: str = "",
securityMode: SecurityMode = SecurityMode.UPDATE,
unique_names=True,
- restricted_path: Optional[list[str]] = None
+ restricted_path: Optional[list[str]] = None,
+ remove_prefix: Optional[str] = None,
+ add_prefix: Optional[str] = None,
):
"""
@@ -1247,7 +1274,7 @@ def crawler_main(crawled_directory_path: str,
dry_run : bool
do not commit any chnages to the server
prefix : str
- remove the given prefix from file paths
+ DEPRECATED, remove the given prefix from file paths
securityMode : int
securityMode of Crawler
unique_names : bool
@@ -1255,6 +1282,10 @@ def crawler_main(crawled_directory_path: str,
restricted_path: optional, list of strings
Traverse the data tree only along the given path. When the end of the given path
is reached, traverse the full tree as normal.
+ remove_prefix : Optional[str]
+ remove the given prefix from file paths
+ add_prefix : Optional[str]
+ add the given prefix to file paths
Returns
-------
@@ -1271,11 +1302,19 @@ def crawler_main(crawled_directory_path: str,
crawler.save_debug_data(provenance_file)
if identifiables_definition_file is not None:
-
ident = CaosDBIdentifiableAdapter()
ident.load_from_yaml_definition(identifiables_definition_file)
crawler.identifiableAdapter = ident
+ if prefix != "":
+ warnings.warn(DeprecationWarning("The prefix argument is deprecated and will be removed "
+ "in the future. Please use `remove_prefix` instead."))
+ if remove_prefix is not None:
+ raise ValueError("Please do not supply the (deprecated) `prefix` and the "
+ "`remove_prefix` argument at the same time. Only use "
+ "`remove_prefix` instead.")
+ remove_prefix = prefix
+
if dry_run:
ins, upd = crawler.synchronize(commit_changes=False)
inserts = [str(i) for i in ins]
@@ -1290,11 +1329,15 @@ def crawler_main(crawled_directory_path: str,
if isinstance(elem, db.File):
# correct the file path:
# elem.file = os.path.join(args.path, elem.file)
- if prefix is None:
- raise RuntimeError(
- "No prefix set. Prefix must be set if files are used.")
- if elem.path.startswith(prefix):
- elem.path = elem.path[len(prefix):]
+ if remove_prefix:
+ if elem.path.startswith(remove_prefix):
+ elem.path = elem.path[len(remove_prefix):]
+ else:
+ raise RuntimeError("Prefix shall be removed from file path but the path "
+ "does not start with the prefix:"
+ f"\n{remove_prefix}\n{elem.path}")
+ if add_prefix:
+ elem.path = add_prefix + elem.path
elem.file = None
# TODO: as long as the new file backend is not finished
# we are using the loadFiles function to insert symlinks.
@@ -1362,8 +1405,12 @@ def parse_args():
parser.add_argument("-u", "--unique-names",
help="Insert or updates entities even if name conflicts exist.")
parser.add_argument("-p", "--prefix",
- help="Remove the given prefix from the paths "
- "of all file objects.")
+ help="DEPRECATED, use --remove-prefix instead. Remove the given prefix "
+ "from the paths of all file objects.")
+ parser.add_argument("--remove-prefix",
+ help="Remove the given prefix from the paths of all file objects.")
+ parser.add_argument("--add-prefix",
+ help="Add the given prefix to the paths of all file objects.")
return parser.parse_args()
@@ -1383,6 +1430,10 @@ def main():
conlogger = logging.getLogger("connection")
conlogger.setLevel(level=logging.ERROR)
+ if args.prefix:
+ print("Please use '--remove-prefix' option instead of '--prefix' or '-p'.")
+ return -1
+
# logging config for local execution
logger.addHandler(logging.StreamHandler(sys.stdout))
if args.debug:
@@ -1405,12 +1456,13 @@ def main():
debug=args.debug,
provenance_file=args.provenance,
dry_run=args.dry_run,
- prefix=args.prefix,
securityMode={"retrieve": SecurityMode.RETRIEVE,
"insert": SecurityMode.INSERT,
"update": SecurityMode.UPDATE}[args.security_mode],
unique_names=args.unique_names,
- restricted_path=restricted_path
+ restricted_path=restricted_path,
+ remove_prefix=args.remove_prefix,
+ add_prefix=args.add_prefix,
))
diff --git a/src/doc/README_SETUP.md b/src/doc/README_SETUP.md
index 1f6e15d408e10e38bce0d9b9fe9b6197ec69bfc3..952a8c94a7dfa24110f320f5dd32b0ad2ac1df01 100644
--- a/src/doc/README_SETUP.md
+++ b/src/doc/README_SETUP.md
@@ -1,63 +1,10 @@
# Getting started with the CaosDB Crawler #
-## Installation ##
-
-### How to install ###
-
-#### Linux ####
-
-Make sure that Python (at least version 3.8) and pip is installed, using your system tools and
-documentation.
-
-Then open a terminal and continue in the [Generic installation](#generic-installation) section.
-
-#### Windows ####
-
-If a Python distribution is not yet installed, we recommend Anaconda Python, which you can download
-for free from [https://www.anaconda.com](https://www.anaconda.com). The "Anaconda Individual Edition" provides most of all
-packages you will ever need out of the box. If you prefer, you may also install the leaner
-"Miniconda" installer, which allows you to install packages as you need them.
-
-After installation, open an Anaconda prompt from the Windows menu and continue in the [Generic
-installation](#generic-installation) section.
-
-#### MacOS ####
-
-If there is no Python 3 installed yet, there are two main ways to
-obtain it: Either get the binary package from
-[python.org](https://www.python.org/downloads/) or, for advanced
-users, install via [Homebrew](https://brew.sh/). After installation
-from python.org, it is recommended to also update the TLS certificates
-for Python (this requires administrator rights for your user):
-
-```sh
-# Replace this with your Python version number:
-cd /Applications/Python\ 3.9/
-
-# This needs administrator rights:
-sudo ./Install\ Certificates.command
-```
-
-After these steps, you may continue with the [Generic
-installation](#generic-installation).
-
-#### Generic installation ####
-
----
-
-Obtain the sources from GitLab and install from there (`git` must be installed for
-this option):
-
-```sh
-git clone https://gitlab.com/caosdb/caosdb-crawler
-cd caosdb-crawler
-pip3 install --user .
-```
-
-**Note**: In the near future, this package will also be made available on PyPi.
-
+## Installation
+see INSTALL.md
## Run Unit Tests
+Run `pytest unittests`.
## Documentation ##
We use sphinx to create the documentation. Docstrings in the code should comply
diff --git a/src/doc/cfood.rst b/src/doc/cfood.rst
index 37f6a8c7d3be9298ec965c50a4ec29110988ddc6..6564ee677f0b363a52c44dd5ceabe5378c255105 100644
--- a/src/doc/cfood.rst
+++ b/src/doc/cfood.rst
@@ -149,6 +149,44 @@ create lists or multi properties instead of single values:
.. code-block:: yaml
Experiment1:
- Measurement: +Measurement <- Element in List (list is cleared before run)
- *Measurement <- Multi Property (properties are removed before run)
- Measurement <- Overwrite
+ Measurement: +Measurement # Element in List (list is cleared before run)
+ *Measurement # Multi Property (properties are removed before run)
+ Measurement # Overwrite
+
+
+File Entities
+-------------
+
+In order to use File Entities, you must set the appropriate ``role: File``.
+Additionally, the path and file keys have to be given, with values that set the
+paths remotely and locally, respectively. You can use the variable
+``<converter name>_path`` that is automatically created by converters that deal
+with file system related StructureElements. The file object itsself is stored
+in a vairable with the same name (as it is the case for other Records).
+
+
+.. code-block:: yaml
+
+ somefile:
+ type: SimpleFile
+ match: ^params.*$ # macht any file that starts with "params"
+ records:
+ fileEntity:
+ role: File # necessary to create a File Entity
+ path: somefile.path # defines the path in CaosDB
+ file: somefile.path # path where the file is found locally
+ SomeRecord:
+ ParameterFile: $fileEntity # creates a reference to the file
+
+Automatically generated keys
+++++++++++++++++++++++++++++
+
+Some variable names are automatically generated and can be used using the
+``$<variable name>`` syntax. Those include:
+
+- ``<converter name>``: access the path of converter names to the current converter
+- ``<converter name>.path``: the file system path to the structure element
+ (file system related converters only; you need curly brackets to use them:
+ ``${<converter name>.path}``)
+- ``<Record key>``: all entities that are created in the ``records`` section
+ are available under the same key
diff --git a/src/doc/concepts.rst b/src/doc/concepts.rst
index 89757f21958f3d94649b33e9f9112593f703191d..0881d9302b621d6b47575e171dd9e8c144e29cd4 100644
--- a/src/doc/concepts.rst
+++ b/src/doc/concepts.rst
@@ -1,6 +1,10 @@
Concepts
))))))))
+The CaosDB Crawler can handle any kind of hierarchical data structure. The typical use case is
+directory tree that is traversed. We use the following terms/concepts to describe how the CaosDB
+Crawler works.
+
Structure Elements
++++++++++++++++++
diff --git a/src/doc/getting_started/INSTALL.md b/src/doc/getting_started/INSTALL.md
new file mode 120000
index 0000000000000000000000000000000000000000..95b6037c7ab329d91e3a8ed4a2b31eba675eef62
--- /dev/null
+++ b/src/doc/getting_started/INSTALL.md
@@ -0,0 +1 @@
+../../../INSTALL.md
\ No newline at end of file
diff --git a/src/doc/getting_started/helloworld.rst b/src/doc/getting_started/helloworld.rst
new file mode 100644
index 0000000000000000000000000000000000000000..ef4a1398322b59d7983b7dff384534cfa501b660
--- /dev/null
+++ b/src/doc/getting_started/helloworld.rst
@@ -0,0 +1,5 @@
+
+Prerequisites
+)))))))))))))
+
+TODO Describe the smallest possible crawler run
diff --git a/src/doc/getting_started/index.rst b/src/doc/getting_started/index.rst
new file mode 100644
index 0000000000000000000000000000000000000000..74ffa7daeff393d05605e1066a5985984c2e9751
--- /dev/null
+++ b/src/doc/getting_started/index.rst
@@ -0,0 +1,15 @@
+Getting Started
++++++++++++++++
+
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+ :hidden:
+
+ Installation<INSTALL>
+ prerequisites
+ helloworld
+
+This section will help you get going! From the first installation steps to the first simple crawl.
+
+Let's go!
diff --git a/src/doc/getting_started/prerequisites.rst b/src/doc/getting_started/prerequisites.rst
new file mode 100644
index 0000000000000000000000000000000000000000..dc8022b6cad99a8508f19f47dc01c601fb676c5b
--- /dev/null
+++ b/src/doc/getting_started/prerequisites.rst
@@ -0,0 +1,6 @@
+
+Prerequisites
+)))))))))))))
+
+TODO Describe what you need to actually do a crawler run: data, CaosDB, ...
+
diff --git a/src/doc/index.rst b/src/doc/index.rst
index b4e30e4728068cabb92626cfac986ab858a0bbb6..d319bf4d24a05a3033b1ae5bbf80433c5ef3646b 100644
--- a/src/doc/index.rst
+++ b/src/doc/index.rst
@@ -7,12 +7,12 @@ CaosDB-Crawler Documentation
:caption: Contents:
:hidden:
- Getting started<README_SETUP>
+ Getting started<getting_started/index>
+ Tutorials<tutorials/index>
Concepts<concepts>
Converters<converters>
CFoods (Crawler Definitions)<cfood>
Macros<macros>
- Tutorials<tutorials/index>
How to upgrade<how-to-upgrade>
API documentation<_apidoc/modules>
diff --git a/src/doc/macros.rst b/src/doc/macros.rst
index d3a3e9b9634a4e1d72228dd46692a824e1d5acfd..7685731d35afab51074bb4d12c51ede0a7ba1b75 100644
--- a/src/doc/macros.rst
+++ b/src/doc/macros.rst
@@ -195,7 +195,7 @@ The example will be expanded to:
Limitation
-----------
+==========
Currently it is not possible to use the same macro twice in the same yaml node, but in different
positions. Consider:
diff --git a/src/doc/tutorials/index.rst b/src/doc/tutorials/index.rst
index 88d598ece284e1aad315a1e0fcae3fdf494b3aad..02371de196cc139776416882aff31bd6fa4dabbe 100644
--- a/src/doc/tutorials/index.rst
+++ b/src/doc/tutorials/index.rst
@@ -1,9 +1,11 @@
Tutorials
+++++++++
+This chapter contains a collection of tutorials.
+
.. toctree::
:maxdepth: 2
:caption: Contents:
- :hidden:
Example CFood<example>
+
diff --git a/unittests/scifolder_cfood.yml b/unittests/scifolder_cfood.yml
index 74fd027563907c5ae416ca389faba0ecd64d5848..dce219b751c3e980662a1eaa4904e1163d9836a0 100644
--- a/unittests/scifolder_cfood.yml
+++ b/unittests/scifolder_cfood.yml
@@ -22,7 +22,7 @@ Data: # name of the converter
parents:
- Project # not needed as the name is equivalent
date: $date
- identifier: $identifier
+ identifier: ${identifier}
subtree:
measurement: # new name for folders on the 3rd level
diff --git a/unittests/test_converters.py b/unittests/test_converters.py
index f72deda18152f9d12161d740e41271f90fcb848c..4d3791fce3ceffaafe529423e4020ebd6a4231ba 100644
--- a/unittests/test_converters.py
+++ b/unittests/test_converters.py
@@ -130,14 +130,11 @@ def test_markdown_converter(converter_registry):
)
)
- converter = MarkdownFileConverter({
- "match": "(.*)"
- }, "TestMarkdownFileConverter",
- converter_registry)
+ converter = MarkdownFileConverter({"match": "(.*)"}, "TestMarkdownFileConverter",
+ converter_registry)
- m = converter.match(File("test_tool.py", rfp(
- "test_tool.py")))
- assert m is None
+ with pytest.raises(ConverterValidationError) as err:
+ converter.create_children(None, File("test_tool.py", rfp("test_tool.py")))
m = converter.match(test_readme)
assert m is not None
@@ -610,3 +607,17 @@ def test_load_converters():
assert "SimpleFile" in converter_registry
assert "Directory" in converter_registry
assert "ListElement" in converter_registry
+
+
+def test_create_path_value(converter_registry):
+ """ test whether the variable containing the path is added to the general store"""
+ dc = Converter.converter_factory(
+ definition={
+ "type": "Directory",
+ "match": ".*"
+ },
+ name="Test", converter_registry=converter_registry)
+ values = GeneralStore()
+ dc.create_values(values, Directory("a", "/a"))
+ assert "Test.path" in values
+ assert values["Test.path"] == "/a"
diff --git a/unittests/test_scalars_cfood.py b/unittests/test_scalars_cfood.py
index 1bf8f0b7d67f00f2018b5b68424d6b9cc17602eb..ac408b2dab0fa151c370d3ec6ffd1dced22c77d7 100644
--- a/unittests/test_scalars_cfood.py
+++ b/unittests/test_scalars_cfood.py
@@ -42,16 +42,23 @@ def test_record_structure_generation(crawler):
subd = crawler.debug_tree[dircheckstr("DataAnalysis")]
assert len(subd) == 2
# variables store on Data Analysis node of debug tree
- assert len(subd[0]) == 3
- assert "Data" in subd[0]
- assert "DataAnalysis" in subd[0]
- assert "RecordThatGetsParentsLater" in subd[0]
+ if "Data" in subd[0]:
+ subddata = subd[0]
+ subdRTGPL = subd[1]
+ else:
+ subddata = subd[1]
+ subdRTGPL = subd[0]
+ assert len(subddata) == 5
+ assert "DataAnalysis" in subddata
+ assert "DataAnalysis.path" in subddata
+ assert "Data.path" in subddata
+ assert "RecordThatGetsParentsLater" in subddata
- prop = subd[0]["RecordThatGetsParentsLater"].get_property("someId")
+ prop = subddata["RecordThatGetsParentsLater"].get_property("someId")
assert type(prop.value) == int
assert prop.value == 23
# record store on Data Analysis node of debug tree
- assert len(subd[1]) == 1
- prop2 = subd[1]["RecordThatGetsParentsLater"].get_property("someId")
+ assert len(subdRTGPL) == 1
+ prop2 = subdRTGPL["RecordThatGetsParentsLater"].get_property("someId")
assert prop == prop2
diff --git a/unittests/test_tool.py b/unittests/test_tool.py
index 23b35f2dc9228eeda9137945198c49c19bf5c474..e15d7cb777ced4b92566df2b25b375e90be39295 100755
--- a/unittests/test_tool.py
+++ b/unittests/test_tool.py
@@ -110,15 +110,17 @@ def ident(crawler):
def test_record_structure_generation(crawler):
+ # TODO How does this test relate to the test function in test_scalars_cfood with the same name?
+ # There seems to be code duplication
subd = crawler.debug_tree[dircheckstr("DataAnalysis")]
subc = crawler.debug_metadata["copied"][dircheckstr("DataAnalysis")]
assert len(subd) == 2
# variables store on Data Analysis node of debug tree
- assert len(subd[0]) == 2
+ assert len(subd[0]) == 4
# record store on Data Analysis node of debug tree
assert len(subd[1]) == 0
assert len(subc) == 2
- assert len(subc[0]) == 2
+ assert len(subc[0]) == 4
assert len(subc[1]) == 0
# The data analysis node creates one variable for the node itself:
@@ -137,7 +139,7 @@ def test_record_structure_generation(crawler):
assert subd[1]["Project"].get_property(
"identifier").value == "climate-model-predict"
- assert len(subd[0]) == 6
+ assert len(subd[0]) == 9
assert subd[0]["date"] == "2020"
assert subd[0]["identifier"] == "climate-model-predict"
assert subd[0]["Project"].__class__ == db.Record
@@ -148,7 +150,7 @@ def test_record_structure_generation(crawler):
assert subc[0]["project_dir"] is False
# Check the copy flags for the first level in the hierarchy:
- assert len(subc[0]) == 6
+ assert len(subc[0]) == 9
assert len(subc[1]) == 1
assert subc[1]["Project"] is False
assert subc[0]["Project"] is False
@@ -161,7 +163,7 @@ def test_record_structure_generation(crawler):
subc = crawler.debug_metadata["copied"][dircheckstr("DataAnalysis",
"2020_climate-model-predict",
"2020-02-08_prediction-errors")]
- assert len(subd[0]) == 8
+ assert len(subd[0]) == 12
assert subd[0]["date"] == "2020-02-08"
assert subd[0]["identifier"] == "prediction-errors"
assert subd[0]["Project"].__class__ == db.Record
@@ -792,8 +794,7 @@ def test_validation_error_print(caplog):
os.path.join(DATADIR, "identifiables.yml"),
True,
None,
- False,
- "/use_case_simple_presentation")
+ False)
assert "Couldn't validate" in caplog.text
caplog.clear()
@@ -965,3 +966,36 @@ def test_split_restricted_path():
assert ["el"] == split_restricted_path("/el")
assert ["el"] == split_restricted_path("/el/")
assert ["el", "el"] == split_restricted_path("/el/el")
+
+
+def test_deprecated_prefix_option():
+ """Test that calling the crawler's main function with the deprecated
+ `prefix` option raises the correct errors and warnings.
+
+ """
+
+ with pytest.deprecated_call():
+ crawler_main("./", rfp("scifolder_cfood.yml"), prefix="to/be/removed")
+
+ with raises(ValueError) as ve:
+ crawler_main("./", rfp("scifolder_cfood.yml"), prefix="to/be/removed",
+ remove_prefix="to/be/removed")
+
+ assert "(deprecated) `prefix` and the `remove_prefix`" in str(ve.value)
+
+
+def test_create_entity_summary():
+ assert "" == Crawler.create_entity_summary([]).strip()
+
+ entities = [
+ db.Record(id=1).add_parent("A"),
+ db.Record(id=4, name='a').add_parent("B"),
+ db.Record(id=5).add_parent("A"),
+ db.Record(id=6, name='b').add_parent("B"),
+ ]
+ text = Crawler.create_entity_summary(entities).strip()
+ assert 'a' in text
+ assert 'b' in text
+ assert 'A:' in text
+ assert 'B:' in text
+ assert "<a href='/Entity/4'>a</a>, <a href='/Entity/6'>b</a>" in text