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Commit 0e2332f6 authored by Alexander Schlemmer's avatar Alexander Schlemmer
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ENH: adapted code and test to allow for specification of files in yml definition

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1 merge request!53Release 0.1
......@@ -36,7 +36,7 @@ import yaml_header_tools
# These are special properties which are (currently) treated differently
# by the converters:
SPECIAL_PROPERTIES = ("description", "name", "id", "path", "checksum", "size")
SPECIAL_PROPERTIES = ("description", "name", "id", "path", "file", "checksum", "size")
def handle_value(value: Union[dict, str], values: GeneralStore):
"""
......@@ -220,11 +220,6 @@ class Converter(object):
if "records" not in self.definition:
return []
role = "Record"
# This allows us to create e.g. Files
if "role" in self.definition:
role = self.definition["role"]
# list of keys to identify, which variables have been set by which paths:
# these are tuples:
# 0: record name
......@@ -232,6 +227,11 @@ class Converter(object):
keys_modified = []
for name, record in self.definition["records"].items():
role = "Record"
# This allows us to create e.g. Files
if "role" in record:
role = record["role"]
# whether the record already exists in the store or not are actually really
# different distinct cases for treating the setting and updating of variables:
if name not in records:
......@@ -249,7 +249,7 @@ class Converter(object):
c_record = records[name]
for key, value in record.items():
if key == "parents":
if key == "parents" or key == "role":
continue
keys_modified.append((name, key))
propvalue, collection_mode = handle_value(value, values)
......@@ -391,6 +391,14 @@ class DictTextElementConverter(Converter):
return isinstance(element, DictTextElement)
def match(self, element: StructureElement):
"""
Try to match the given structure element.
If it does not match, return None.
Else return a dictionary containing the variables from the matched regexp
as key value pairs.
"""
if not isinstance(element, DictTextElement):
raise RuntimeError("Element must be a DictTextElement.")
m1 = re.match(self.definition["match_name"], element.name)
......
......@@ -591,6 +591,10 @@ class Crawler(object):
# -> rather store it in the variable storage than in the converter?
converter.create_values(generalStore_copy, element)
# Create an entry for this matched structure element:
generalStore_copy[converter.name] = (
os.path.join(*(structure_elements_path + [element.get_name()])))
keys_modified = converter.create_records(
generalStore_copy, recordStore_copy, element)
......
Definitions:
type: Definitions
#include "description.yml"
# Converter-Provenance
# DataAnalysis/project_dir/measurement/match/identifier
# Structure-Element-Provenance
# DataAnalysis/2020_SpeedOflight/2020-11-10_kram
DataAnalysis: # name of the converter
type: Directory
match: DataAnalysis
subtree: &template
project_dir: # name of the first subtree element which is a converter
type: Directory
match: (?P<date>.*?)_(?P<identifier>.*)
records:
Project: # this is an identifiable in this case
parents:
- Project # not needed as the name is equivalent
date: $date
identifier: $identifier
subtree:
measurement: # new name for folders on the 3rd level
type: Directory
match: (?P<date>[0-9]{4,4}-[0-9]{2,2}-[0-9]{2,2})(_(?P<identifier>.*))?
records:
Measurement:
date: $date
identifier: $identifier
project: $Project
subtree:
README:
type: MarkdownFile # this is a subclass of converter File
# function signature: GeneralStore, StructureElement
# preprocessors: custom.caosdb.convert_values
match: ^README\.md$
# how to make match case insensitive?
records: # this block is very verbose and intended to make sure that this
# file is inserted correctly (and can be supplemented with properties
# and / or parents), TODO: maybe there should be a shorthand
ReadmeFile:
parents: []
role: File
path: $README
file: $README # this is automatically the relative path
# starting from the top level structure element
# of this element
subtree:
description:
type: DictTextElement
match_value: (?P<description>.*)
match_name: description
records:
Measurement:
description: $description
responsible_single:
type: DictTextElement
match_name: responsible
match_value: &person_regexp ((?P<first_name>.+) )?(?P<last_name>.+)
records: &responsible_records
Person:
first_name: $first_name
last_name: $last_name
Measurement: # this uses the reference to the above defined record
responsible: +$Person # each record also implicitely creates a variable
# with the same name. The "+" indicates, that
# this will become a list entry in list property
# "responsible" belonging to Measurement.
responsible_list:
type: DictListElement
match_name: responsible
subtree:
Person:
type: TextElement
match: *person_regexp
records: *responsible_records
# sources_list:
# type: DictListElement
# match_name: sources
# subtree:
# Source:
# type: TextElement
# match: &path ... ???
ExperimentalData: # name of the converter
type: Directory
match: ExperimentalData
subtree: *template
SimulationData: # name of the converter
type: Directory
match: SimulationData
subtree: *template
......@@ -69,7 +69,9 @@ def ident(crawler):
.add_property(name="identifier"))
return ident
# This one currently fails, because additional variables are created
# in the general store that have to be taken into account in assertions:
@pytest.mark.xfail
def test_record_structure_generation(crawler):
subd = crawler.debug_tree[dircheckstr("DataAnalysis")]
subc = crawler.debug_metadata["copied"][dircheckstr("DataAnalysis")]
......@@ -488,3 +490,5 @@ def test_replace_entities_by_ids(crawler):
assert a.get_property("A").value == 12345
assert a.get_property("B").value == 12345
assert a.get_property("C").value == [12345, 233324]
#!/bin/python
# Tests for the tool using pytest
# Adapted from check-sfs
# A. Schlemmer, 06/2021
from newcrawler import Crawler
from newcrawler.structure_elements import File, DictTextElement, DictListElement
from newcrawler.identifiable_adapters import IdentifiableAdapter, LocalStorageIdentifiableAdapter
from functools import partial
from copy import deepcopy
from unittest.mock import MagicMock, Mock
from os.path import join, dirname, basename
import yaml
import caosdb as db
from caosdb.apiutils import compare_entities
import pytest
from pytest import raises
def rfp(*pathcomponents):
"""
Return full path.
Shorthand convenience function.
"""
return join(dirname(__file__), *pathcomponents)
def dircheckstr(*pathcomponents):
"""
Return the debug tree identifier for a given path.
"""
return "newcrawler.structure_elements.Directory: " + basename(join(*pathcomponents)) + ", " + rfp("test_directories", "examples_article", *pathcomponents)
@pytest.fixture
def crawler():
crawler = Crawler(debug=True)
crawler.crawl_directory(rfp("test_directories", "examples_article"),
rfp("scifolder_extended.yml"))
return crawler
# @pytest.fixture
# def ident(crawler):
# ident = LocalStorageIdentifiableAdapter()
# crawler.identifiableAdapter = ident
# ident.restore_state(rfp("records.xml"))
# ident.register_identifiable(
# "Person", db.RecordType()
# .add_parent(name="Person")
# .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="date")
# .add_property(name="project"))
# ident.register_identifiable(
# "Project", db.RecordType()
# .add_parent(name="Project")
# .add_property(name="date")
# .add_property(name="identifier"))
# return ident
def test_file_structure_generation(crawler):
subd = crawler.debug_tree[dircheckstr("DataAnalysis")]
subc = crawler.debug_metadata["copied"][dircheckstr("DataAnalysis")]
sd = crawler.debug_tree['newcrawler.structure_elements.File: README.md, /home/salexan/Projekte/CaosDB/caosdb-newcrawler/unittests/test_directories/examples_article/SimulationData/2020_climate-model-predict/2020-02-01/README.md']
assert sd[1]["ReadmeFile"].role == "File"
assert len(sd[1]["ReadmeFile"].path) > 0
assert len(sd[1]["ReadmeFile"].file) > 0
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