From 8a5cb5c964c72bd1c3071349182422d49bb39ad3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Tue, 3 Nov 2020 13:18:01 +0000
Subject: [PATCH] F xls readme
---
CHANGELOG.md | 3 +
integrationtests/crawl.py | 4 +-
.../2019-02-03_something/README.md | 24 --
.../2019-02-03_something/README.xlsx | Bin 0 -> 5303 bytes
.../2019-02-03_V1.0-rc1/README.xlsx | Bin 0 -> 5255 bytes
.../2019-02-03_V1.0-rc1/analyse.py | 1 +
.../2019-02-03_V1.0-rc1/calc.py | 1 +
.../2019-02-03_v0.1/README.md | 15 ++
.../2019-02-03_v0.1/example.deb | 1 +
.../2010_TestSoftware/2019-02-03_v0.1/plot.py | 0
.../2020NewProject0X/2020-02-03/README.md | 15 ++
.../2020NewProject0X/2020-02-03/calc.py | 0
.../2020NewProject0X/2020-02-03/plot.py | 0
.../2020-02-03_second/README.xlsx | Bin 0 -> 5168 bytes
.../2020-02-03_second/analyse.py | 0
.../2020-02-03_second/release.deb | 1 +
.../2020NewProject0X/2020-02-04/README.md | 15 ++
.../2020NewProject0X/2020-02-04/example.deb | 1 +
.../2020NewProject0X/2020-02-04/plot.py | 0
integrationtests/filldb.sh | 1 +
integrationtests/insert_model.py | 6 +
integrationtests/model.yml | 8 +
integrationtests/test_cache.py | 71 +++---
integrationtests/test_crawler_with_cfoods.py | 212 ++++++++++++++++++
src/caosadvancedtools/cfood.py | 49 +++-
src/caosadvancedtools/crawler.py | 5 +-
src/caosadvancedtools/utils.py | 19 +-
27 files changed, 380 insertions(+), 72 deletions(-)
delete mode 100644 integrationtests/extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.md
create mode 100644 integrationtests/extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx
create mode 100644 integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_V1.0-rc1/README.xlsx
create mode 100644 integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_V1.0-rc1/analyse.py
create mode 100644 integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_V1.0-rc1/calc.py
create mode 100644 integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/README.md
create mode 100644 integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/example.deb
create mode 100644 integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/plot.py
create mode 100644 integrationtests/extroot/Software/2020NewProject0X/2020-02-03/README.md
create mode 100644 integrationtests/extroot/Software/2020NewProject0X/2020-02-03/calc.py
create mode 100644 integrationtests/extroot/Software/2020NewProject0X/2020-02-03/plot.py
create mode 100644 integrationtests/extroot/Software/2020NewProject0X/2020-02-03_second/README.xlsx
create mode 100644 integrationtests/extroot/Software/2020NewProject0X/2020-02-03_second/analyse.py
create mode 100644 integrationtests/extroot/Software/2020NewProject0X/2020-02-03_second/release.deb
create mode 100644 integrationtests/extroot/Software/2020NewProject0X/2020-02-04/README.md
create mode 100644 integrationtests/extroot/Software/2020NewProject0X/2020-02-04/example.deb
create mode 100644 integrationtests/extroot/Software/2020NewProject0X/2020-02-04/plot.py
diff --git a/CHANGELOG.md b/CHANGELOG.md
index cb8662e1..7c458aed 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -16,6 +16,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
output
- New class for collecting information for exporting tables, e.g., to
metadata repositories
+- new name parsing
+- new test for software folder structure
+- new assure_name_is function
### Changed ###
diff --git a/integrationtests/crawl.py b/integrationtests/crawl.py
index e439510f..2bec8b0a 100755
--- a/integrationtests/crawl.py
+++ b/integrationtests/crawl.py
@@ -33,7 +33,7 @@ from caosadvancedtools.cfood import fileguide
from caosadvancedtools.crawler import FileCrawler
from caosadvancedtools.guard import INSERT, UPDATE
from scifolder import (AnalysisCFood, ExperimentCFood, ProjectCFood,
- PublicationCFood, SimulationCFood)
+ PublicationCFood, SimulationCFood, SoftwareCFood)
try:
from sss_helper import get_argument_parser, print_success
@@ -87,7 +87,7 @@ if __name__ == "__main__":
c = FileCrawler(files=files, use_cache=True,
interactive=False, hideKnown=False,
cfood_types=[ProjectCFood,
- ExperimentCFood, AnalysisCFood,
+ ExperimentCFood, AnalysisCFood, SoftwareCFood,
PublicationCFood, SimulationCFood,
])
diff --git a/integrationtests/extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.md b/integrationtests/extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.md
deleted file mode 100644
index 4470e62b..00000000
--- a/integrationtests/extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.md
+++ /dev/null
@@ -1,24 +0,0 @@
----
-responsible:
-- First Person
-description: A description of an example analysis.
-
-results:
-- file: "images/*.png"
- description: an example reference to a results file
-
-sources:
-- file: /ExperimentalData/2010_TestProject/2019-02-03_something/
- description: an example reference to an experiment
-
-revisionOf:
-- ../2019-02-03
-
-scripts:
-- analyse.py
-
-tags:
-- collagen
-- time sweep
-- frequency sweep
-...
diff --git a/integrationtests/extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx b/integrationtests/extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx
new file mode 100644
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diff --git a/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_V1.0-rc1/analyse.py b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_V1.0-rc1/analyse.py
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--- /dev/null
+++ b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_V1.0-rc1/analyse.py
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diff --git a/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_V1.0-rc1/calc.py b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_V1.0-rc1/calc.py
new file mode 100644
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--- /dev/null
+++ b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_V1.0-rc1/calc.py
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diff --git a/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/README.md b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/README.md
new file mode 100644
index 00000000..d844a2dd
--- /dev/null
+++ b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/README.md
@@ -0,0 +1,15 @@
+---
+responsible: Responsible, Only
+description: A description of this example analysis.
+
+sources:
+- file: "/ExperimentalData/2010_TestProject/2019-02-03/*.dat"
+ description: an example reference to a results file
+
+sourceCode:
+- file: plot.py
+ description: a plotting script
+binaries:
+- file: example.deb
+ description: the binary file
+...
diff --git a/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/example.deb b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/example.deb
new file mode 100644
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diff --git a/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/plot.py b/integrationtests/extroot/Software/2010_TestSoftware/2019-02-03_v0.1/plot.py
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diff --git a/integrationtests/extroot/Software/2020NewProject0X/2020-02-03/README.md b/integrationtests/extroot/Software/2020NewProject0X/2020-02-03/README.md
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index 00000000..a47ea6e1
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+++ b/integrationtests/extroot/Software/2020NewProject0X/2020-02-03/README.md
@@ -0,0 +1,15 @@
+---
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+- Only Responsible MPI DS
+description: A description of this example analysis.
+
+sources:
+- file: "/ExperimentalData/2010_TestProject/2019-02-03/*.dat"
+ description: an example reference to a results file
+
+sourceCode:
+- file: plot.py
+ description: a plotting script
+- file: calc.py
+ description: a calc script
+...
diff --git a/integrationtests/extroot/Software/2020NewProject0X/2020-02-03/calc.py b/integrationtests/extroot/Software/2020NewProject0X/2020-02-03/calc.py
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diff --git a/integrationtests/extroot/Software/2020NewProject0X/2020-02-03_second/analyse.py b/integrationtests/extroot/Software/2020NewProject0X/2020-02-03_second/analyse.py
new file mode 100644
index 00000000..e69de29b
diff --git a/integrationtests/extroot/Software/2020NewProject0X/2020-02-03_second/release.deb b/integrationtests/extroot/Software/2020NewProject0X/2020-02-03_second/release.deb
new file mode 100644
index 00000000..92861e91
--- /dev/null
+++ b/integrationtests/extroot/Software/2020NewProject0X/2020-02-03_second/release.deb
@@ -0,0 +1 @@
+kdjf
diff --git a/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/README.md b/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/README.md
new file mode 100644
index 00000000..97b7137a
--- /dev/null
+++ b/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/README.md
@@ -0,0 +1,15 @@
+---
+responsible:
+- Some Responsible
+- Responsible, No, MPI DS
+description: A description of this example analysis.
+
+sources:
+- file: "/ExperimentalData/2010_TestProject/2019-02-03/*.dat"
+ description: an example reference to a results file
+
+sourceCode: plot.py
+binaries:
+- file: example.deb
+ description: the binary file
+...
diff --git a/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/example.deb b/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/example.deb
new file mode 100644
index 00000000..685dc927
--- /dev/null
+++ b/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/example.deb
@@ -0,0 +1 @@
+binary file
diff --git a/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/plot.py b/integrationtests/extroot/Software/2020NewProject0X/2020-02-04/plot.py
new file mode 100644
index 00000000..e69de29b
diff --git a/integrationtests/filldb.sh b/integrationtests/filldb.sh
index da1abc70..98d22347 100755
--- a/integrationtests/filldb.sh
+++ b/integrationtests/filldb.sh
@@ -5,5 +5,6 @@ python3 -m caosadvancedtools.loadFiles /opt/caosdb/mnt/extroot/ExperimentalData
python3 -m caosadvancedtools.loadFiles /opt/caosdb/mnt/extroot/DataAnalysis
python3 -m caosadvancedtools.loadFiles /opt/caosdb/mnt/extroot/SimulationData
python3 -m caosadvancedtools.loadFiles /opt/caosdb/mnt/extroot/Publications
+python3 -m caosadvancedtools.loadFiles /opt/caosdb/mnt/extroot/Software
python3 insert_model.py
python3 crawl.py /
diff --git a/integrationtests/insert_model.py b/integrationtests/insert_model.py
index 1dcf5bdb..2289f72e 100755
--- a/integrationtests/insert_model.py
+++ b/integrationtests/insert_model.py
@@ -1,5 +1,11 @@
#!/usr/bin/env python3
+import caosdb as db
from caosmodels.parser import parse_model_from_yaml
model = parse_model_from_yaml("model.yml")
model.sync_data_model(noquestion=True)
+
+if len(db.execute_query("FIND Property alias")) == 0:
+ al = db.Property(name="alias")
+ al.add_parent(name="name")
+ al.insert()
diff --git a/integrationtests/model.yml b/integrationtests/model.yml
index 35f5ef24..39659c00 100644
--- a/integrationtests/model.yml
+++ b/integrationtests/model.yml
@@ -10,6 +10,14 @@ Experiment:
#recommended_properties:
responsible:
Project:
+SoftwareVersion:
+ recommended_properties:
+ version:
+ datatype: TEXT
+ description: 'First name of a Person.'
+ binaries:
+ sourceCode:
+ Software:
Person:
obligatory_properties:
firstName:
diff --git a/integrationtests/test_cache.py b/integrationtests/test_cache.py
index cb9c174e..4b0a6ced 100644
--- a/integrationtests/test_cache.py
+++ b/integrationtests/test_cache.py
@@ -22,45 +22,54 @@
#
# ** end header
+import os
+import unittest
+from tempfile import NamedTemporaryFile
+
import caosdb as db
from caosadvancedtools.cache import UpdateCache
-def setup():
- try:
- db.execute_query("FIND Test*").delete()
- except Exception:
- pass
-
+class CacheTest(unittest.TestCase):
+ def empty_db(self):
+ try:
+ db.execute_query("FIND Test*").delete()
+ except Exception:
+ pass
-def teardown():
- setup()
+ def setUp(self):
+ self.cache = NamedTemporaryFile(delete=False).name
+ os.remove(self.cache)
+ self.empty_db()
+ def tearDown(self):
+ self.empty_db()
+ os.remove(self.cache)
-def test_same_old_different_new():
- """Formerly, inserting two containers with different changes to the
- same entity into the update cache would result in an
- IntegrityException.
+ def test_same_old_different_new(self):
+ """Formerly, inserting two containers with different changes to the
+ same entity into the update cache would result in an
+ IntegrityException.
- """
- rt = db.RecordType(name="TestType").insert()
- db.Property(name="TestProp1", datatype=db.TEXT).insert()
- db.Property(name="TestProp2", datatype=db.TEXT).insert()
- rec = db.Record(name="TestRecord").add_parent(rt).insert()
+ """
+ rt = db.RecordType(name="TestType").insert()
+ db.Property(name="TestProp1", datatype=db.TEXT).insert()
+ db.Property(name="TestProp2", datatype=db.TEXT).insert()
+ rec = db.Record(name="TestRecord").add_parent(rt).insert()
- # add TestProp1 to TestRecord
- rec.add_property(name="TestProp1", value="blub")
- cont = db.Container().append(rec)
+ # add TestProp1 to TestRecord
+ rec.add_property(name="TestProp1", value="blub")
+ cont = db.Container().append(rec)
- update = UpdateCache()
- run_id = "a"
- update.insert(cont, run_id)
- assert len(update.get_updates(run_id)) == 1
+ update = UpdateCache(db_file=self.cache)
+ run_id = "a"
+ update.insert(cont, run_id)
+ assert len(update.get_updates(run_id)) == 1
- # duplicate and add TestProp2 to TestRecord
- rec = db.execute_query("FIND Record TestRecord", unique=True)
- rec.add_property(name="TestProp2", value="bla")
- cont = db.Container().append(rec)
- # same old digest, different new digest
- update.insert(cont, run_id)
- assert len(update.get_updates(run_id)) == 2
+ # duplicate and add TestProp2 to TestRecord
+ rec = db.execute_query("FIND Record TestRecord", unique=True)
+ rec.add_property(name="TestProp2", value="bla")
+ cont = db.Container().append(rec)
+ # same old digest, different new digest
+ update.insert(cont, run_id)
+ assert len(update.get_updates(run_id)) == 2
diff --git a/integrationtests/test_crawler_with_cfoods.py b/integrationtests/test_crawler_with_cfoods.py
index cc6f0677..c39c3fc6 100755
--- a/integrationtests/test_crawler_with_cfoods.py
+++ b/integrationtests/test_crawler_with_cfoods.py
@@ -266,3 +266,215 @@ class CrawlerTest(unittest.TestCase):
# Test type
self.assertEqual(pub.parents[0].name, "Thesis")
+
+ def test_software(self):
+ ########################
+ # # overall software # #
+ ########################
+
+ sw = db.execute_query("FIND Record Software")
+ assert len(sw) == 5
+
+ ps = db.execute_query("FIND RecordType Software with name!='Software'")
+ assert len(ps) == 2
+
+ ##############################
+ # # first software version # #
+ ##############################
+ ana = db.execute_query(
+ "FIND Software with version='V1.0-rc1'", unique=True)
+
+ sw = db.execute_query(
+ "FIND Software with name='2010_TestSoftware'", unique=True)
+ assert sw.get_property("alias").value == "TestSoftware"
+
+ # The software record should inherit from the correct software
+ assert sw.id == ana.get_parents()[0].id
+ assert ana.name == "TestSoftware_V1.0-rc1"
+
+ # There should not be a file as binary
+ self.assertIsNone(ana.get_property("binaries"))
+
+ # There should be a file as script attached with path plot.py
+ datfile = get_entity_with_id(ana.get_property("sourceCode").value[0])
+ datfile2 = get_entity_with_id(ana.get_property("sourceCode").value[1])
+
+ for d in [datfile, datfile2]:
+ if datfile.path.endswith("analyse.py"):
+ assert datfile.description == "a simple script"
+ elif datfile.path.endswith("calc.py"):
+ assert datfile.description == "some calculation"
+ else:
+ raise Exception("unkown file")
+
+ # Should have two responsible person
+ self.assertIsNotNone(ana.get_property("responsible"))
+ person = db.Record(id=ana.get_property("responsible").value[0])
+ person.retrieve()
+ person2 = db.Record(id=ana.get_property("responsible").value[1])
+ person2.retrieve()
+
+ for fn in ["Second", "First"]:
+ found = False
+
+ for p in [person, person2]:
+ if p.get_property("firstname").value == fn:
+ found = True
+
+ if not found:
+ raise Exception("Did not find person")
+
+ # Should have a description
+ self.assertIsNotNone(ana.description)
+
+ #######################
+ # # second software version # #
+ #######################
+ ana = db.execute_query(
+ "FIND Software with version='v0.1'", unique=True)
+
+ sw = db.execute_query(
+ "FIND Software with name='2010_TestSoftware'", unique=True)
+
+ # The software record should inherit from the correct software
+ assert sw.id == ana.get_parents()[0].id
+ # The software should have the date
+ assert "2019-02-03" == ana.get_property("date").value
+
+ # There should be a file as binary attached with path release.deb
+ datfile_id = ana.get_property("binaries").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "example.deb"
+
+ # There should be a file as script attached with path plot.py
+ datfile_id = ana.get_property("sourceCode").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "plot.py"
+
+ # Should have a responsible person
+ self.assertIsNotNone(ana.get_property("responsible"))
+ person = db.Record(id=ana.get_property("responsible").value[0])
+ person.retrieve()
+ self.assertEqual("Only", person.get_property("firstname").value)
+
+ # Should have a description
+ assert "example" in ana.description
+
+ #######################
+ # # third software version # #
+ #######################
+ ana = db.execute_query(
+ "FIND Software with date='2020-02-04' and not version",
+ unique=True)
+
+ sw = db.execute_query(
+ "FIND Software with name='2020NewProject0X'", unique=True)
+
+ # The software record should inherit from the correct software
+ assert sw.id == ana.get_parents()[0].id
+ # The software should have the date
+ assert "2020-02-04" == ana.get_property("date").value
+
+ # There should be a file as binary attached with path release.deb
+ datfile_id = ana.get_property("binaries").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "example.deb"
+
+ # There should be a file as script attached with path plot.py
+ datfile_id = ana.get_property("sourceCode").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "plot.py"
+
+ # Should have two responsible person
+ self.assertIsNotNone(ana.get_property("responsible"))
+ person = db.Record(id=ana.get_property("responsible").value[0])
+ person.retrieve()
+ person2 = db.Record(id=ana.get_property("responsible").value[1])
+ person2.retrieve()
+
+ for fn in ["Some", "No"]:
+ found = False
+
+ for p in [person, person2]:
+ if p.get_property("firstname").value == fn:
+ found = True
+
+ if not found:
+ raise Exception("Did not find person")
+
+ # Should have a description
+ assert "example" in ana.description
+
+ #######################
+ # # fourth software version # #
+ #######################
+ ana = db.execute_query(
+ "FIND Software with date='2020-02-03' and not version",
+ unique=True)
+
+ sw = db.execute_query(
+ "FIND Software with name='2020NewProject0X'", unique=True)
+ assert sw.get_property("alias").value == "NewProject0X"
+
+ # The software record should inherit from the correct software
+ assert sw.id == ana.get_parents()[0].id
+ # The software should have the date
+ assert "2020-02-03" == ana.get_property("date").value
+
+ # There should not be a file as binary
+ self.assertIsNone(ana.get_property("binaries"))
+
+ # There should be a file as script attached with path plot.py
+ datfile = get_entity_with_id(ana.get_property("sourceCode").value[0])
+ datfile2 = get_entity_with_id(ana.get_property("sourceCode").value[1])
+
+ for d in [datfile, datfile2]:
+ if datfile.path.endswith("plot.py"):
+ assert datfile.description == "a plotting script"
+ elif datfile.path.endswith("calc.py"):
+ assert datfile.description == "a calc script"
+ else:
+ raise Exception("unkown file")
+
+ # Should have a responsible person
+ self.assertIsNotNone(ana.get_property("responsible"))
+ person = db.Record(id=ana.get_property("responsible").value[0])
+ person.retrieve()
+ self.assertEqual("Only", person.get_property("firstname").value)
+ self.assertEqual("Responsible", person.get_property("lastname").value)
+
+ # Should have a description
+ assert "example" in ana.description
+
+ ##############################
+ # # fifth software version # #
+ ##############################
+ ana = db.execute_query(
+ "FIND Software with version='second'", unique=True)
+
+ sw = db.execute_query(
+ "FIND Software with name='2020NewProject0X'", unique=True)
+ assert sw.get_property("alias").value == "NewProject0X"
+
+ # The software record should inherit from the correct software
+ assert sw.id == ana.get_parents()[0].id
+ assert ana.name == "NewProject0X_second"
+
+ # There should be a file as binary attached with path release.deb
+ datfile_id = ana.get_property("binaries").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "release.deb"
+
+ # There should be a file as script attached with path plot.py
+ datfile_id = ana.get_property("sourceCode").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "analyse.py"
+
+ # Should have a responsible person
+ self.assertIsNotNone(ana.get_property("responsible"))
+ person = db.Record(id=ana.get_property("responsible").value[0])
+ person.retrieve()
+ self.assertEqual("First", person.get_property("firstname").value)
+
+ # Should have a description
+ self.assertIsNotNone(ana.description)
diff --git a/src/caosadvancedtools/cfood.py b/src/caosadvancedtools/cfood.py
index 341594cf..54a6b809 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -412,24 +412,24 @@ def assure_object_is_in_list(obj, containing_object, property_name,
to_be_updated.append(containing_object)
-# TOOD rename to is
-# switch arugments and check for old sequence
-def assure_has_description(entity, description, to_be_updated=None,
- force=False):
+def assure_special_is(entity, value, kind, to_be_updated=None, force=False):
"""
- Checks whether `entity` has the description that is passed.
+ Checks whether `entity` has the name or description that is passed.
If this is the case this function ends. Otherwise the entity is assigned
- a new description. The list to_be_updated is supplied, the entity is added to
+ a new name. The list to_be_updated is supplied, the entity is added to
the list in order to indicate, that the entity `entity` should be updated.
Otherwise it is directly updated
"""
- if entity.description == description:
+ if kind not in ["name", "description"]:
+ raise RuntimeError("Function cannot be used to set {}".format(kind))
+
+ if entity.__getattribute__(kind) == value:
return
- logger.debug("UPDATE: set description of entity {}".format(entity.id))
- entity.description = description
+ logger.debug("UPDATE: set {} of entity {}".format(kind, entity.id))
+ entity.__setattr__(kind, value)
if to_be_updated is None:
if force:
@@ -440,6 +440,37 @@ def assure_has_description(entity, description, to_be_updated=None,
to_be_updated.append(entity)
+def assure_name_is(entity, name, to_be_updated=None, force=False):
+ """
+ Checks whether `entity` has the name that is passed.
+
+ If this is the case this function ends. Otherwise the entity is assigned
+ a new name. The list to_be_updated is supplied, the entity is added to
+ the list in order to indicate, that the entity `entity` should be updated.
+ Otherwise it is directly updated
+ """
+
+ assure_special_is(entity, name, "name", to_be_updated=to_be_updated,
+ force=force)
+
+
+# TOOD rename to is
+# switch arugments and check for old sequence
+def assure_has_description(entity, description, to_be_updated=None,
+ force=False):
+ """
+ Checks whether `entity` has the description that is passed.
+
+ If this is the case this function ends. Otherwise the entity is assigned
+ a new description. The list to_be_updated is supplied, the entity is added to
+ the list in order to indicate, that the entity `entity` should be updated.
+ Otherwise it is directly updated
+ """
+
+ assure_special_is(entity, description, "description",
+ to_be_updated=to_be_updated, force=force)
+
+
def assure_has_parent(entity, parent, to_be_updated=None,
force=False, unique=True):
"""
diff --git a/src/caosadvancedtools/crawler.py b/src/caosadvancedtools/crawler.py
index e5bb738c..6d706bb3 100644
--- a/src/caosadvancedtools/crawler.py
+++ b/src/caosadvancedtools/crawler.py
@@ -45,10 +45,10 @@ import subprocess
import traceback
import uuid
from datetime import datetime
+from sqlite3 import IntegrityError
import caosdb as db
from caosdb.exceptions import TransactionError
-from sqlite3 import IntegrityError
from .cache import Cache, UpdateCache, get_pretty_xml
from .cfood import RowCFood, add_files, get_ids_for_entities_with_names
@@ -293,7 +293,7 @@ class Crawler(object):
except Exception as e:
try:
DataModelProblems.evaluate_exception(e)
- except BaseException:
+ except Exception:
pass
logger.info("Failed during execution of {}!".format(
cfood.__class__.__name__))
@@ -365,6 +365,7 @@ ____________________\n""".format(i+1, len(pending_changes)) + str(el[3]))
"""
from xml.sax.saxutils import escape
+
# TODO move path related stuff to sss_helper
form = """
<html>
diff --git a/src/caosadvancedtools/utils.py b/src/caosadvancedtools/utils.py
index cb790a51..2504f569 100644
--- a/src/caosadvancedtools/utils.py
+++ b/src/caosadvancedtools/utils.py
@@ -4,7 +4,8 @@
# ** header v3.0
# This file is a part of the CaosDB Project.
#
-# Copyright (C) 2019 Henrik tom Wörden
+# Copyright (C) 2020 IndiScale GmbH <info@indiscale.com>
+# Copyright (C) 2020 Henrik tom Wörden <h.tomwoerden@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
@@ -58,10 +59,20 @@ def string_to_person(person):
"""
Creates a Person Record from a string.
- Currently only the format <Firstname> <Lastname> <*> is supported.
+ The following formats are supported:
+ - `<Firstname> <Lastname> <*>`
+ - `<Lastname(s)>,<Firstname(s)>,<*>`
+
+ The part after the name can be used for an affiliation for example.
"""
- firstname = person.split(" ")[0]
- lastname = person.split(" ")[1]
+
+ if "," in person:
+ firstname = person.split(",")[1].strip()
+ lastname = person.split(",")[0].strip()
+ else:
+ firstname = person.split(" ")[0].strip()
+ lastname = person.split(" ")[1].strip()
+
pr = db.Record()
pr.add_parent("Person")
pr.add_property("lastname", lastname)
--
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