From 44a157fa82f632752f6353cc78c9cdcac7ce5a5d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Henrik=20tom=20W=C3=B6rden?= <h.tomwoerden@indiscale.com>
Date: Thu, 6 Apr 2023 10:37:22 +0200
Subject: [PATCH] MAINT: refactor due to new default entity role(RECORD)
---
integrationtests/test_assure_functions.py | 8 ++--
.../test_base_table_exporter_integration.py | 4 +-
integrationtests/test_cache.py | 2 +-
.../test_crawl_with_datamodel_problems.py | 2 +-
integrationtests/test_crawler_basics.py | 2 +-
integrationtests/test_crawler_with_cfoods.py | 40 +++++++++----------
integrationtests/test_data_model.py | 2 +-
integrationtests/test_im_und_export.py | 6 +--
integrationtests/test_table.py | 8 ++--
integrationtests/update_analysis.py | 2 +-
src/caosadvancedtools/cache.py | 2 +-
src/caosadvancedtools/export_related.py | 2 +-
src/caosadvancedtools/models/parser.py | 2 +-
13 files changed, 41 insertions(+), 41 deletions(-)
diff --git a/integrationtests/test_assure_functions.py b/integrationtests/test_assure_functions.py
index b1c731db..e04d481f 100644
--- a/integrationtests/test_assure_functions.py
+++ b/integrationtests/test_assure_functions.py
@@ -33,7 +33,7 @@ from caosadvancedtools.guard import (global_guard, RETRIEVE, UPDATE)
def setup():
"""Delete all test entities."""
- db.execute_query("FIND Test*").delete(raise_exception_on_error=False)
+ db.execute_query("FIND ENTITY Test*").delete(raise_exception_on_error=False)
def setup_module():
@@ -105,13 +105,13 @@ def test_add_to_empty_list():
db.Record(name="TestReferencingRecord").add_parent(
referencing_rt).add_property(list_prop, value=[]).insert()
- referenced_rec = db.execute_query("FIND TestReferencedRecord", unique=True)
+ referenced_rec = db.execute_query("FIND ENTITY TestReferencedRecord", unique=True)
referencing_rec = db.execute_query(
- "FIND TestReferencingRecord", unique=True)
+ "FIND ENTITY TestReferencingRecord", unique=True)
assure_object_is_in_list(referenced_rec, referencing_rec, list_prop.name)
referencing_rec = db.execute_query(
- "FIND TestReferencingRecord", unique=True)
+ "FIND ENTITY TestReferencingRecord", unique=True)
assert referencing_rec.get_property(list_prop.name).value == [
referenced_rec.id]
diff --git a/integrationtests/test_base_table_exporter_integration.py b/integrationtests/test_base_table_exporter_integration.py
index 9d79e857..5af9caa3 100644
--- a/integrationtests/test_base_table_exporter_integration.py
+++ b/integrationtests/test_base_table_exporter_integration.py
@@ -81,7 +81,7 @@ def insert_entities():
def setup_module():
"""Clear all test entities"""
try:
- db.execute_query("FIND Test*").delete()
+ db.execute_query("FIND ENTITY Test*").delete()
except BaseException:
pass
@@ -146,7 +146,7 @@ def test_queries():
"Test_Property_2").value
# test guessing of selector
- del(export_dict["Test_Property_2"]["selector"])
+ del (export_dict["Test_Property_2"]["selector"])
my_exporter = te.BaseTableExporter(
export_dict=export_dict, record=rec1, raise_error_if_missing=True)
assert my_exporter.export_dict["Test_Property_2"]["selector"] == "Test_Property_2"
diff --git a/integrationtests/test_cache.py b/integrationtests/test_cache.py
index 4b0a6ced..da1824e8 100644
--- a/integrationtests/test_cache.py
+++ b/integrationtests/test_cache.py
@@ -33,7 +33,7 @@ from caosadvancedtools.cache import UpdateCache
class CacheTest(unittest.TestCase):
def empty_db(self):
try:
- db.execute_query("FIND Test*").delete()
+ db.execute_query("FIND ENTITY Test*").delete()
except Exception:
pass
diff --git a/integrationtests/test_crawl_with_datamodel_problems.py b/integrationtests/test_crawl_with_datamodel_problems.py
index 0c6a145a..8623d57d 100644
--- a/integrationtests/test_crawl_with_datamodel_problems.py
+++ b/integrationtests/test_crawl_with_datamodel_problems.py
@@ -74,7 +74,7 @@ def test_crawler_with_data_model_problems():
deleted_entities = {"Experiment", "Poster", "results"}
for ent in deleted_entities:
- db.execute_query("FIND "+ent).delete()
+ db.execute_query("FIND ENTITY "+ent).delete()
# Do the crawling
def access(x): return "extroot" + x
diff --git a/integrationtests/test_crawler_basics.py b/integrationtests/test_crawler_basics.py
index 7da90844..60c09d73 100644
--- a/integrationtests/test_crawler_basics.py
+++ b/integrationtests/test_crawler_basics.py
@@ -40,7 +40,7 @@ def setup_module():
"""Clear all test entities. Allow insertions."""
guard.set_level(INSERT)
try:
- db.execute_query("FIND Test*").delete()
+ db.execute_query("FIND ENTITY Test*").delete()
except Exception:
pass
diff --git a/integrationtests/test_crawler_with_cfoods.py b/integrationtests/test_crawler_with_cfoods.py
index 19b1f8ff..1fa5eaa5 100755
--- a/integrationtests/test_crawler_with_cfoods.py
+++ b/integrationtests/test_crawler_with_cfoods.py
@@ -30,7 +30,7 @@ from caosdb.apiutils import retrieve_entity_with_id
def get_entity_with_id(eid):
- return db.execute_query("FIND "+str(eid), unique=True)
+ return db.execute_query("FIND ENTITY "+str(eid), unique=True)
class LoadFilesTest(unittest.TestCase):
@@ -49,7 +49,7 @@ class CrawlerTest(unittest.TestCase):
# # dummy for dependency test experiment # #
########################
exp = db.execute_query(
- "FIND Experiment with date=2019-02-04 and identifier=empty_identifier",
+ "FIND ENTITY Experiment with date=2019-02-04 and identifier=empty_identifier",
unique=True)
########################
@@ -59,7 +59,7 @@ class CrawlerTest(unittest.TestCase):
# vanishing of the property
# thus an x is used here. Needs to be fixed.
exp = db.execute_query(
- "FIND Experiment with date=2019-02-03 and identifier=empty_identifier",
+ "FIND ENTITY Experiment with date=2019-02-03 and identifier=empty_identifier",
unique=True)
# There should be a Project with name TestProject which is referenced
@@ -99,7 +99,7 @@ class CrawlerTest(unittest.TestCase):
# # second experiment # #
#########################
exp = db.execute_query(
- "FIND Experiment with date=2019-02-03 and identifier='something'",
+ "FIND ENTITY Experiment with date=2019-02-03 and identifier='something'",
unique=True)
# Should be the same project
@@ -120,7 +120,7 @@ class CrawlerTest(unittest.TestCase):
# # first analysis # #
######################
ana = db.execute_query(
- "FIND Analysis with date=2019-02-03 and identifier='empty_identifier'",
+ "FIND ENTITY Analysis with date=2019-02-03 and identifier='empty_identifier'",
unique=True)
# There should be a Project with name TestProject which is referenced
@@ -164,7 +164,7 @@ class CrawlerTest(unittest.TestCase):
# # second analysis # #
#######################
ana = db.execute_query(
- "FIND Analysis with date=2019-02-03 and identifier='something'",
+ "FIND ENTITY Analysis with date=2019-02-03 and identifier='something'",
unique=True)
# Should be the same project
@@ -197,7 +197,7 @@ class CrawlerTest(unittest.TestCase):
# # first simulation # #
######################
sim = db.execute_query(
- "FIND Simulation with date=2019-02-03 and identifier='empty_identifier'",
+ "FIND ENTITY Simulation with date=2019-02-03 and identifier='empty_identifier'",
unique=True)
# There should be a Project with name TestProject which is referenced
@@ -228,7 +228,7 @@ class CrawlerTest(unittest.TestCase):
# # second simulation # #
#########################
sim = db.execute_query(
- "FIND Simulation with date=2019-02-03 and identifier='something'",
+ "FIND ENTITY Simulation with date=2019-02-03 and identifier='something'",
unique=True)
sources = [get_entity_with_id(el) for el in
@@ -273,7 +273,7 @@ class CrawlerTest(unittest.TestCase):
#########################
# # first publication # #
#########################
- pub = db.execute_query("FIND *really_cool_finding", unique=True)
+ pub = db.execute_query("FIND ENTITY *really_cool_finding", unique=True)
# There should be a file as result attached with path poster.pdf
datfile_id = pub.get_property("results").value[0]
@@ -291,7 +291,7 @@ class CrawlerTest(unittest.TestCase):
##########################
# # second publication # #
##########################
- pub = db.execute_query("FIND *paper_on_exciting_stuff ", unique=True)
+ pub = db.execute_query("FIND ENTITY *paper_on_exciting_stuff ", unique=True)
# Test type
self.assertEqual(pub.parents[0].name, "Thesis")
@@ -311,10 +311,10 @@ class CrawlerTest(unittest.TestCase):
# # first software version # #
##############################
ana = db.execute_query(
- "FIND Software with version='V1.0-rc1'", unique=True)
+ "FIND ENTITY Software with version='V1.0-rc1'", unique=True)
sw = db.execute_query(
- "FIND Software with name='2010_TestSoftware'", unique=True)
+ "FIND ENTITY Software with name='2010_TestSoftware'", unique=True)
assert sw.get_property("alias").value == "TestSoftware"
# The software record should inherit from the correct software
@@ -360,10 +360,10 @@ class CrawlerTest(unittest.TestCase):
# # second software version # #
#######################
ana = db.execute_query(
- "FIND Software with version='v0.1'", unique=True)
+ "FIND ENTITY Software with version='v0.1'", unique=True)
sw = db.execute_query(
- "FIND Software with name='2010_TestSoftware'", unique=True)
+ "FIND ENTITY Software with name='2010_TestSoftware'", unique=True)
# The software record should inherit from the correct software
assert sw.id == ana.get_parents()[0].id
@@ -393,11 +393,11 @@ class CrawlerTest(unittest.TestCase):
# # third software version # #
#######################
ana = db.execute_query(
- "FIND Software with date='2020-02-04' and not version",
+ "FIND ENTITY Software with date='2020-02-04' and not version",
unique=True)
sw = db.execute_query(
- "FIND Software with name='2020NewProject0X'", unique=True)
+ "FIND ENTITY Software with name='2020NewProject0X'", unique=True)
# The software record should inherit from the correct software
assert sw.id == ana.get_parents()[0].id
@@ -438,11 +438,11 @@ class CrawlerTest(unittest.TestCase):
# # fourth software version # #
#######################
ana = db.execute_query(
- "FIND Software with date='2020-02-03' and not version",
+ "FIND ENTITY Software with date='2020-02-03' and not version",
unique=True)
sw = db.execute_query(
- "FIND Software with name='2020NewProject0X'", unique=True)
+ "FIND ENTITY Software with name='2020NewProject0X'", unique=True)
assert sw.get_property("alias").value == "NewProject0X"
# The software record should inherit from the correct software
@@ -479,10 +479,10 @@ class CrawlerTest(unittest.TestCase):
# # fifth software version # #
##############################
ana = db.execute_query(
- "FIND Software with version='second'", unique=True)
+ "FIND ENTITY Software with version='second'", unique=True)
sw = db.execute_query(
- "FIND Software with name='2020NewProject0X'", unique=True)
+ "FIND ENTITY Software with name='2020NewProject0X'", unique=True)
assert sw.get_property("alias").value == "NewProject0X"
# The software record should inherit from the correct software
diff --git a/integrationtests/test_data_model.py b/integrationtests/test_data_model.py
index 2949fa81..5bf168cd 100644
--- a/integrationtests/test_data_model.py
+++ b/integrationtests/test_data_model.py
@@ -57,7 +57,7 @@ class DataModelTest(unittest.TestCase):
def tearDown(self):
try:
- tests = db.execute_query("FIND test*")
+ tests = db.execute_query("FIND ENTITY test*")
tests.delete()
except Exception:
pass
diff --git a/integrationtests/test_im_und_export.py b/integrationtests/test_im_und_export.py
index 8ea45fd2..cd6782c2 100644
--- a/integrationtests/test_im_und_export.py
+++ b/integrationtests/test_im_und_export.py
@@ -8,12 +8,12 @@ from caosadvancedtools.import_from_xml import import_xml
if __name__ == "__main__":
print("Conducting im- and export tests")
- rec = db.execute_query("FIND 2019-02-03_really_cool_finding", unique=True)
+ rec = db.execute_query("FIND ENTITY 2019-02-03_really_cool_finding", unique=True)
directory = TemporaryDirectory()
export_related_to(rec.id, directory=directory.name)
# delete everything
print("Clearing database")
- recs = db.execute_query("FIND entity with id>99")
+ recs = db.execute_query("FIND ENTITY entity with id>99")
recs.delete()
assert 0 == len(db.execute_query("FIND File which is stored at "
"**/poster.pdf"))
@@ -22,7 +22,7 @@ if __name__ == "__main__":
# The following tests the existence of some required entities.
# However, this is not a full list.
- db.execute_query("FIND 2019-02-03_really_cool_finding", unique=True)
+ db.execute_query("FIND ENTITY 2019-02-03_really_cool_finding", unique=True)
db.execute_query("FIND RecordType Poster", unique=True)
db.execute_query("FIND RecordType Analysis", unique=True)
db.execute_query("FIND RecordType Person", unique=True)
diff --git a/integrationtests/test_table.py b/integrationtests/test_table.py
index 15b851fb..b8dfe349 100644
--- a/integrationtests/test_table.py
+++ b/integrationtests/test_table.py
@@ -34,14 +34,14 @@ if __name__ == "__main__":
table = pd.read_csv("example_table.csv")
- assert 0 == len(db.execute_query("FIND Person with firstname=Henrik"))
+ assert 0 == len(db.execute_query("FIND ENTITY Person with firstname=Henrik"))
first = table.loc[table.firstName == "Henrik"]
tcr = TableCrawler(table=first, unique_cols=["firstName", "lastName"],
recordtype="Person", interactive=False)
tcr.crawl(security_level=UPDATE)
- assert 1 == len(db.execute_query("FIND Person with firstname=Henrik"))
+ assert 1 == len(db.execute_query("FIND ENTITY Person with firstname=Henrik"))
tcr = TableCrawler(table=table, unique_cols=["firstName", "lastName"],
recordtype="Person", interactive=False)
tcr.crawl(security_level=UPDATE)
- assert 1 == len(db.execute_query("FIND Person with firstname=Henrik"))
- assert 1 == len(db.execute_query("FIND Person with firstname=Max"))
+ assert 1 == len(db.execute_query("FIND ENTITY Person with firstname=Henrik"))
+ assert 1 == len(db.execute_query("FIND ENTITY Person with firstname=Max"))
diff --git a/integrationtests/update_analysis.py b/integrationtests/update_analysis.py
index bd18ab37..ddebc049 100644
--- a/integrationtests/update_analysis.py
+++ b/integrationtests/update_analysis.py
@@ -39,7 +39,7 @@ from caosadvancedtools.serverside.generic_analysis import run
def main():
- da = db.execute_query("FIND Analysis with identifier=TEST", unique=True)
+ da = db.execute_query("FIND ENTITY Analysis with identifier=TEST", unique=True)
run(da)
diff --git a/src/caosadvancedtools/cache.py b/src/caosadvancedtools/cache.py
index db189b16..2b79f9ae 100644
--- a/src/caosadvancedtools/cache.py
+++ b/src/caosadvancedtools/cache.py
@@ -344,7 +344,7 @@ class UpdateCache(AbstractCache):
old_ones = db.Container()
for ent in cont:
- old_ones.append(db.execute_query("FIND {}".format(ent.id),
+ old_ones.append(db.execute_query("FIND ENTITY {}".format(ent.id),
unique=True))
return old_ones
diff --git a/src/caosadvancedtools/export_related.py b/src/caosadvancedtools/export_related.py
index 69b588c3..7ae3a4db 100755
--- a/src/caosadvancedtools/export_related.py
+++ b/src/caosadvancedtools/export_related.py
@@ -99,7 +99,7 @@ def invert_ids(entities):
def export_related_to(rec_id, directory="."):
if not isinstance(rec_id, int):
raise ValueError("rec_id needs to be an integer")
- ent = db.execute_query("FIND {}".format(rec_id), unique=True)
+ ent = db.execute_query("FIND ENTITY {}".format(rec_id), unique=True)
cont = recursively_collect_related(ent)
export(cont, directory=directory)
diff --git a/src/caosadvancedtools/models/parser.py b/src/caosadvancedtools/models/parser.py
index c9b890de..658fe5e9 100644
--- a/src/caosadvancedtools/models/parser.py
+++ b/src/caosadvancedtools/models/parser.py
@@ -260,7 +260,7 @@ class Parser(object):
for role in ("Property", "RecordType", "Record", "File"):
if db.execute_query("COUNT {} {}".format(role, name)) > 0:
self.model[name] = db.execute_query(
- "FIND {} WITH name={}".format(role, name), unique=True)
+ "FIND ENTITY {} WITH name={}".format(role, name), unique=True)
break
else:
raise Exception("Did not find {}".format(name))
--
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