diff --git a/CHANGELOG.md b/CHANGELOG.md
index 6e381333581953a15a4fe533ced131121dc0569d..ebd856357bfb25d4e03ee3550458e590f4a38610 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -17,6 +17,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
### Removed ###
### Fixed ###
+- refactored to work with the new default key word in FIND queries: RECORD
### Security ###
diff --git a/integrationtests/test.sh b/integrationtests/test.sh
index 36730cc948d308659f01f6153f86a917ab1909d0..9f8d003c9219f7e243fd50c5d846b9a7450b9c7b 100755
--- a/integrationtests/test.sh
+++ b/integrationtests/test.sh
@@ -43,21 +43,23 @@ mv DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx \
DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx_back
cd ..
echo "run crawler"
-./crawl.py / | tee $OUT
+./crawl.py / | tee "$OUT"
# rename the moved file
mv extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx_back \
extroot/DataAnalysis/2010_TestProject/2019-02-03_something/README.xlsx
# check whether there was something UNAUTHORIZED
-grep "There where unauthorized changes" $OUT
+grep "There where unauthorized changes" "$OUT"
# get the id of the run which is the last field of the output string
-RUN_ID=$(grep "run id:" $OUT | awk '{ print $NF }')
+RUN_ID=$(grep "run id:" "$OUT" | awk '{ print $NF }')
echo $RUN_ID
echo "run crawler again"
echo "./crawl.py -a $RUN_ID /"
-./crawl.py -a $RUN_ID / | tee $OUT
+./crawl.py -a $RUN_ID / | tee "$OUT"
set +e
-if grep "There where unauthorized changes" $OUT
+if grep "There where unauthorized changes" "$OUT"
then
+ echo "There still were unauthorized changes, which should not have happend!"
+ echo "Test FAILED"
exit 1
fi
set -e
diff --git a/integrationtests/test_assure_functions.py b/integrationtests/test_assure_functions.py
index b1c731dbbf25f33b54fc3a005402f292525d2d05..e04d481f230936ae96b02fe910401f50e7138a01 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 9d79e857fe706d78103ade3b92ee38498a2a1607..5af9caa3e83184f77c37c24073d85ee5aae2184b 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 4b0a6cedc390b1268e8d2d89393e19a27a83b3be..da1824e8c3cdf3f68bb82f8c7f39e6eecb111f92 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 0c6a145afdab682f82af09a17fb9aa0770769959..8623d57d60ded38987953ffaf78b1d30e15a8011 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 7da90844f14cf0d1eaded9d4fc8f37320da46aad..60c09d73e954c39d752b5fa4ae5e272d28000ca1 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 19b1f8ff10e365031d6940c7b904e3656eda2861..1fa5eaa5a4f050d7282b863aae626982ff738c43 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 2949fa81727a6c61a8646a48c249204fa87542d8..5bf168cd25873975d73cbbaa0249f2fd4c21299b 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_datamodel_problems.py b/integrationtests/test_datamodel_problems.py
index 3bca302dd2a337cee7fd023ee6a64c5185bc99f5..855170338fbc81493e407fbe235415d60958c0f0 100644
--- a/integrationtests/test_datamodel_problems.py
+++ b/integrationtests/test_datamodel_problems.py
@@ -39,7 +39,7 @@ def setup_module():
"""Clear problem sets and delete possible test entities"""
DataModelProblems.missing.clear()
try:
- db.execute_query("FIND Test*").delete()
+ db.execute_query("FIND Entity Test*").delete()
except Exception as delete_exc:
print(delete_exc)
diff --git a/integrationtests/test_im_und_export.py b/integrationtests/test_im_und_export.py
index 8ea45fd2cebbcb2c3be6c8cb79805204486f7862..407faa1a1d3eb609ffd01b9c78d74f1c6a9b231b 100644
--- a/integrationtests/test_im_und_export.py
+++ b/integrationtests/test_im_und_export.py
@@ -8,13 +8,14 @@ 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.delete()
+ if len(recs) > 0:
+ recs.delete()
assert 0 == len(db.execute_query("FIND File which is stored at "
"**/poster.pdf"))
print("Importing stored elements")
@@ -22,7 +23,7 @@ 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 15b851fb5c81611d0faba93edfc58f46f9d75e79..b8dfe349f3dac3be9bb741f937f2be4f73b6b2af 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 bd18ab375437bec02320dcfd269896c2ba7e2bb0..ddebc049f449026400278a26226d341d64e678c8 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 db189b16e5755094ff0d6816aa0806b197b1e883..2b79f9ae7eedaf6e7d6896450a8e7b14e1dc9b30 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/cfood.py b/src/caosadvancedtools/cfood.py
index 4a9f955a17fc429deb6cdd10c3645700e579b4df..c0da4f0156dc2af48a4ba80b4d0af69c62cd5c3e 100644
--- a/src/caosadvancedtools/cfood.py
+++ b/src/caosadvancedtools/cfood.py
@@ -807,7 +807,7 @@ class RowCFood(AbstractCFood):
def update_identifiables(self):
rec = self.identifiables[0]
- for key, value in self.item.iteritems():
+ for key, value in self.item.items():
if key in self.unique_cols:
continue
assure_property_is(rec, key,
diff --git a/src/caosadvancedtools/crawler.py b/src/caosadvancedtools/crawler.py
index 7b81b81ee9a717c226de7f3f3c0e5f28e3e6e789..5e84bc8a60c1b358150c4db389efb62656af0631 100644
--- a/src/caosadvancedtools/crawler.py
+++ b/src/caosadvancedtools/crawler.py
@@ -212,15 +212,14 @@ class Crawler(object):
new_cont.insert(unique=False)
logger.info("Successfully inserted {} records!".format(len(new_cont)))
all_inserts += len(new_cont)
- logger.info("Finished with authorized updates.")
+ logger.info("Finished with authorized inserts.")
changes = cache.get_updates(run_id)
for _, _, old, new, _ in changes:
- new_cont = db.Container()
- new_cont = new_cont.from_xml(new)
+ new_cont = db.Container.from_xml(new)
ids = []
- tmp = []
+ tmp = db.Container()
update_incomplete = False
# remove duplicate entities
for el in new_cont:
@@ -230,14 +229,14 @@ class Crawler(object):
else:
update_incomplete = True
new_cont = tmp
- if new[0].version:
+ if new_cont[0].version:
valids = db.Container()
nonvalids = db.Container()
for ent in new_cont:
remote_ent = db.Entity(id=ent.id).retrieve()
if ent.version == remote_ent.version:
- valids.append(remote_ent)
+ valids.append(ent)
else:
update_incomplete = True
nonvalids.append(remote_ent)
diff --git a/src/caosadvancedtools/export_related.py b/src/caosadvancedtools/export_related.py
index 69b588c34cc7c8123ab4291f6d8f76f06e7400be..7ae3a4dbba65faed551f75a1627eb504a3275f48 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 c9b890de570d29e4a013b14ebe4579e956277ed2..bb06823a7398dd4846712077afa0b35d0713185d 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)
+ f"FIND {role} WITH name={name}", unique=True)
break
else:
raise Exception("Did not find {}".format(name))
diff --git a/src/caosadvancedtools/scifolder/utils.py b/src/caosadvancedtools/scifolder/utils.py
index afa671af85506a57a06ad5198bec4495823c76f1..50e897c7d2f19c6269ec622489c5a2c6ce1a28e0 100644
--- a/src/caosadvancedtools/scifolder/utils.py
+++ b/src/caosadvancedtools/scifolder/utils.py
@@ -154,7 +154,7 @@ def create_files_list(df, ftype):
files = []
for indx, src in df.loc[ftype,
- pd.notnull(df.loc[ftype])].iteritems():
+ pd.notnull(df.loc[ftype])].items():
desc = df.loc[ftype+" description", indx]
if pd.notnull(desc):
diff --git a/src/caosadvancedtools/table_converter.py b/src/caosadvancedtools/table_converter.py
index 76f4dfcdb5f040d81d923289a7a730806ad8681b..4b8591ed009ee8e63b328ad43e0d458b3e805ce7 100644
--- a/src/caosadvancedtools/table_converter.py
+++ b/src/caosadvancedtools/table_converter.py
@@ -79,7 +79,7 @@ def from_table(spreadsheet, recordtype):
rec = db.Record()
rec.add_parent(name=recordtype)
- for key, value in row.iteritems():
+ for key, value in row.items():
if key.lower() == "description":
rec.description = value
continue
diff --git a/src/caosadvancedtools/table_importer.py b/src/caosadvancedtools/table_importer.py
index e5f6579fe2826c589f648d1d2812c04d620576f2..1931c0477fc89584aff8f24fb873d0bf9e98553d 100755
--- a/src/caosadvancedtools/table_importer.py
+++ b/src/caosadvancedtools/table_importer.py
@@ -339,7 +339,7 @@ class TableImporter():
df[key] = df[key].astype(datatype)
# Now check each element
- for idx, val in df.loc[pd.notnull(df.loc[:, key]), key].iteritems():
+ for idx, val in df.loc[pd.notnull(df.loc[:, key]), key].items():
if not isinstance(val, datatype):
msg = (