diff --git a/integrationtests/full_test/crawl.py b/integrationtests/full_test/crawl.py
index fd162731f784850425d15cbc9755bf0c7f9418f9..62ca8eac18475f7778ccc34372cba7dbfbc3587b 100755
--- a/integrationtests/full_test/crawl.py
+++ b/integrationtests/full_test/crawl.py
@@ -56,7 +56,7 @@ if __name__ == "__main__":
print("Query done...")
config = db.configuration.get_config()
c = Crawler(use_cache=True, access=access,
- verbosity=INFO,
+ verbosity=DEBUG,
food=[ProjectCFood,
AnalysisCFood, ExperimentCFood,
PublicationCFood, SimulationCFood,
diff --git a/integrationtests/full_test/extroot/DataAnalysis/TestProject/2019-02-03/README.md b/integrationtests/full_test/extroot/DataAnalysis/TestProject/2019-02-03/README.md
index e557f2035e34f7f96975454223b15ebe0dd6f79c..1c3d6935026481fb6a62fce17941d1a02be64314 100644
--- a/integrationtests/full_test/extroot/DataAnalysis/TestProject/2019-02-03/README.md
+++ b/integrationtests/full_test/extroot/DataAnalysis/TestProject/2019-02-03/README.md
@@ -3,7 +3,7 @@ responsible:
- Only Responsible
description: A description of another example analysis.
-data:
+source:
- filename: "/ExperimentalData/TestProject/2019-02-03/*.dat"
description: an example reference to a results file
diff --git a/integrationtests/full_test/extroot/DataAnalysis/TestProject/2019-02-03_something/README.md b/integrationtests/full_test/extroot/DataAnalysis/TestProject/2019-02-03_something/README.md
index c342053aaa94a474f59a714209b3066c084c706e..c62e216b51144cb741e0363c4ce82c5d3e7f7bc7 100644
--- a/integrationtests/full_test/extroot/DataAnalysis/TestProject/2019-02-03_something/README.md
+++ b/integrationtests/full_test/extroot/DataAnalysis/TestProject/2019-02-03_something/README.md
@@ -7,9 +7,12 @@ results:
- filename: "images/*.png"
description: an example reference to a results file
-data:
-- filename: /ExperimentalData/TestProject/2019-02-03_something/use*.xlsx
- description: an example reference to data files
+source:
+- filename: /ExperimentalData/TestProject/2019-02-03_something/
+ description: an example reference to an experiment
+
+revisionOf:
+- ../2019-02-03
scripts:
- analyse.py
diff --git a/integrationtests/full_test/extroot/Publications/Posters/2019-02-03_really_cool_finding/README.md b/integrationtests/full_test/extroot/Publications/Posters/2019-02-03_really_cool_finding/README.md
index 348a6fec3c00ad19a28a9e6b86e668aa36cd73eb..68bebf70be96d400a5e9bc31eb78adbb7168bb23 100644
--- a/integrationtests/full_test/extroot/Publications/Posters/2019-02-03_really_cool_finding/README.md
+++ b/integrationtests/full_test/extroot/Publications/Posters/2019-02-03_really_cool_finding/README.md
@@ -3,7 +3,9 @@ responsible:
- Only Responsible
description: A description of another example experiment.
+source:
+- /home/professional/CaosDB/caosdb-deploy/profiles/empty/custom/extroot/DataAnalysis/TestProject/2019-02-03/results.pdf
+
results:
-- filename: "/ExperimentalData/TestProject/2019-02-03/*.dat"
- description: an example reference to a results file
+- "*.pdf"
...
diff --git a/integrationtests/full_test/extroot/Publications/Posters/2019-02-03_really_cool_finding/datafile.dat b/integrationtests/full_test/extroot/Publications/Posters/2019-02-03_really_cool_finding/datafile.dat
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/integrationtests/full_test/extroot/Publications/Theses/2019_paper_on_exciting_stuff/README.md b/integrationtests/full_test/extroot/Publications/Theses/2019_paper_on_exciting_stuff/README.md
index 9e63c07cf8a943637c62d63f61faba489aa8c4f0..5bd4e2733c450251ab7a014dd88b08ef788da5c2 100644
--- a/integrationtests/full_test/extroot/Publications/Theses/2019_paper_on_exciting_stuff/README.md
+++ b/integrationtests/full_test/extroot/Publications/Theses/2019_paper_on_exciting_stuff/README.md
@@ -1,12 +1,9 @@
---
responsible:
- First Person
-- Second Person
description: A description of an example experiment.
-results:
-- filename: "*.xlsx"
- description: an example reference to a results file
+
tags:
- collagen
diff --git a/integrationtests/full_test/extroot/Publications/Theses/2019_paper_on_exciting_stuff/usefull.xlsx b/integrationtests/full_test/extroot/Publications/Theses/2019_paper_on_exciting_stuff/usefull.xlsx
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/integrationtests/full_test/extroot/Publications/Theses/2019_paper_on_exciting_stuff/useless.xlsx b/integrationtests/full_test/extroot/Publications/Theses/2019_paper_on_exciting_stuff/useless.xlsx
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/integrationtests/full_test/extroot/SimulationData/TestProject/2019-02-03/README.md b/integrationtests/full_test/extroot/SimulationData/TestProject/2019-02-03/README.md
index 348a6fec3c00ad19a28a9e6b86e668aa36cd73eb..048b64e81ea5c641aa03af827e07fbd04bbd0e60 100644
--- a/integrationtests/full_test/extroot/SimulationData/TestProject/2019-02-03/README.md
+++ b/integrationtests/full_test/extroot/SimulationData/TestProject/2019-02-03/README.md
@@ -4,6 +4,9 @@ responsible:
description: A description of another example experiment.
results:
-- filename: "/ExperimentalData/TestProject/2019-02-03/*.dat"
+- filename: "*.dat"
description: an example reference to a results file
+
+scripts:
+- sim.py
...
diff --git a/integrationtests/full_test/extroot/SimulationData/TestProject/2019-02-03_something/README.md b/integrationtests/full_test/extroot/SimulationData/TestProject/2019-02-03_something/README.md
index 9e63c07cf8a943637c62d63f61faba489aa8c4f0..3c984cb2246af2b31013295dfaa48cc3e0094d23 100644
--- a/integrationtests/full_test/extroot/SimulationData/TestProject/2019-02-03_something/README.md
+++ b/integrationtests/full_test/extroot/SimulationData/TestProject/2019-02-03_something/README.md
@@ -5,8 +5,18 @@ responsible:
description: A description of an example experiment.
results:
-- filename: "*.xlsx"
- description: an example reference to a results file
+- filename: "*.npy"
+ description: time series
+
+scripts:
+- "parameters.p"
+- "large_sim.py"
+
+revisonOf:
+- ../2019-02-03
+
+source:
+- /extroot/ExperimentalData/TestProject/2019-02-03
tags:
- collagen
diff --git a/integrationtests/full_test/test_crawler.py b/integrationtests/full_test/test_crawler.py
index d610d6217a98ae9dd3953ba82c476c8c7a5984ba..70821deb9e0ae8fbfe286f7e94e73ec00bc5da3d 100755
--- a/integrationtests/full_test/test_crawler.py
+++ b/integrationtests/full_test/test_crawler.py
@@ -30,8 +30,19 @@ class CrawlerTest(unittest.TestCase):
# There should be a datafile as result attached with path datafile.dat
datfile_id = exp.get_property("results").value[0]
datfile = get_entity_with_id(datfile_id)
+ self.assertEqual("A description of another example experiment.",
+ datfile.description)
assert os.path.basename(datfile.path) == "datafile.dat"
+ # Should have a responsible person
+ self.assertIsNotNone(exp.get_property("Responsible"))
+ person = db.Record(id=exp.get_property("Responsible").value)
+ person.retrieve()
+ self.assertEqual("Only", person.get_property("FirstName").value)
+
+ # Should have a description
+ self.assertIsNotNone(exp.description)
+
#########################
# # second experiment # #
#########################
@@ -75,6 +86,28 @@ class CrawlerTest(unittest.TestCase):
datfile = get_entity_with_id(datfile_id)
assert os.path.basename(datfile.path) == "plot.py"
+ # There should be a file as script attached with path plot.py
+ datfile_id = ana.get_property("source").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "datafile.dat"
+ self.assertEqual(datfile.description,
+ "an example reference to a results file")
+
+ # Should have a responsible person
+ self.assertIsNotNone(ana.get_property("Responsible"))
+ person = db.Record(id=ana.get_property("Responsible").value)
+ person.retrieve()
+ self.assertEqual("Only", person.get_property("FirstName").value)
+
+ # Should have a description
+ self.assertIsNotNone(ana.description)
+
+ # Should reference an experiment
+ self.assertIsNotNone(ana.get_property("Experiment"))
+ person = db.Record(id=ana.get_property("Responsible").value)
+ person.retrieve()
+ self.assertEqual("2019-02-03", person.get_property("date").value)
+
#######################
# # second analysis # #
#######################
@@ -85,30 +118,120 @@ class CrawlerTest(unittest.TestCase):
# Should be the same project
assert project_id == ana.get_property("Project").value
- # Should have two data files
- datfile_ids = ana.get_property("results").value
- datafile_names = []
+ # There should be a file as script attached with path plot.py
+ datfile_id = ana.get_property("scripts").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "analyse.py"
- for did in datfile_ids:
- datfile = get_entity_with_id(did)
- datafile_names.append(os.path.basename(datfile.path))
- assert "lol1.png" in datafile_names
- assert "lol2.png" in datafile_names
+ # Should reference an experiment
+ self.assertIsNotNone(ana.get_property("Experiment"))
+ person = db.Record(id=ana.get_property("Responsible").value)
+ person.retrieve()
+ self.assertEqual("2019-02-03", person.get_property("date").value)
+
+ def test_simulation(self):
+ ######################
+ # # first simulation # #
+ ######################
+ sim = db.execute_query(
+ "FIND Simulation with date=2019-02-03 and identifier='empty_identifier'",
+ unique=True)
+
+ # There should be a Project with name TestProject which is referenced
+ project_id = sim.get_property("Project").value
+ project = get_entity_with_id(project_id)
+ assert "Project" in [p.name for p in project.get_parents()]
+
+ # There should be a file as result attached with path results.pdf
+ datfile_id = sim.get_property("results").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "snapshots.dat"
# There should be a file as script attached with path plot.py
- datfile_id = ana.get_property("scripts").value[0]
+ datfile_id = sim.get_property("scripts").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "sim.py"
+
+ # Should have a responsible person
+ self.assertIsNotNone(sim.get_property("Responsible"))
+ person = db.Record(id=sim.get_property("Responsible").value)
+ person.retrieve()
+ self.assertEqual("Only", person.get_property("FirstName").value)
+
+ # Should have a description
+ self.assertIsNotNone(sim.description)
+
+ #########################
+ # # second simulation # #
+ #########################
+ sim = db.execute_query(
+ "FIND Simulation with date=2019-02-03 and identifier='something'",
+ unique=True)
+
+ # There should be a file as script attached with path plot.py
+ exp = get_entity_with_id(sim.get_property("source").value)
+ self.assertEqual(exp.parents[0].name, "Experiment")
+
+ # Should be the same project
+ assert project_id == sim.get_property("Project").value
+
+ # Should have two responsible persons
+ self.assertIsNotNone(sim.get_property("Responsible"))
+ self.assertEqual(len(sim.get_property("Responsible").value), 2)
+
+ # Should have revision
+ osim = get_entity_with_id(sim.get_property("revisionOf").value[0])
+ self.assertEqual(osim.parents[0].name, "Simulation")
+ self.assertNotEqual(osim.id, sim.id)
+
+ # Should have data file
+ datfile_id = sim.get_property("results").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "timeseries.npy"
+
+ # There should be a file as script attached with path plot.py
+ datfile_id = sim.get_property("scripts").value[0]
datfile = get_entity_with_id(datfile_id)
assert os.path.basename(datfile.path) == "analyse.py"
+ # Should have two scritps files
+ datfile_ids = exp.get_property("scripts").value
+ datafile_names = []
+
+ for did in datfile_ids:
+ datfile = get_entity_with_id(did)
+ datafile_names.append(os.path.basename(datfile.path))
+ assert "parameters.p" in datafile_names
+ assert "large_sim.py" in datafile_names
+
def test_publication(self):
#########################
# # first publication # #
#########################
pub = db.execute_query("FIND *really_cool_finding", unique=True)
- # There should be a Project with name TestProject which is referenced
+ # There should be a file as result attached with path results.pdf
+ datfile_id = pub.get_property("results").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "poster.pdf"
+
+ # There should be a file as data attached with path plot.py
+ datfile_id = pub.get_property("sources").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "results.pdf"
+
+ # Test type
+ self.assertEqual(pub.parents[0].name, "Poster")
##########################
# # second publication # #
##########################
pub = db.execute_query("FIND *paper_on_exciting_stuff ", unique=True)
+
+ # There should be a file as data attached with path plot.py
+ datfile_id = pub.get_property("sources").value[0]
+ datfile = get_entity_with_id(datfile_id)
+ assert os.path.basename(datfile.path) == "results.pdf"
+
+ # Test type
+ self.assertEqual(pub.parents[0].name, "Poster")