update tests

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,

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
 

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

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"
 ...

integrationtests/full_test/extroot/Publications/Theses/2019_paper_on_exciting_stuff/README.md

 ---
 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

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
 ...

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

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")