Merge branch 'integrationtest' into 'master'

Integrationtest

See merge request bmp-caosdb/caosdb-advanced-user-tools!4

integrationtests/model.yml

+Experiment:
+  obligatory_properties:
+    date:
+      datatype: DATETIME 
+      description: 'date of the experiment'
+    identifier:
+      datatype: TEXT 
+      description: 'identifier of the experiment'
+  # TODO empty  recommended_properties is a problem
+  #recommended_properties:
+    responsible:
+Project:
+Person:
+  obligatory_properties:
+    firstName:
+      datatype: TEXT 
+      description: 'First name of a Person.'
+    lastName:
+      datatype: TEXT 
+      description: 'LastName of a Person.'
+    responsible:
+responsible:
+  datatype: REFERENCE
+results:
+  datatype: REFERENCE
+data:
+  datatype: REFERENCE
+scripts:
+  datatype: REFERENCE
+Source:
+Simulation:
+  obligatory_properties:
+    date:
+    identifier:
+    responsible:
+Analysis:
+  obligatory_properties:
+    date:
+    identifier:
+    responsible:
+Publication:
+Thesis:
+  inherit_from_suggested:
+  - Publication
+Article:
+  inherit_from_suggested:
+  - Publication
+Poster:
+  inherit_from_suggested:
+  - Publication
+Presentation:
+  inherit_from_suggested:
+  - Publication
+Report:
+  inherit_from_suggested:
+  - Publication

integrationtests/test.sh

+./filldb.sh
+py.test-3 test_crawler.py

integrationtests/test_crawler.py

+#!/usr/bin/env python3
+import os
+import unittest
+
+import caosdb as db
+
+
+def get_entity_with_id(eid):
+    return db.execute_query("FIND "+str(eid), unique=True)
+
+
+class CrawlerTest(unittest.TestCase):
+    def test_experiment(self):
+        ########################
+        # # first experiment # #
+        ########################
+        # TODO saving an empty string as value in a text property leads to a
+        # 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='x'",
+            unique=True)
+
+        # There should be a Project with name TestProject which is referenced
+        project_id = exp.get_property("Project").value
+        project = get_entity_with_id(project_id)
+        assert project.name == "TestProject"
+        assert "Project" in [p.name for p in project.get_parents()]
+
+        # 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)
+        assert os.path.basename(datfile.path) == "datafile.dat"
+
+        #########################
+        # # second experiment # #
+        #########################
+        exp = db.execute_query(
+            "FIND Experiment with date=2019-02-03 and identifier='something'",
+            unique=True)
+
+        # Should be the same project
+        assert project_id == exp.get_property("Project").value
+
+        # Should have two data files
+        datfile_ids = exp.get_property("results").value
+        datafile_names = []
+
+        for did in datfile_ids:
+            datfile = get_entity_with_id(did)
+            datafile_names.append(os.path.basename(datfile.path))
+        assert "usefull.xlsx" in datafile_names
+        assert "useless.xlsx" in datafile_names
+
+    def test_analysis(self):
+        ######################
+        # # first analysis # #
+        ######################
+        ana = db.execute_query(
+            "FIND Analysis with date=2019-02-03 and identifier='x'",
+            unique=True)
+
+        # There should be a Project with name TestProject which is referenced
+        project_id = ana.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 = ana.get_property("results").value[0]
+        datfile = get_entity_with_id(datfile_id)
+        assert os.path.basename(datfile.path) == "results.pdf"
+
+        # 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) == "plot.py"
+
+        #######################
+        # # second analysis # #
+        #######################
+        ana = db.execute_query(
+            "FIND Analysis with date=2019-02-03 and identifier='something'",
+            unique=True)
+
+        # 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 = []
+
+        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
+
+        # 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"
+
+    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
+
+        ##########################
+        # # second publication # #
+        ##########################
+        pub = db.execute_query("FIND paper_on_exciting_stuff ", unique=True)

src/caosadvancedtools/cfood.py

@@ -31,9 +31,10 @@ from copy import deepcopy
 from datetime import datetime
 
 import caosdb as db
-from caosadvancedtools.cache import Cache
 from caosdb.exceptions import TransactionError
 
+from caosadvancedtools.cache import Cache
+
 ENTITIES = {}
 
 
@@ -108,7 +109,8 @@ class AbstractCFood(object):
 
             if identifiable is None:
                 print("THIS IS STRANGE. No identifiables found in {}.".format(
-                    crawled_file})
+                    crawled_file))
+
                 continue
             existing = None
 
@@ -209,7 +211,7 @@ class AbstractCFood(object):
         # is using the unique keyword
         try:
             r = q.execute(unique=True)
-        except TransactionError as er:
+        except TransactionError:
             r = None
 
         if r is not None:

src/caosadvancedtools/crawler.py

@@ -57,5 +57,3 @@ class Crawler(object):
         print("{} FILES TO BE PROCESSED.".format(len(files)))
 
         return files
-
-

src/caosadvancedtools/read_md_header.py

@@ -57,6 +57,7 @@ def _clean_header(header):
 class NoValidHeader(Exception):
     pass
 
+
 def get_header(filename):
     """Open an md file identified by filename and read out the yaml
 header.

src/programs/crawl.py

@@ -29,6 +29,7 @@ import argparse
 import caosdb as db
 from argparse import RawTextHelpFormatter
 
+
 def get_parser():
     parser = argparse.ArgumentParser(description=__doc__,
                                      formatter_class=RawTextHelpFormatter)

src/programs/example_cfood.py

@@ -27,6 +27,7 @@ import caosdb as db
 
 from caosadvancedtools.cfood import AbstractCFood
 
+
 class ExampleCFood(AbstractCFood):
     def create_identifiables(self, crawled_file, match):
         print("create_identifiables")

unittests/create_filetree.py

@@ -62,11 +62,6 @@ def main(folder, dry=True):
                         os.system("touch "+d_path)
 
 
-
-
-
-
-
 def get_parser():
     parser = argparse.ArgumentParser(description=__doc__,
                                      formatter_class=RawTextHelpFormatter)

unittests/test_cfood.py

@@ -39,6 +39,7 @@ class CFoodTest(unittest.TestCase):
     def test_check_existence(self):
         assert AbstractCFood.find_existing(self.exp) is None
 
+
 class CFoodTestExist(CFoodTest):
     def setUp(self):
         super().setUp()

unittests/test_table_converter.py

@@ -82,6 +82,7 @@ class ToTsvTest(unittest.TestCase):
 class IntegrationTest(unittest.TestCase):
     """ converts  tsv to a container and back and compares origin with
     result """
+
     def test_backandforth(self):
         cont = from_tsv(TEST_TABLE, "Measurement")
         tempfile = NamedTemporaryFile(delete=False)