Merge bddf0b5 into 4b3a598

4dn-dcic · Nov 29, 2016 · 34eb899 · 34eb899
2 parents 4b3a598 + bddf0b5
commit 34eb899
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Showing 13 changed files with 317 additions and 251 deletions.
diff --git a/.gitignore b/.gitignore
@@ -15,3 +15,7 @@ dist/
 Submit4DN.egg-info/*
 coverage.xml
 
+
+fields_ordered.xls
+
+fields.xls
diff --git a/README.md b/README.md
@@ -86,13 +86,13 @@ get_field_info --type Biosample --comments --outfile biosample.xls
 
 Complete list of sheets:
 ~~~~
-get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type Image --comments --outfile AllItems.xls
+get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentSetReplicate --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type Image --comments --outfile AllItems.xls
 
 ~~~~
 
 Complete list of sheets: (using python scripts)
 ~~~~
-python3 -m wranglertools.get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type Image --comments --outfile AllItems.xls
+python3 -m wranglertools.get_field_info --type Publication --type Document --type Vendor --type Protocol --type BiosampleCellCulture --type Biosource --type Enzyme --type Construct --type TreatmentChemical --type TreatmentRnai --type Modification --type Biosample --type FileFastq --type FileSet --type IndividualHuman --type IndividualMouse --type ExperimentHiC --type ExperimentCaptureC --type Target --type GenomicRegion --type ExperimentSet --type ExperimentSetReplicate --type Image --comments --outfile AllItems.xls
 
 ~~~~
 

diff --git a/README.rst b/README.rst
diff --git a/setup.cfg b/setup.cfg
@@ -2,20 +2,20 @@
 max-line-length = 120
 [coverage:run]
 branch = True
-omit = 
+omit =
     */__pycache__/*
     */Data_Files/*
     */System_Files/*
     */tests/*
-include = 
-	*/wranglertools/*	
+include =
+	*/wranglertools/*
 [aliases]
 test=pytest
 
 [tool:pytest]
-addopts = 
+addopts =
         --cov
         --cov-report term
         --cov-report xml
 	--cov-report html
-	--cov-fail-under 89 
+	--cov-fail-under 85 
diff --git a/tests/data_files/Exp_HiC_insert.xls b/tests/data_files/Exp_HiC_insert.xls
diff --git a/tests/data_files/Exp_Set_Replicate_insert.xls b/tests/data_files/Exp_Set_Replicate_insert.xls
diff --git a/tests/data_files/Exp_Set_insert.xls b/tests/data_files/Exp_Set_insert.xls
diff --git a/tests/test_fdnDCIC.py b/tests/test_fdnDCIC.py
@@ -191,15 +191,14 @@ def test_switch_fields():
             [['cell_line_tier', 'cell_line', 'SOP_cell_line'], 'Biosource'],
             [['start_coordinate', 'start_location', 'location_description',
               'end_location', 'end_coordinate'], "GenomicRegion"],
-            [['experiment_relation.relationship_type', 'experiment_sets|3', 'files', 'average_fragment_size',
-              'experiment_sets|1', 'fragment_size_range', 'documents', 'experiment_relation.experiment',
-              'experiment_sets|2', 'filesets', 'experiment_sets|0'], "Experiment"]
+            [['experiment_relation.relationship_type', 'files', 'average_fragment_size',
+              'fragment_size_range', 'documents', 'experiment_relation.experiment',
+              'filesets'], "Experiment"]
             ]
     result_list = [['cell_line', 'cell_line_tier', 'SOP_cell_line'],
                    ['location_description', 'start_location', 'end_location', 'start_coordinate', 'end_coordinate'],
                    ['average_fragment_size', 'fragment_size_range', 'files', 'filesets',
-                    'experiment_relation.relationship_type', 'experiment_relation.experiment', 'experiment_sets|0',
-                    'experiment_sets|1', 'experiment_sets|2', 'experiment_sets|3', 'documents']]
+                    'experiment_relation.relationship_type', 'experiment_relation.experiment', 'documents']]
     for n, (a, b) in enumerate(cases):
         assert result_list[n] == fdnDCIC.switch_fields(a, b)
 
@@ -210,6 +209,7 @@ def test_fetch_all_items_mock(connection, mocker, returned_vendor_items):
         all_vendor_items = fdnDCIC.fetch_all_items('Vendor', fields, connection)
         for vendor in all_vendor_items:
             assert len(vendor) == len(fields)
+            print(vendor)
             assert vendor[0].startswith("#")
 
 

diff --git a/tests/test_get_field_info.py b/tests/test_get_field_info.py
@@ -38,9 +38,8 @@ def test_dotted_field_name_no_parent():
 def test_build_field_list(item_properties):
     field_list = gfi.build_field_list(item_properties, required_fields=["title", "pi"])
     assert field_list
-    assert len(field_list) == 16
+    assert len(field_list) == 13
     names = [i.name for i in field_list]
-    assert 'experiment_sets|0' in names
     assert '*title' in names