Merge pull request #56 from lgoldbach/debug

base_name -> basename for restframework compatibility

.gitignore

@@ -1,3 +1,6 @@
+# Django (temporary)
+manage.py   # locally need to change manage.py but shouldnt change on git atm, unless explicitly requested
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -67,3 +70,6 @@ docs/_build/
 /staticfiles/
 /media/
 /logs/
+
+# PyCharm
+.idea

report/views.py

@@ -174,7 +174,7 @@ def get_sequencers_list(self):
 
     def get_pi_sequencer_counts(self):
         sequencer_mapping = {}
-        for flowcell in self.flowcells:
+        for flowcell in self.flowcells:    # gets records from flowcell
             sequencer_name = flowcell.sequencer.name
             pools = {x.pool for x in flowcell.fetched_lanes}
             for pool in pools:
@@ -186,19 +186,22 @@ def get_pi_sequencer_counts(self):
         items = sequencer_mapping.keys()
 
         pi_mapping = {}
-        for req in self.requests:
+        for req in self.requests:    # gets records from requests
             pi = req.user.pi
             pi_name = pi.name if pi else 'None'
             records = req.fetched_libraries + req.fetched_samples
+
             pi_mapping.update({
                 record: pi_name for record in records if record in items
             })
 
-        pairs = [
-            (pi_mapping[k], sequencer_name)
-            for k, v in sequencer_mapping.items() for sequencer_name in v
-        ]
-
+        pairs = []
+        for k, v in sequencer_mapping.items():
+            for sequencer_name in v:
+                try:
+                    pairs.append((pi_mapping[k], sequencer_name))
+                except KeyError:    # KeyError if record exists under flowcell but the correspond. request was deleted.
+                    pass    # could add a warning pop-up here
         counts = Counter(pairs)
 
         data = {}

requirements/base.txt

@@ -19,7 +19,7 @@ sphinx-rtd-theme
 xlwt
 fpdf
 numpy
-pandas
+pandas==0.24
 jupyter
 bioblend
 python-docx

wui/api.py

@@ -38,44 +38,44 @@
 
 router = routers.DefaultRouter()
 
-router.register(r'requests', RequestViewSet, base_name='request')
-router.register(r'cost_units', CostUnitsViewSet, base_name='cost-units')
-router.register(r'organisms', OrganismViewSet, base_name='organism')
-router.register(r'read_lengths', ReadLengthViewSet, base_name='read-length')
-router.register(r'concentration_methods', ConcentrationMethodViewSet, base_name='concentration-method')
-router.register(r'index_types', IndexTypeViewSet, base_name='index-type')
-router.register(r'generator_index_types', GeneratorIndexTypeViewSet, base_name='generator-index-type')
-router.register(r'indices', IndexViewSet, base_name='index')
-router.register(r'library_protocols', LibraryProtocolViewSet, base_name='library-protocol')
-router.register(r'library_protocols_invoicing', LibraryProtocolInvoicingViewSet, base_name='library-protocol-invoicing')
-router.register(r'read_lengths_invoicing',ReadLengthInvoicingViewSet, base_name='read-lengths-invoicing')
-router.register(r'library_types', LibraryTypeViewSet, base_name='library-type')
-router.register(r'nucleic_acid_types', NucleicAcidTypeViewSet, base_name='nucleic-acid-type')
-router.register(r'pool_sizes', PoolSizeViewSet, base_name='pool-size')
+router.register(r'requests', RequestViewSet, basename='request')
+router.register(r'cost_units', CostUnitsViewSet, basename='cost-units')
+router.register(r'organisms', OrganismViewSet, basename='organism')
+router.register(r'read_lengths', ReadLengthViewSet, basename='read-length')
+router.register(r'concentration_methods', ConcentrationMethodViewSet, basename='concentration-method')
+router.register(r'index_types', IndexTypeViewSet, basename='index-type')
+router.register(r'generator_index_types', GeneratorIndexTypeViewSet, basename='generator-index-type')
+router.register(r'indices', IndexViewSet, basename='index')
+router.register(r'library_protocols', LibraryProtocolViewSet, basename='library-protocol')
+router.register(r'library_protocols_invoicing', LibraryProtocolInvoicingViewSet, basename='library-protocol-invoicing')
+router.register(r'read_lengths_invoicing',ReadLengthInvoicingViewSet, basename='read-lengths-invoicing')
+router.register(r'library_types', LibraryTypeViewSet, basename='library-type')
+router.register(r'nucleic_acid_types', NucleicAcidTypeViewSet, basename='nucleic-acid-type')
+router.register(r'pool_sizes', PoolSizeViewSet, basename='pool-size')
 
-router.register(r'libraries_and_samples', LibrarySampleTree, base_name='libraries-and-samples')
-router.register(r'libraries', LibraryViewSet, base_name='libraries')
-router.register(r'samples', SampleViewSet, base_name='samples')
+router.register(r'libraries_and_samples', LibrarySampleTree, basename='libraries-and-samples')
+router.register(r'libraries', LibraryViewSet, basename='libraries')
+router.register(r'samples', SampleViewSet, basename='samples')
 
-router.register(r'incoming_libraries', IncomingLibrariesViewSet, base_name='incoming-libraries')
+router.register(r'incoming_libraries', IncomingLibrariesViewSet, basename='incoming-libraries')
 
-router.register(r'index_generator', IndexGeneratorViewSet, base_name='index-generator')
+router.register(r'index_generator', IndexGeneratorViewSet, basename='index-generator')
 
-router.register(r'library_preparation', LibraryPreparationViewSet, base_name='library-preparation')
+router.register(r'library_preparation', LibraryPreparationViewSet, basename='library-preparation')
 
-router.register(r'pooling', PoolingViewSet, base_name='pooling')
+router.register(r'pooling', PoolingViewSet, basename='pooling')
 
-router.register(r'sequencers', SequencerViewSet, base_name='sequencers')
-router.register(r'flowcells', FlowcellViewSet, base_name='flowcells')
-router.register(r'pools', PoolViewSet, base_name='pools')
+router.register(r'sequencers', SequencerViewSet, basename='sequencers')
+router.register(r'flowcells', FlowcellViewSet, basename='flowcells')
+router.register(r'pools', PoolViewSet, basename='pools')
 
-router.register(r'invoicing', InvoicingViewSet, base_name='invoicing')
-router.register(r'fixed_costs', FixedCostsViewSet, base_name='fixed-costs')
-router.register(r'library_preparation_costs', LibraryPreparationCostsViewSet, base_name='library-preparation-costs')
-router.register(r'sequencing_costs', SequencingCostsViewSet, base_name='sequencing-costs')
+router.register(r'invoicing', InvoicingViewSet, basename='invoicing')
+router.register(r'fixed_costs', FixedCostsViewSet, basename='fixed-costs')
+router.register(r'library_preparation_costs', LibraryPreparationCostsViewSet, basename='library-preparation-costs')
+router.register(r'sequencing_costs', SequencingCostsViewSet, basename='sequencing-costs')
 
-router.register(r'run_statistics', RunStatisticsViewSet, base_name='run-statistics')
-router.register(r'sequences_statistics', SequencesStatisticsViewSet, base_name='sequences-statistics')
-router.register(r'analysis_list', FlowcellAnalysisViewSet, base_name='analysis_list')
+router.register(r'run_statistics', RunStatisticsViewSet, basename='run-statistics')
+router.register(r'sequences_statistics', SequencesStatisticsViewSet, basename='sequences-statistics')
+router.register(r'analysis_list', FlowcellAnalysisViewSet, basename='analysis_list')
 
-router.register(r'metadata_exporter', MetadataExporterViewSet, base_name='metadata_exporter')
+router.register(r'metadata_exporter', MetadataExporterViewSet, basename='metadata_exporter')

wui/settings/base.py

@@ -126,7 +126,7 @@
 
 
 ADMINS = [
-    ('Bioinfo Core', 'bioinfo-core@ie-freiburg.mpg.de'),
+    ('goldbach', 'leander.goldbach@gmail.com'),
 ]