updating a few things // switching branches

Author: ecpantalone

ingest/templates/ingest/metadata_questions.html

@@ -46,7 +46,8 @@ <h3>Step 2 of 3: What does your data look like?</h3>
         <input type="radio" id="ingest_method_5" name="ingest_method" value="ingest_5">
       </td>
       <td> 
-      <p>5.	SWC (description TBD)</p>
+      <p>5.	Reconstructed neurons in standardized swc format. All reconstructions were generated from one specimen. There should be one line listed in the specimen tab. There should be one line listed in the dataset tab. No information should be listed in the image tab. File format specification: <a href="http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html">http://www.neuronland.org/NLMorphologyConverter/MorphologyFormats/SWC/Spec.html</a>
+      </p>
       </td>
     </tr>
   </table>

ingest/views.py

@@ -1434,7 +1434,7 @@ def check_swc_sheet(filename):
     workbook=xlrd.open_workbook(filename)
     sheetname = 'SWC'
     swc_sheet = workbook.sheet_by_name(sheetname)
-    colheads=['tracingFile', 'sourceData', 'sourceDataSample', 'sourceDataSubmission', 'coordinates', 'coordinatesRegistration', 'brainRegion', 'brainRegionAtlas', 'brainRegionAtlasName', 'brainRegionAxonalProjection', 'brainRegionDendriticProjection', 'neuronType', 'segmentTags', 'proofreadingLevel', 'notes']
+    colheads=['tracingFile', 'sourceData', 'sourceDataSample', 'sourceDataSubmission', 'coordinates', 'coordinatesRegistration', 'brainRegion', 'brainRegionAtlas', 'brainRegionAtlasName', 'brainRegionAxonalProjection', 'brainRegionDendriticProjection', 'neuronType', 'segmentTags', 'proofreadingLevel', 'Notes']
     cellcols=['A','B','C','D','E', 'F', 'G', 'H', 'I', 'J', 'K', 'L', 'M', 'N', 'O']
     coordinatesRegistration = ['Yes', 'No']
     cols=swc_sheet.row_values(3)
@@ -1643,12 +1643,12 @@ def save_swc_sheet(swcs, sheet, saved_datasets):
 
             swc = SWC(tracingFile=tracingFile, sourceData=sourceData, sourceDataSample=sourceDataSample, sourceDataSubmission=sourceDataSubmission, coordinates=coordinates, coordinatesRegistration=coordinatesRegistration,  brainRegion=brainRegion, brainRegionAtlas=brainRegionAtlas, brainRegionAtlasName=brainRegionAtlasName, brainRegionAxonalProjection=brainRegionAxonalProjection, brainRegionDendriticProjection=brainRegionDendriticProjection, neuronType=neuronType, segmentTags=segmentTags, proofreadingLevel=proofreadingLevel, notes=notes, data_set_id=data_set_id,sheet_id=sheet.id)
             swc_no_uuid = swc.save()
-            print(swc_no_uuid.id)
+            print('swc id: ' + swc_no_uuid.id)
 
 
             swc_uuid = Mne.num_to_mne(swc_no_uuid.id)
 
-            print(swc_uuid)
+            print('swc_uuid: '+ swc_uuid)
 
             this_swc = SWC.objects.get(id=swc_no_uuid.id)
             # this_swc(swc_uuid=swc_uuid)
@@ -2028,7 +2028,7 @@ def save_specimen_sheet_method_4(specimen_set, sheet):
 
 def save_specimen_sheet_method_5(specimen_set, sheet):
     # 1 datasets, 1 instruments, 0 images
-    # single specimen
+    # 1 specimen
     try:
         for s in specimen_set:
             localid = s['LocalID']
@@ -2392,12 +2392,12 @@ def save_all_sheets_method_4(instruments, specimen_set, images, datasets, sheet,
         saved = False
 
 def save_all_sheets_method_5(instruments, specimen_set, datasets, sheet, contributors, funders, publications, swcs):
-	  # if swc tab filled out we don't want images
-		# 1 dataset row should be filled out
-		# many SWC : 1 dataset
+	# if swc tab filled out we don't want images
+	# 1 dataset row should be filled out
+	# many SWC : 1 dataset
     # 1 specimen
     # 1 instrument
-		# 1 datasest
+	# 1 datasest
 
     try:
         specimen_object_method_5 = save_specimen_sheet_method_5(specimen_set, sheet)
@@ -2435,7 +2435,8 @@ def metadata_version_check(filename):
         version1 = True
     return version1
 
-def check_all_sheets(filename):
+def check_all_sheets(filename, ingest_method):
+    ingest_method = ingest_method
     errormsg = check_contributors_sheet(filename)
     if errormsg != '':
         return errormsg
@@ -2454,12 +2455,14 @@ def check_all_sheets(filename):
     errormsg = check_specimen_sheet(filename)
     if errormsg != '':
         return errormsg
-    errormsg = check_image_sheet(filename)
-    if errormsg != '':
-        return errormsg
-    errormsg = check_swc_sheet(filename)
-    if errormsg != '':
-        return errormsg
+    if ingest_method != 'ingest_5':
+        errormsg = check_image_sheet(filename)
+        if errormsg != '':
+            return errormsg
+    if ingest_method == 'ingest_5':
+        errormsg = check_swc_sheet(filename)
+        if errormsg != '':
+            return errormsg
     return errormsg
 
 @login_required
@@ -2493,7 +2496,7 @@ def descriptive_metadata_upload(request):
             # datapath = '/home/shared_bil_dev/testetc/' 
 
             # for development locally
-            datapath = '/Users/luketuite/Desktop/bil_metadata_uploads' 
+            datapath = '/Users/ecp/Desktop/bil_metadata_uploads' 
 
             spreadsheet_file = request.FILES['spreadsheet_file']
 
@@ -2514,7 +2517,7 @@ def descriptive_metadata_upload(request):
 
             # using new metadata model
             elif version1 == False:
-                errormsg = check_all_sheets(filename)
+                errormsg = check_all_sheets(filename, ingest_method)
                 if errormsg != '':
                     messages.error(request, errormsg)
                     return redirect('ingest:descriptive_metadata_upload')