Merge pull request #167 from macarthur-lab/hotfix-phenotips_pdf_view-…

…0.01

Hotfix phenotips pdf view 0.01

xbrowse_server/api/urls.py

@@ -46,4 +46,5 @@
 
     #phenotips related
     url(r'^phenotips/proxy/edit/(?P<eid>[\w|-]+)$', 'xbrowse_server.phenotips.views.fetch_phenotips_edit_page', name='fetch_phenotips_edit_page'),
+    url(r'^phenotips/proxy/view/(?P<eid>[\w|-]+)$', 'xbrowse_server.phenotips.views.fetch_phenotips_pdf_page', name='fetch_phenotips_pdf_page'),
 )

xbrowse_server/base/views/project_views.py

@@ -36,9 +36,17 @@
 from xbrowse_server.mall import get_reference
 from xbrowse_server import mall
 from xbrowse_server.gene_lists.views import download_response as gene_list_download_response
+from xbrowse_server.phenotips.reporting_utilities import get_phenotype_entry_metrics_for_project
+from xbrowse_server.phenotips.reporting_utilities import categorize_phenotype_counts
+from xbrowse_server.phenotips.reporting_utilities import aggregate_phenotype_counts_into_bins
+from xbrowse_server.decorators import log_request
+import logging
+
+logger = logging.getLogger(__name__)
 
 
 @login_required
+@log_request('project_views')
 def project_home(request, project_id):
 
     project = get_object_or_404(Project, project_id=project_id)
@@ -58,7 +66,25 @@ def project_home(request, project_id):
     else:
         raise Exception("Authx - how did we get here?!?")
 
+    phenotips_supported=False
+    if project_id in settings.PHENOTIPS_SUPPORTED_PROJECTS:
+      phenotips_supported=True
+
+    indiv_phenotype_counts=[]
+    binned_counts={}
+    categorized_phenotype_counts={}
+    if phenotips_supported:
+      try:
+        indiv_phenotype_counts= get_phenotype_entry_metrics_for_project(project_id)
+        binned_counts=aggregate_phenotype_counts_into_bins(indiv_phenotype_counts)
+        categorized_phenotype_counts=categorize_phenotype_counts(binned_counts)
+      except Exception as e:
+        print 'error looking for project information in PhenoTips:logging & moving,there might not be any data'
+        logger.error('project_views:'+str(e))
+
     return render(request, 'project.html', {
+        'categorized_phenotype_counts':categorized_phenotype_counts,
+        'phenotips_supported':phenotips_supported,
         'project': project,
         'auth_level': auth_level,
         'can_edit': project.can_edit(request.user),

xbrowse_server/phenotips/reporting_utilities.py

@@ -0,0 +1,193 @@
+from xbrowse_server.base.models import Project
+from xbrowse_server.phenotips.utilities import get_uname_pwd_for_project
+import os
+from django.conf import settings
+import requests
+from requests.auth import HTTPBasicAuth
+
+def get_phenotype_entry_metrics_for_project(project_id):
+  '''
+    Processes the given project
+    Inputs:
+    project: a project ID
+  '''
+  try:
+      project = Project.objects.get(project_id=project_id)
+      individuals=[]
+      for individual in project.get_individuals():
+        individuals.append(individual.indiv_id)
+      return get_phenotype_entry_details_for_individuals(individuals,project_id)
+  except Exception as e:
+    print '\nsorry, we encountered an error finding project:',e,'\n'
+    raise
+
+def aggregate_phenotype_counts_into_bins(phenotype_counts):
+  '''
+    Given a list of individual phenotype counts, aggregates these into
+    bins of counts
+    Input:
+    A list of dicts that have indiv ID and how many phenotypes entered
+    [{}, ....]
+    Ex:
+    [{'eid': u'NA19675', 'num_phenotypes_entered': 1},....]
+    
+    Output:
+    A dict that resembles (the "count" here is derived from "num_phenotypes_entered":
+    {count: [indiv1, indiv2, indiv3 ..indivs with this many phenotypes entered],
+    count2: [indivX,...]}
+  '''
+  aggregated={}
+  for count in phenotype_counts:
+    if aggregated.has_key(count['num_phenotypes_entered']):
+      aggregated[count['num_phenotypes_entered']].append(count['eid'])
+    else:
+      aggregated[count['num_phenotypes_entered']] = [count['eid']]
+  return aggregated
+
+
+
+def get_phenotype_entry_details_for_individuals(individuals,project_id):
+  '''
+    Process this list of individuals
+    
+    Inputs:
+    individuals: a list of individuals
+  '''
+  all_patients=[]
+  try:
+    for individual in individuals:
+      phenotype_count_for_indiv=phenotype_entry_metric_for_individual(individual,project_id)
+      all_patients.append({'eid':individual,'num_phenotypes_entered':phenotype_count_for_indiv})
+    return all_patients
+  except Exception as e:
+    raise
+
+
+
+
+def print_details_to_stdout(proj_dets,summarize):
+  '''
+    Print details to STDOUT
+    
+    Inputs:
+    proj_dets: a project details structure
+    summarize: True/False whether to summarize view
+  '''
+  category_names=self.get_phenotype_count_categorie_names()
+  if summarize:
+      print '{:20s} {:20s} {:20s} {:20s} {:20s} {:20s}'.format('Project',*category_names)
+  try:
+    for proj_id,dets in proj_dets.iteritems():
+      phenotype_counts={}
+      for patient_det in dets:
+        if not summarize:
+          print patient_det['eid'],patient_det['num_phenotypes_entered']
+        if summarize:
+          if phenotype_counts.has_key(patient_det['num_phenotypes_entered']):
+            phenotype_counts[patient_det['num_phenotypes_entered']].append(patient_det['eid'])
+          else:
+            phenotype_counts[patient_det['num_phenotypes_entered']]=[patient_det['eid']]
+      if summarize:
+        data=categorize_phenotype_counts(phenotype_counts)
+        print '{:20s}'.format(proj_id),
+        for category_name in category_names:
+          print '{:20s}'.format(str(len(data[category_name]))),
+        print
+  except Exception as e:
+    raise
+
+
+def categorize_phenotype_counts(phenotype_counts):
+  '''
+    Bin counts in categories for easy reporting in columns
+    
+    Categories are:
+    0
+    0-10
+    10-20
+    >30
+    
+    Notes:
+    If you add any new categories, remember to update method
+    get_phenotype_count_categorie_names.
+    
+    Inputs:
+    A dict of number of patients to number of phenotypes 
+    entered for each patient 
+    
+    Outputs:
+    -A dict with keys of above categories and values being count
+    of each.
+    -A tuple with category names
+  '''
+  category_names=get_phenotype_count_categorie_names()
+  data={}
+  for c in category_names:
+    data[c]=[]
+  for phenotype_count,patients in phenotype_counts.iteritems():
+    if phenotype_count ==0:
+      data['0'].extend(patients)
+    if phenotype_count>0 and phenotype_count<11:
+      data['1to10'].extend(patients) 
+    if phenotype_count>=11 and phenotype_count<=20:
+      data['11to20'].extend(patients)
+    if phenotype_count>=21 and phenotype_count<=30:
+      data['21to30'].extend(patients)
+    if phenotype_count>=31:
+      data['larger_than_31'].extend(patients)
+  return data
+
+
+def get_phenotype_count_categorie_names():
+  '''
+    Return a tuple of category names used
+    categorize_phenotype_counts.
+    Notes:
+    Any updates to this function must coincide with method
+    
+  '''
+  return ('0','1to10','11to20','21to30','larger_than_31')
+
+
+
+
+
+def get_phenotypes_entered_for_individual(indiv_id,project_id):
+  '''
+    Get phenotype data enterred for this individual.
+    
+    Inputs:
+    indiv_id: an individual ID (ex: PIE-OGI855-001726)
+  '''
+  try:  
+    uname,pwd = get_uname_pwd_for_project(project_id,read_only=True)
+    url = os.path.join(settings.PHENOPTIPS_HOST_NAME,'rest/patients/eid/' + indiv_id)
+    response = requests.get(url, auth=HTTPBasicAuth(uname,pwd))
+    return response.json()
+  except Exception as e:
+    print 'patient phenotype export error:',e
+    raise
+
+
+
+
+
+def phenotype_entry_metric_for_individual(indiv_id, project_id):
+  '''
+    Determine a metric that describes the level of phenotype entry for this
+    individual.
+    
+    Notes:
+      1. Phenotype terms appear in both features (where HPO terms exist)
+         and in nonstandard_features where phenotypes were defined in 
+         regular text where HPO might not have existed.
+    
+    Inputs:
+    indiv_id: an individual ID (ex: PIE-OGI855-001726)
+  '''
+  entered_phenotypes=get_phenotypes_entered_for_individual(indiv_id,project_id)
+  count=0
+  for k,v in entered_phenotypes.iteritems():
+    if k=='features' or k=='nonstandard_features':
+      count = count + len(v)
+  return count

xbrowse_server/phenotips/views.py

@@ -109,6 +109,44 @@ def fetch_phenotips_edit_page(request,eid):
 
 
 
+@log_request('phenotips_proxy_pdf_page')
+@login_required
+@csrf_exempt
+def fetch_phenotips_pdf_page(request,eid):
+  '''
+    A proxy for phenotips view and edit patient pages
+    Notes: 
+      - Exempting csrf here since phenotips doesn't have this support
+      - Each call to this endpoint is atomic, no session information is kept
+        between calls. Each call to this is from within a new Frame, hence no
+        notion of session is kept. Each is a new login into PhenoTips.
+  '''  
+  try:
+    current_user = request.user
+    project_id=request.GET['project']  
+    uname,pwd = get_uname_pwd_for_project(project_id,read_only=True)
+    ext_id=convert_internal_id_to_external_id(eid,uname,pwd)
+    auth_level=get_auth_level(project_id,request.user)
+    if auth_level == 'unauthorized':
+      return HttpResponse('unauthorized')
+    url=  settings.PHENOPTIPS_HOST_NAME + '/bin/export/data/' + ext_id + '?format=pdf&pdfcover=0&pdftoc=0&pdftemplate=PhenoTips.PatientSheetCode'
+    response,curr_session = do_authenticated_call_to_phenotips(url,uname,pwd)
+    http_response=HttpResponse(response.content)
+    for header in response.headers.keys():
+      if header != 'connection' and header != 'transfer-encoding': #these hop-by-hop headers are not allowed by Django
+        http_response[header]=response.headers[header]
+    return http_response
+  except Exception as e:
+    print e
+    raise Http404 
+
+
+
+
+
+
+
+
 @log_request('proxy_get')
 @login_required
 @csrf_exempt

xbrowse_server/templates/family/family_home.html

@@ -131,7 +131,7 @@ <h4 class="section-header">Individuals</h4>
                             <th>Mother</th>
                             <th>Father</th>
                             {% if phenotips_supported %}
-                            	<th>Phenotips</th>
+                            	<th>PhenoTips</th>
                             {% endif %}
                         </tr>
                     </thead>
@@ -145,7 +145,12 @@ <h4 class="section-header">Individuals</h4>
                         <td>{% if indiv.maternal_id %}{{ indiv.maternal_id }}{% else %}-{% endif %}</td>
                         <td>{% if indiv.paternal_id %}{{ indiv.paternal_id }}{% else %}-{% endif %}</td>
                         {% if phenotips_supported %}
-                        	<td><button id={{ indiv }} type="button" class="btn btn-info btn-sm phenotipsEditModalBtn">Edit in Phenotips</button></td>
+                        	<td>
+                        		{% if user_is_admin %}
+                        			<button id={{ indiv }} type="button" class="btn btn-info btn-sm phenotipsEditModalBtn">Edit</button>
+                        		{% endif %}
+                        		<button id={{ indiv }} type="button" class="btn btn-info btn-sm phenotipsViewModalBtn">View</button>
+                        	</td>
                         {% endif %}
                     </tr>
                     {% endfor %}
@@ -161,7 +166,7 @@ <h4 class="section-header">Individuals</h4>
 				<div class="modal-content">
 					<div class="modal-header">
 						<button type="button" class="close" data-dismiss="modal">&times;</button>
-						<h4 class="modal-title">Phenotips</h4>
+						<h4 class="modal-title">PhenoTips</h4>
 					</div>
 					<div class="modal-body"">
 						<iframe name="phenotipsEditPatientFrame" id="phenotipsEditPatientFrame" src="" width=1000 height=800 frameborder="0"></iframe>
@@ -170,18 +175,27 @@ <h4 class="modal-title">Phenotips</h4>
 			</div>
 		</div>
 		<script>
+		<!-- Edit page -->
 		$('.phenotipsEditModalBtn').on('click',function(event) {
 			var patientId=this.id;
 			var project_name="{{ project.project_id }}";
 			showEditPageForThisPatient(patientId,project_name);
 		});
-
 		//to capture modal close event relating to editing/viewing a phenotips patient page
 		$("#phenotipsModal").on("hidden.bs.modal",function() {
 			//clear up the existing frame so frame is black before next page loads
 			$('#phenotipsEditPatientFrame').attr('src', "about:blank");
 		});
 		</script>
+
+		<script>
+		<!-- View ONLY PDF page -->
+		$('.phenotipsViewModalBtn').on('click',function(event) {
+			var patientId=this.id;
+			var project_name="{{ project.project_id }}";
+			showViewPageForThisPatient(patientId,project_name);
+		});
+		</script>
 
 
 
@@ -202,6 +216,11 @@ <h4 class="modal-title">Phenotips</h4>
 			$('#phenotipsEditPatientFrame').attr('src', uri);
 			$('#phenotipsModal').modal('show');
 		}
+		function showViewPageForThisPatient(patientId,project) {
+			var uri = '/api/phenotips/proxy/view/' + patientId + '?' + 'project=' + project;
+			$('#phenotipsEditPatientFrame').attr('src', uri);
+			$('#phenotipsModal').modal('show');
+		}
 		</script>
 
 		<style>

xbrowse_server/templates/project.html

@@ -76,6 +76,34 @@ <h4 class="section-header">Results</h4>
                         <h5><a href="{% url 'add_tag' project.project_id %}">Create tag</a></h5>
                     </div>
                 </div>
+
+
+                {% if phenotips_supported and auth_level == 'admin'%}
+                	<h4 class="section-header">Phenotype entry metrics</h4>
+                	<div class="row">
+                		<table class="table table-hover">
+                			<tr>
+                				<td><p>Count of HPO terms<p></td>
+                				<td><p>0<p></td>
+                				<td><p>1 to 10</p></td>
+                				<td><p>11 to 20</p></td>
+                				<td><p>21 to 30</p></td>
+                				<td><p>More than 30</p></td>
+                			</tr>
+                			<tr>
+                				<td><p>Individuals</p></td>
+                				<td><p>{{ categorized_phenotype_counts.0|length }}</p></td>
+                				<td><p>{{ categorized_phenotype_counts.1to10|length }}</p></td>
+                				<td><p>{{ categorized_phenotype_counts.11to20|length }}</p></td>
+                				<td><p>{{ categorized_phenotype_counts.21to30|length }}</p></td>
+                				<td><p>{{ categorized_phenotype_counts.larger_than_31|length }}</p></td>
+                			</tr>
+                		</table>
+                	</div>
+                {% endif %}
+
+
+
             </div>
             <div class="col-sm-4">
                 <h4 class="section-header">Project Settings</h4>