Merge pull request #95 from NHS-NGS/development

Development

CHANGELOG.md

@@ -1,4 +1,53 @@
-## [0.4.5]- 2018-08-2X
+## [0.5.5]- 2018-10-XX
+### Added
+- Case alert feature
+- Case code flag
+
+### Changed
+- Made cancer tweaks to proband page
+- Proband page now shows related GELIRs
+
+## [0.5.4]- 2018-10-03
+### Added
+- Cancer germline selection
+
+### Changes
+- Improved MDT selection page
+
+## [0.5.3]- 2018-09-14
+### Added 
+- Added binning to case updates
+
+### Changed
+- UI improvements
+- Nicer display during update process
+- Patched security flaws
+
+## [0.5.2]- 2018-09-03
+### Added 
+- Report history feature
+
+### Changed
+- Fixed cancer MDT page bug
+
+## [0.5.1]- 2018-07-26
+### Changed 
+- Updated reporting templates
+
+## [0.5.0]- 2018-07-11
+### Added
+- PVFlag feature to describe variant flags
+
+### Changed
+- Labkey speed up
+- Removed T0 feature
+- speed improvements to updates
+
+## [0.4.6]- 2018-06-18
+### Changed
+- Fixed minor bug where export buttons removed pagination
+
+## [0.4.5]- 2018-06-18
 ### Added
 - History tab to cases which shows history of changes to cases, ordered by oldest to newest
 

gelweb/gel2mdt/api/serializers.py

@@ -284,5 +284,6 @@ class Meta:
             'recruiting_disease',
             'sex',
             'nhs_num',
-            'disease_subtype'
+            'disease_subtype',
+            'case_code'
         )

gelweb/gel2mdt/database_utils/case_handler.py

@@ -218,10 +218,19 @@ def get_tools_and_versions(self):
         :return: A dictionary of tools and versions used for the case
         '''
         if self.json['sample_type'] == 'raredisease':
-            tools_dict = {'genome_build': self.json_request_data["genomeAssemblyVersion"]}
+            if self.json_request_data['genomeAssemblyVersion'].startswith('GRCh37'):
+                genome_build = 'GRCh37'
+            elif self.json_request_data['genomeAssemblyVersion'].startswith('GRCh38'):
+                genome_build = 'GRCh38'
         elif self.json['sample_type'] == 'cancer':
-            tools_dict = {'genome_build': self.json["assembly"]}
-        return tools_dict
+            if self.json["assembly"].startswith('GRCh37'):
+                genome_build = 'GRCh37'
+            elif self.json["assembly"].startswith('GRCh38'):
+                genome_build = 'GRCh38'
+        else:
+            raise Exception(f'{self.request_id} has unknown genome build')
+
+        return {'genome_build': genome_build}
 
     def get_status_json(self):
         """

gelweb/gel2mdt/database_utils/multiple_case_adder.py

@@ -157,8 +157,6 @@ def __init__(self, sample_type, head=None, test_data=False,
                         set(self.cases_to_update)
                     self.update_database()
 
-                    print("Finished processing bin", bin_count, "of", len(bins))
-
                     for case in self.cases_to_add:
                         del case
                     for case in self.cases_to_update:
@@ -217,6 +215,8 @@ def update_database(self):
             listupdate.reports_added.add(*added_cases)
             listupdate.reports_updated.add(*updated_cases)
 
+            # Add in case alert
+
     def fetch_test_data(self):
         """
         This will run and convert our test data to a list of jsons if
@@ -234,13 +234,14 @@ def fetch_test_data(self):
                 logger.info("Found case json at " + file_path + " for testing.")
                 with open(file_path) as json_file:
                     json_data = json.load(json_file)
-                    list_of_cases.append(Case(
-                        case_json=json_data,
-                        panel_manager=self.panel_manager,
-                        variant_manager=self.variant_manager,
-                        gene_manager=self.gene_manager,
-                        skip_demographics=self.skip_demographics,
-                        pullt3=self.pullt3))
+                    if json_data['sample_type'] == self.sample_type:
+                        list_of_cases.append(Case(
+                            case_json=json_data,
+                            panel_manager=self.panel_manager,
+                            variant_manager=self.variant_manager,
+                            gene_manager=self.gene_manager,
+                            skip_demographics=self.skip_demographics,
+                            pullt3=self.pullt3))
         logger.info("Found " + str(len(list_of_cases)) +  " test cases.")
         return list_of_cases
 
@@ -304,20 +305,22 @@ def check_cases_to_update(self):
         cases_to_update = []
         # use set subtraction to get only cases that haven't already been added
         cases_to_check = set(self.list_of_cases) - set(self.cases_to_add)
+        all_latest_reports = GELInterpretationReport.objects.latest_cases_by_sample_type(sample_type=self.sample_type)
         try:
-            latest_report_list = [
-                GELInterpretationReport.objects.filter(
-                    ir_family=InterpretationReportFamily.objects.get(
-                        ir_family_id=case.request_id
-                    )).latest("updated") for case in cases_to_check]
+            latest_report_list = []
+            for case in cases_to_check:
+                for report in all_latest_reports:
+                    if case.request_id == report.ir_family.ir_family_id:
+                        latest_report_list.append(report)
 
             latest_hashes = {
                 ir.ir_family.ir_family_id: ir.sha_hash
                 for ir in latest_report_list
             }
 
             for case in cases_to_check:
-                if case.json_hash != latest_hashes[case.request_id]:
+                latest_hash = latest_hashes.get(case.request_id, None)
+                if not latest_hash or case.json_hash != latest_hash:
                     cases_to_update.append(case)
 
         except GELInterpretationReport.DoesNotExist as e:

gelweb/gel2mdt/exports.py

@@ -95,7 +95,10 @@ def write_mdt_outcome_template(report):
                   + ' ' \
                   + str(report.ir_family.participant_family.proband.surname)
     row[1].text = str(report.ir_family.participant_family.proband.date_of_birth.date())
-    row[2].text = report.ir_family.participant_family.proband.nhs_number
+    try:
+        row[2].text = report.ir_family.participant_family.proband.nhs_number
+    except TypeError:
+        row[2].text = ''
     if report.ir_family.participant_family.proband.local_id:
         row[3].text = report.ir_family.participant_family.proband.local_id
 

gelweb/gel2mdt/forms.py

@@ -107,7 +107,7 @@ class GELIRForm(forms.ModelForm):
     '''
     class Meta:
         model = GELInterpretationReport
-        fields = ['case_status', 'mdt_status', 'pilot_case', 'case_sent', 'no_primary_findings']
+        fields = ['case_status', 'mdt_status', 'pilot_case', 'case_sent', 'no_primary_findings', 'case_code']
 
     def save(self):
         gelir = self.instance
@@ -117,6 +117,7 @@ def save(self):
         gelir.pilot_case = data['pilot_case']
         gelir.case_sent = data['case_sent']
         gelir.no_primary_findings = data['no_primary_findings']
+        gelir.case_code = data['case_code']
         gelir.save(overwrite=True)
 
 
@@ -380,3 +381,17 @@ class GenomicsEnglandform(forms.Form):
 
 class GeneSearchForm(forms.Form):
     gene = forms.CharField(max_length=25, widget = forms.TextInput(attrs={'style': 'width:200px'}))
+
+
+class AddCaseAlert(forms.ModelForm):
+
+    def clean_gel_id(self):
+        if self.cleaned_data['gel_id'].isdigit() and len(self.cleaned_data['gel_id']) >= 8:
+            return self.cleaned_data['gel_id'].strip()
+        else:
+            forms.ValidationError("Doesn't look like a GELID")
+
+
+    class Meta:
+        model = CaseAlert
+        fields = ['gel_id', 'comment', 'sample_type']

gelweb/gel2mdt/models.py

@@ -323,6 +323,8 @@ class GELInterpretationReport(models.Model):
         ('R', 'Required'), ('N', 'Not Required'), ('I', 'In Progress'), ('D', 'Done'),), default='U')
     pilot_case = models.BooleanField(default=False)
     no_primary_findings = models.BooleanField(default=False)
+    case_code = models.CharField(max_length=20, null=True, blank=True, choices=(
+        ('REANALYSE', 'REANALYSE'), ('URGENT', 'URGENT')), )
 
     def save(self, overwrite=False, *args, **kwargs):
         """
@@ -352,6 +354,7 @@ def save(self, overwrite=False, *args, **kwargs):
                 latest_report.no_primary_findings = self.no_primary_findings
                 latest_report.archived_version = self.archived_version
                 latest_report.has_germline_variant = self.has_germline_variant
+                latest_report.case_code = self.case_code
                 super(GELInterpretationReport, latest_report).save(*args, **kwargs)
             else:
                 self.assigned_user = latest_report.assigned_user
@@ -362,6 +365,7 @@ def save(self, overwrite=False, *args, **kwargs):
                 self.polled_at_datetime = timezone.now()
                 self.user = latest_report.user
                 self.no_primary_findings = latest_report.no_primary_findings
+                self.case_code = latest_report.case_code
                 # update the latest saved version.
                 self.archived_version = latest_report.archived_version + 1
                 super(GELInterpretationReport, self).save(*args, **kwargs)
@@ -400,7 +404,7 @@ def __str__(self):
     class Meta:
         managed = True
         db_table = 'ClinicalScientist'
-        app_label= 'gel2mdt'
+        app_label = 'gel2mdt'
 
 
 class Proband(models.Model):
@@ -890,4 +894,16 @@ class MDTReport(models.Model):
     class Meta:
         managed = True
         db_table = 'MDTReport'
-        app_label= 'gel2mdt'
+        app_label = 'gel2mdt'
+
+
+class CaseAlert(models.Model):
+    gel_id = models.CharField(max_length=30)
+    comment = models.CharField(max_length=255)
+    sample_type = models.CharField(max_length=20, choices=(('cancer', 'cancer'),
+                                                           ('raredisease', 'raredisease')))
+
+    class Meta:
+        managed = True
+        db_table = 'GELAlert'
+        app_label = 'gel2mdt'

gelweb/gel2mdt/tasks.py

@@ -203,6 +203,46 @@ def update_for_t3(report_id):
                       pullt3=True,
                       sample=report.ir_family.participant_family.proband.gel_id)
 
+@task
+def case_alert_email():
+    '''
+    Utility function designed to be run with celery. Emails GELTeam nightly about CaseAlert cases
+    :param report_id: GEL InterpretationReport ID
+    :return: Nothing
+    '''
+    sample_types = {'raredisease': False, 'cancer': False}
+    matching_cases = {}
+    for s_type in sample_types:
+        case_alerts = CaseAlert.objects.filter(sample_type=s_type)
+        gel_reports = GELInterpretationReport.objects.latest_cases_by_sample_type(
+            sample_type=s_type).prefetch_related('ir_family__participant_family__proband')
+        matching_cases[s_type] = {}
+        for case in case_alerts:
+            matching_cases[s_type][case.id] = []
+            for report in gel_reports:
+                try:
+                    if report.ir_family.participant_family.proband.gel_id == str(case.gel_id):
+                        matching_cases[s_type][case.id].append((report.id,
+                                                                report.ir_family.ir_family_id))
+                    sample_types[s_type] = True
+                except Proband.DoesNotExist:
+                    pass
+
+    text_content = ''
+    if sample_types['cancer'] or sample_types['raredisease']:
+        for s_type in sample_types:
+            if matching_cases[s_type]:
+                text_content += f'{s_type} Case Alert:\n'
+                for case in matching_cases[s_type]:
+                    case_alert = CaseAlert.objects.get(id=case)
+                    text_content += f'Case {case_alert.gel_id} with CIP-ID of {matching_cases[s_type][case][0][1]} ' \
+                                    f'has been added to the database. CaseAlert comment: {case_alert.comment}\n'
+        subject, from_email, to = f'GeL2MDT CaseAlert', '[email protected]', '[email protected]'
+        msg = EmailMessage(subject, text_content, from_email, [to])
+        try:
+            msg.send()
+        except Exception as e:
+            pass
 
 @task
 def listupdate_email():

gelweb/gel2mdt/templates/gel2mdt/base.html

@@ -109,6 +109,9 @@
                     <ul class="nav navbar-nav">
                         <li><a href="{% url 'validation-list' sample_type=sample_type %}" ><i class="fas fa-check-circle"></i> Validation</a></li>
                         </ul>
+                     <ul class="nav navbar-nav">
+                        <li><a href="{% url 'case-alert' sample_type=sample_type %}" ><i class="fas fa-bell"></i> Case Alerts</a></li>
+                        </ul>
                     {% endif %}
 
 

gelweb/gel2mdt/templates/gel2mdt/cancer_main.html

@@ -272,7 +272,7 @@ <h4 name="filter-spec" class="panel-title">
                             <th>Surname</th>
                             <th>NHS No.</th>
                             <th>Date of Birth</th>
-                            <th>Max Tier</th>
+                            <th>Max Domain</th>
                             <th>Assembly</th>
                             <th>Status</th>
                             <th>Pilot</th>
@@ -282,11 +282,13 @@ <h4 name="filter-spec" class="panel-title">
                             <th>Priority</th>
                             <th>Recruiting Disease</th>
                             <th>CIP ID</th>
-                            <th>GMC</th>
+                            <th>LDP</th>
                             <th>Clinician</th>
+                            <th>Case Code</th>
                             <th>Gender</th>
                             <th>Disease Subtype</th>
                             <th>NHS number</th>
+
                         </tr>
                     </thead>
                     </table>
@@ -558,6 +560,7 @@ <h4 name="filter-spec" class="panel-title">
                 {"data": "cip_id"},
                 {"data": "gmc"},
                 {"data": "clinician"},
+                {"data": "case_code"},
                 {
                     "data": "sex",
                     "visible": false