#3539 added lab compare export option (#944)

classification/templates/classification/classification_export.html

@@ -101,6 +101,11 @@
         } else if (labSelectionMode === 'include') {
             inputError = 'You must include at least 1 lab';
         }
+        if (format === 'lab_compare'){
+            if (selectedLabs.length !== 2) {
+                inputError = 'You must select 2 labs';
+            }
+        }
 
         let selectedOrgs = $("input[name='org_selection']:checked");
         if (selectedOrgs.length) {

classification/views/classification_export_view.py

@@ -83,6 +83,7 @@ def export_view(request: HttpRequest) -> Response:
     format_clinvar_expert_compare = {'id': 'clinvar_compare_expert', 'name': 'ClinVar Expert Panel Compare', 'admin_only': True}
     format_json = {'id': 'json', 'name': 'JSON'}
     format_spelling = {'id': 'spelling', 'name': 'Spelling Report', 'admin_only': True}
+    format_lab_compare = {'id': 'lab_compare', 'name': 'Lab Compare', 'admin_only': True}
     format_redcap = {'id': 'redcap', 'name': 'REDCap'}
     format_vcf = {'id': 'vcf', 'name': 'VCF'}
     formats = [
@@ -91,6 +92,7 @@ def export_view(request: HttpRequest) -> Response:
         format_clinvar_compare,
         format_clinvar_expert_compare,
         format_spelling,
+        format_lab_compare,
         format_json,
         format_mvl
     ]

classification/views/exports/__init__.py

@@ -8,3 +8,4 @@
 from classification.views.exports.classification_export_formatter_redcap import ClassificationExportFormatterRedCap
 from classification.views.exports.classification_export_formatter_spelling import ClassificationExportFormatterSpelling
 from classification.views.exports.classification_export_formatter_vcf import ClassificationExportFormatterVCF
+from classification.views.exports.classification_export_formatter_lab_compare import ClassificationExportInternalCompare

classification/views/exports/classification_export_formatter_lab_compare.py

@@ -0,0 +1,92 @@
+from typing import List
+
+from django.http import HttpRequest
+from django.urls.base import reverse
+
+from classification.enums import SpecialEKeys
+from classification.views.exports.classification_export_decorator import register_classification_exporter
+from classification.views.exports.classification_export_filter import ClassificationFilter, AlleleData
+from classification.views.exports.classification_export_formatter import ClassificationExportFormatter
+from library.django_utils import get_url_from_view_path
+from library.utils import ExportRow, export_column, delimited_row
+
+
+class ClassificationlabCompareRow(ExportRow):
+
+    def __init__(self,  AlleleData, lab1, lab2):
+        self.AlleleData = AlleleData
+        self.lab1 = lab1
+        self.lab2 = lab2
+
+    @export_column("Allele URL")
+    def allele_url(self):
+        url = get_url_from_view_path(reverse('view_allele', kwargs={"allele_id": self.AlleleData}))
+        return url
+
+    @export_column("Lab 1")
+    def lab_clinical_significance(self):
+        return self.lab1
+
+    @export_column("Lab 2")
+    def lab2_clinical_significance(self):
+        return self.lab2
+
+    @export_column("Difference")
+    def difference(self, lab_name1, lab_name2):
+        if (self.lab1 != '' and self.lab2 != '') and self.lab1 == self.lab2:
+            return 'Same'
+        elif self.lab1 == '' and self.lab2 != '':
+            return lab_name2
+        elif self.lab1 != '' and self.lab2 == '':
+            return lab_name1
+        elif self.lab1 != self.lab2:
+            return 'Different'
+        elif self.lab1 == '' and self.lab2 == '':
+            return 'No data'
+
+
+@register_classification_exporter("lab_compare")
+class ClassificationExportInternalCompare(ClassificationExportFormatter):
+
+    @classmethod
+    def from_request(cls, request: HttpRequest) -> 'ClassificationExportInternalCompare':
+        return ClassificationExportInternalCompare(
+            classification_filter=ClassificationFilter.from_request(request),
+        )
+
+    def content_type(self) -> str:
+        return "text/csv"
+
+    def extension(self) -> str:
+        return "csv"
+
+    def header(self) -> List[str]:
+        if self.classification_filter.include_sources and len(self.classification_filter.include_sources) == 2:
+            lab_names = sorted([str(lab) for lab in self.classification_filter.include_sources])
+            return [delimited_row(['Allele URL', lab_names[0], lab_names[1], 'Difference'], ',')]
+        else:
+            raise ValueError("Must specify 2 labs to compare")
+
+    def footer(self) -> List[str]:
+        return []
+
+    def row(self, allele_data: AlleleData) -> List[str]:
+        rows: List[str] = []
+        lab1 = set()
+        lab2 = set()
+        if self.classification_filter.include_sources:
+            lab_name1, lab_name2 = sorted(self.classification_filter.include_sources)
+            for cm in allele_data.cms_regardless_of_issues:
+                if cm.lab == lab_name1 and cm.clinical_significance is not None:
+                    lab1.add(cm.get(SpecialEKeys.CLINICAL_SIGNIFICANCE))
+                if cm.lab == lab_name2 and cm.clinical_significance is not None:
+                    lab2.add(cm.get(SpecialEKeys.CLINICAL_SIGNIFICANCE))
+
+            lab1_set = ','.join(lab1)
+            lab2_set = ','.join(lab2)
+            row = ClassificationlabCompareRow(AlleleData=allele_data.allele_id, lab1=lab1_set, lab2=lab2_set)
+            rows.append(delimited_row([row.allele_url(), row.lab_clinical_significance(),
+                                       row.lab2_clinical_significance(), row.difference(lab_name1, lab_name2)], ','))
+        else:
+            raise ValueError("Error comparing labs")
+        return rows