Remove some commented out code

api/routes/project_insights.py

@@ -23,8 +23,8 @@ async def get_project_insights_summary(
     """
     Get summary stats for a list of projects and sequencing types
     """
-    spslayer = ProjectInsightsLayer(connection)
-    projects_insights_stats = await spslayer.get_project_insights_summary(
+    pilayer = ProjectInsightsLayer(connection)
+    projects_insights_stats = await pilayer.get_project_insights_summary(
         project_ids=project_ids, sequencing_types=sequencing_types
     )
 
@@ -44,8 +44,8 @@ async def get_project_insights_details(
     """
     Get extensive sequencing group details for a list of projects and sequencing types
     """
-    spslayer = ProjectInsightsLayer(connection)
-    projects_insights_details = await spslayer.get_project_insights_details(
+    pilayer = ProjectInsightsLayer(connection)
+    projects_insights_details = await pilayer.get_project_insights_details(
         project_ids=project_ids, sequencing_types=sequencing_types
     )
 

db/python/layers/project_insights.py

@@ -480,7 +480,7 @@ async def get_project_insights_summary(
             user=self.author, project_ids=project_ids, readonly=True
         )
 
-        (   # each of these is keyed by (project_id, sequencing_type)
+        (
             total_families_by_project_id_and_seq_fields,
             total_participants_by_project_id_and_seq_fields,
             total_samples_by_project_id_and_seq_fields,
@@ -503,13 +503,9 @@ async def get_project_insights_summary(
         )
 
         # Get the sequencing groups for each of the analyses in the grouped analyses rows
-        # (latest_annotate_dataset and latest_es_indices)
-        # TODO: Add multiQC and other grouped analyses to this
         analysis_sequencing_groups = await self.get_analysis_sequencing_groups([latest_annotate_dataset_by_project_id_and_seq_type, latest_es_indices_by_project_id_and_seq_type_and_stage])
 
-        # sequencing_platforms = await SequencingPlatformTable(self._connection).get()
         sequencing_technologies = await SequencingTechnologyTable(self._connection).get()
-        # sequencing_types = await SequencingTypeTable(self._connection).get()
 
         # Get all possible permutations of the projects, sequencing types, and sequencing technologies
         permutations = itertools.product(projects, sequencing_types, sequencing_technologies)
@@ -612,13 +608,10 @@ async def get_project_insights_details(
             ),
         )
         # Get the sequencing groups for each of the analyses in the grouped analyses rows
-        # (latest_annotate_dataset and latest_es_indices)
-        # TODO: Add multiQC and other grouped analyses to this
         analysis_sequencing_groups = await self.get_analysis_sequencing_groups([latest_annotate_dataset_by_project_id_and_seq_type, latest_es_indices_by_project_id_and_seq_type_and_stage])
 
         sequencing_platforms = await SequencingPlatformTable(self._connection).get()
         sequencing_technologies = await SequencingTechnologyTable(self._connection).get()
-        # sequencing_types = await SequencingTypeTable(self._connection).get()
 
         # Get all possible permutations of the projects, sequencing types, sequencing platforms, and sequencing technologies
         permutations = itertools.product(projects, sequencing_types, sequencing_platforms, sequencing_technologies)
@@ -631,7 +624,6 @@ async def get_project_insights_details(
                 continue
 
             if sequencing_technology == 'short-read':
-                # The grouped analyses rows are keyed by (project_id, sequencing_type)
                 latest_annotate_dataset = latest_annotate_dataset_by_project_id_and_seq_type[(project.id, sequencing_type)]
                 latest_snv_es_index = latest_es_indices_by_project_id_and_seq_type_and_stage[(project.id, sequencing_type, 'MtToEs')]
                 if sequencing_type == 'genome':

db/python/layers/web.py

@@ -1,4 +1,4 @@
-# pylint: disable=too-many-locals, too-many-instance-attributes, too-many-lines
+# pylint: disable=too-many-locals, too-many-instance-attributes
 import asyncio
 import itertools
 import json

web/src/index.css

@@ -311,7 +311,7 @@ html[data-theme='dark-mode'] .ui.table {
     font-weight: bold;
 }
 
-/* seqr projects stats dashboard */
+/* Project Insights dashboard */
 .html-tooltip .MuiTooltip-tooltip {
     background-color: #f5f5f9;
     color: rgba(0, 0, 0, 0.87);
@@ -327,11 +327,9 @@ html[data-theme='dark-mode'] .ui.table {
 .ui.table .table-cell {
     text-align: center;
     vertical-align: middle;
-    /* font-size: 0.8em; */
     color: var(--color-text-primary) !important;
     word-wrap: break-word !important;
     overflow-wrap: break-word !important;
-    /* white-space: normal !important; */
 }
 
 .ui.table .header-cell {

web/src/pages/projectInsights/Details.tsx

@@ -116,26 +116,12 @@ const Details: React.FC = () => {
                 selectedSampleExtIds.includes(item.sample_ext_ids[0])) &&
             (selectedSequencingGroupIds.length === 0 ||
                 selectedSequencingGroupIds.includes(item.sequencing_group_id)) &&
-            // (selectedCompletedCram.length === 0 ||
-            //     (selectedCompletedCram.includes('Yes') && item.completed_cram) ||
-            //     (selectedCompletedCram.includes('No') && !item.completed_cram)) &&
             (selectedCompletedCram.length === 0 ||
                 selectedCompletedCram.includes(item.completed_cram ? 'Yes' : 'No')) &&
-            // (selectedInLatestAnnotateDataset.length === 0 ||
-            //     (selectedInLatestAnnotateDataset.includes('Yes') &&
-            //         item.in_latest_annotate_dataset) ||
-            //     (selectedInLatestAnnotateDataset.includes('No') &&
-            //         !item.in_latest_annotate_dataset)) &&
             (selectedInLatestAnnotateDataset.length === 0 ||
                 selectedInLatestAnnotateDataset.includes(
                     item.in_latest_annotate_dataset ? 'Yes' : 'No'
                 )) &&
-            // (selectedInLatestSnvEsIndex.length === 0 ||
-            //     (selectedInLatestSnvEsIndex.includes('Yes') && item.in_latest_snv_es_index) ||
-            //     (selectedInLatestSnvEsIndex.includes('No') && !item.in_latest_snv_es_index)) &&
-            // (selectedInLatestSvEsIndex.length === 0 ||
-            //     (selectedInLatestSvEsIndex.includes('Yes') && item.in_latest_sv_es_index) ||
-            //     (selectedInLatestSvEsIndex.includes('No') && !item.in_latest_sv_es_index)) &&
             (selectedInLatestSnvEsIndex.length === 0 ||
                 selectedInLatestSnvEsIndex.includes(item.in_latest_snv_es_index ? 'Yes' : 'No')) &&
             (selectedInLatestSvEsIndex.length === 0 ||