Merge branch 'release/0.3.1'

assets/js/pages/gwas_upload.js

@@ -13,7 +13,7 @@ import { _isHeader } from 'locuszoom/esm/ext/lz-parsers/gwas/sniffers';
 import { makeGWASParser } from 'locuszoom/esm/ext/lz-parsers';
 
 const PREVIEW_BYTES = 5000;  // enough for 50-100 lines
-const MAX_UPLOAD_SIZE = 1048576 * 1000; // 1000 MiB # FIXME: Currently upload limit is only implemented in the frontend
+const MAX_UPLOAD_SIZE = 1048576 * 1250; // 1250 MiB # FIXME: Currently upload limit is only implemented in the frontend
 
 
 class BaseReader {

assets/vue/gwas_region.vue

@@ -8,7 +8,7 @@
     import RegionPicker from 'localzoom/src/components/RegionPicker.vue';
     import { DATA_TYPES } from 'localzoom/src/util/constants';
     import { activateUserLD } from 'localzoom/src/util/lz-helpers';
-    import {setup_feature_metrics} from 'localzoom/src/util/metrics';
+    import {count_add_track, setup_feature_metrics} from 'localzoom/src/util/metrics';
 
     const MAX_REGION_SIZE = 1000000;
 
@@ -95,6 +95,8 @@
                     }
                 }
 
+                count_add_track(data_type);
+                this.known_tracks.push({data_type, filename, display_name});
             },
         },
         components: { BatchSpec, BatchScroller, GwasToolbar, PlotPanes, RegionPicker }

compose/production/django/Dockerfile

@@ -6,7 +6,7 @@ FROM node:fermium as jsbuilder
 COPY ./package.json ./package-lock.json /build/
 COPY . /build/
 WORKDIR /build/
-RUN npm install ci && npm run prod
+RUN npm ci && npm run prod
 
 
 # Step 2 (main): Django app. Install python dependencies, add volume mounts, and run.

locuszoom_plotting_service/templates/gwas/gwas_summary.html

@@ -142,8 +142,9 @@ <h3>QQ Plot:</h3>
     {% else %}
       <p>We were unable to process your uploaded GWAS file. Please review the logs for the cause, and contact us
         if you believe the problem is an error.</p>
-      <p>You can verify that you uploaded the correct file by comparing the checksum (SHA256):<br>
-        <span class="text-muted">{{ gwas.files.file_sha256.hex }}</span></p>
+      {# FIXME: At present, metadata.files is only set at conclusion of a successful upload (tasks.py). This makes it difficult to show the SHA, which lives in the associated "this is the file for a study" record. #}
+      {#      <p>You can verify that you uploaded the correct file by comparing the checksum (SHA256):<br>#}
+      {#        <span class="text-muted">{{ gwas.files.file_sha256.hex }}</p>#}
       {%  if request.user == gwas.owner %}
         <form method="post" action="{% url 'gwas:rerun' gwas.slug %}" class="form-horizontal">
           {% csrf_token %}

requirements/base.txt

@@ -25,5 +25,5 @@ pyyaml  # Required for OpenAPI rendering
 boltons~=20.2.1
 scipy~=1.5.3
 python-magic==0.4.18
-zorp[perf,lookups]==0.3.3
+zorp[perf,lookups]==0.3.4
 genelocator==1.1.2

util/ingest/validators.py

@@ -57,11 +57,11 @@ def _validate_data_rows(self, reader) -> bool:
 
             if cur_chrom == prev_chrom and cp[1] < prev_pos:
                 # Positions not in correct order for Pheweb to use
-                raise v_exc.ValidationException('Positions must be sorted prior to uploading')
+                raise v_exc.ValidationException(f'Positions must be sorted prior to uploading. Position chr{cur_chrom}:{cp[1]} should not follow chr{prev_chrom}:{prev_pos}')
 
             if cur_chrom != prev_chrom:
                 if cur_chrom in chrom_seen:
-                    raise v_exc.ValidationException('Chromosomes must be sorted (so that all variants for the same chromosome are contiguous)')  # noqa
+                    raise v_exc.ValidationException(f'Chromosomes must be sorted (so that all variants for the same chromosome are contiguous). Error at position: chr{cur_chrom}:{cp[1]}')  # noqa
                 else:
                     chrom_seen.add(cur_chrom)