update to v2.0.3 (#168)

afrubin · EstelleDa · web-flow · commit b2ab9615274b · 2021-10-26T12:28:29.000+11:00
* Update SRA identifier field name (#152) * don't accept ArrayExpress arrays as raw reads * prefer DOIs over DOI identifer or DOI accession in text * prefer PubMed IDs over PubMed identifiers in text * prefer Raw reads accessions over SRA identifiers in text * migrations for verbose name changes * fix raw reads label in html * fix count column ordering bug (#164) * fix score column ordering bug (#167) * fix target sequence accession auto-fill (#166) * fix public score set metadata editing (#165) * update version * tag the correct postgres image Co-authored-by: EstelleDa <baishenlonger@live.com.sg>
diff --git a/core/static/core/mavedb/scoreset-form.js b/core/static/core/mavedb/scoreset-form.js
@@ -269,14 +269,14 @@ function initializeScoresetForm ({ newForm = true, privateDateset = true }) {
       }
 
       let id = this.value;
-      let uniprotSelect = $('#id_uniprot-identifier');
-      let uniprotOffsetElem = $('#id_uniprot-offset');
+      let uniprotSelect = $('#id_uniprot-offset-identifier');
+      let uniprotOffsetElem = $('#id_uniprot-offset-offset');
 
-      let refseqSelect = $('#id_refseq-identifier');
-      let refseqOffsetElem = $('#id_refseq-offset');
+      let refseqSelect = $('#id_refseq-offset-identifier');
+      let refseqOffsetElem = $('#id_refseq-offset-offset');
 
-      let ensemblSelect = $('#id_ensembl-identifier');
-      let ensemblOffsetElem = $('#id_ensembl-offset');
+      let ensemblSelect = $('#id_ensembl-offset-identifier');
+      let ensemblOffsetElem = $('#id_ensembl-offset-offset');
 
       let nameElem = document.getElementById('id_name');
       let categoryElem = document.getElementById('id_category');
@@ -322,7 +322,6 @@ function initializeScoresetForm ({ newForm = true, privateDateset = true }) {
               $(uniprotSelect).val('').trigger('change');
               $(uniprotOffsetElem).val(0);
             }
-
             // Change RefSeq
             if (refseq_id) {
               $(refseqSelect).val(refseq_id).trigger('change');
diff --git a/data/main/site_info.json b/data/main/site_info.json
@@ -6,5 +6,5 @@
   "md_privacy": "",
   "md_terms": "",
   "md_usage_guide": "",
-  "version": "2.0.2"
+  "version": "2.0.3"
 }
diff --git a/dataset/forms/base.py b/dataset/forms/base.py
@@ -86,7 +86,7 @@ def __init__(self, *args, **kwargs):
         self.fields["sra_ids"] = FlexibleModelMultipleChoiceField(
             klass=SraIdentifier,
             to_field_name="identifier",
-            label="SRA identifiers",
+            label="Raw reads accessions",
             required=False,
             queryset=SraIdentifier.objects.all(),
             widget=forms.SelectMultiple(
@@ -96,7 +96,7 @@ def __init__(self, *args, **kwargs):
         self.fields["doi_ids"] = FlexibleModelMultipleChoiceField(
             klass=DoiIdentifier,
             to_field_name="identifier",
-            label="DOI identifiers",
+            label="DOIs",
             required=False,
             queryset=DoiIdentifier.objects.all(),
             widget=forms.SelectMultiple(
@@ -106,7 +106,7 @@ def __init__(self, *args, **kwargs):
         self.fields["pubmed_ids"] = FlexibleModelMultipleChoiceField(
             klass=PubmedIdentifier,
             to_field_name="identifier",
-            label="PubMed identifiers",
+            label="PubMed IDs",
             required=False,
             queryset=PubmedIdentifier.objects.all(),
             widget=forms.SelectMultiple(
diff --git a/dataset/migrations/0017_auto_20210825_1634.py b/dataset/migrations/0017_auto_20210825_1634.py
@@ -0,0 +1,105 @@
+# -*- coding: utf-8 -*-
+# Generated by Django 1.11.29 on 2021-08-25 06:34
+from __future__ import unicode_literals
+
+from django.db import migrations, models
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ("dataset", "0016_auto_20200923_1616"),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name="experiment",
+            name="doi_ids",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="associated_experiments",
+                to="metadata.DoiIdentifier",
+                verbose_name="DOIs",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experiment",
+            name="pubmed_ids",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="associated_experiments",
+                to="metadata.PubmedIdentifier",
+                verbose_name="PubMed IDs",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experiment",
+            name="sra_ids",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="associated_experiments",
+                to="metadata.SraIdentifier",
+                verbose_name="Raw reads accessions",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experimentset",
+            name="doi_ids",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="associated_experimentsets",
+                to="metadata.DoiIdentifier",
+                verbose_name="DOIs",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experimentset",
+            name="pubmed_ids",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="associated_experimentsets",
+                to="metadata.PubmedIdentifier",
+                verbose_name="PubMed IDs",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="experimentset",
+            name="sra_ids",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="associated_experimentsets",
+                to="metadata.SraIdentifier",
+                verbose_name="Raw reads accessions",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="scoreset",
+            name="doi_ids",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="associated_scoresets",
+                to="metadata.DoiIdentifier",
+                verbose_name="DOIs",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="scoreset",
+            name="pubmed_ids",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="associated_scoresets",
+                to="metadata.PubmedIdentifier",
+                verbose_name="PubMed IDs",
+            ),
+        ),
+        migrations.AlterField(
+            model_name="scoreset",
+            name="sra_ids",
+            field=models.ManyToManyField(
+                blank=True,
+                related_name="associated_scoresets",
+                to="metadata.SraIdentifier",
+                verbose_name="Raw reads accessions",
+            ),
+        ),
+    ]
diff --git a/dataset/models/base.py b/dataset/models/base.py
@@ -208,19 +208,19 @@ def tracked_fields(cls):
     sra_ids = models.ManyToManyField(
         SraIdentifier,
         blank=True,
-        verbose_name="SRA identifiers",
+        verbose_name="Raw reads accessions",
         related_name="associated_%(class)ss",
     )
     doi_ids = models.ManyToManyField(
         DoiIdentifier,
         blank=True,
-        verbose_name="DOI identifiers",
+        verbose_name="DOIs",
         related_name="associated_%(class)ss",
     )
     pubmed_ids = models.ManyToManyField(
         PubmedIdentifier,
         blank=True,
-        verbose_name="PubMed identifiers",
+        verbose_name="PubMed IDs",
         related_name="associated_%(class)ss",
     )
 
diff --git a/dataset/templates/dataset/base/base.html b/dataset/templates/dataset/base/base.html
@@ -413,7 +413,7 @@ <h2 id="metadata" class="underline left-align section-heading">
 
         {% if is_experiment %}
           {% if instance.sra_ids.count %}
-            <strong>SRA:</strong>
+            <strong>Raw reads:</strong>
             <ul>
               {% for sra in instance.sra_ids.all %}
                 <li>
@@ -423,7 +423,7 @@ <h2 id="metadata" class="underline left-align section-heading">
               {% endfor %}
             </ul>
           {% else %}
-            <p><strong>SRA:</strong> No associated SRAs </p>
+            <p><strong>Raw reads:</strong> No associated raw reads </p>
           {% endif %}
         {% endif %}
       {% endif %}
diff --git a/dataset/views/scoreset.py b/dataset/views/scoreset.py
@@ -63,6 +63,7 @@ def get_context_data(self, **kwargs):
         order_by = "id"  # instance.primary_hgvs_column
         variants = instance.children.order_by("{}".format(order_by))[:10]
         context["variants"] = variants
+        # instance get the count_column from dataset, while instance.children get the count_column from variant.
         context["score_columns"] = instance.score_columns
         context["count_columns"] = instance.count_columns
 
@@ -107,9 +108,26 @@ def get_ajax(self, *args, **kwargs):
         for variant in variants:
             row = {}
             if type_ == "counts":
-                v_data = variant.count_data
+                # Reorder the columns cause variants have different order from score set.
+                variant_dict = variant.data["count_data"]
+                correct_order = instance.count_columns[3:]
+                ordered_dict_items = [
+                    (k, variant_dict[k]) for k in correct_order
+                ]
+                v_data = variant.count_data[:3]
+                for o in ordered_dict_items:
+                    v_data.append(o[1])
+                # v_data = variant.count_data
             else:
-                v_data = variant.score_data
+                # Reorder the columns because variants have different order from score set table.
+                variant_dict = variant.data["score_data"]
+                correct_order = instance.score_columns[3:]
+                ordered_dict_items = [
+                    (k, variant_dict[k]) for k in correct_order
+                ]
+                v_data = variant.score_data[:3]
+                for o in ordered_dict_items:
+                    v_data.append(o[1])
 
             for i, data in enumerate(v_data):
                 if isinstance(data, float):
@@ -167,7 +185,6 @@ def form_valid(self, form: Dict[str, Any]) -> HttpResponseRedirect:
             profile = self.request.user.profile
             profile.clear_submission_errors()
             profile.save()
-
             self.save_forms(form)
             messages.success(self.request, self.get_success_message())
         except Exception as error:
@@ -220,7 +237,6 @@ def get_success_message(self) -> str:
     @transaction.atomic()
     def save_forms(self, forms: Dict[str, Any]) -> Dict[str, Any]:
         scoreset_form: ScoreSetForm = forms["scoreset_form"]
-
         with create_revision():
             scoreset: ScoreSet = scoreset_form.save(commit=True)
             self.object: ScoreSet = scoreset
@@ -357,6 +373,7 @@ def dispatch(self, request, *args, **kwargs) -> HttpResponseRedirect:
 
         return super().dispatch(request, *args, **kwargs)
 
+    # Create a new scoreset will call this method
     def post(self, request, *args, **kwargs):
         """
         Handles POST requests, instantiating a form instance with the passed
@@ -373,7 +390,6 @@ def post(self, request, *args, **kwargs):
 
         scoreset_form: ScoreSetForm = forms.pop("scoreset_form")
         valid &= scoreset_form.is_valid(targetseq=target_form.get_targetseq())
-
         # Check that if AA sequence, dataset defined pro variants only.
         if (
             target_form.sequence_is_protein
@@ -392,7 +408,6 @@ def post(self, request, *args, **kwargs):
         # Put forms back into forms dictionary.
         forms["scoreset_form"] = scoreset_form
         forms["target_gene_form"] = target_form
-
         if valid:
             return self.form_valid(forms)
         else:
@@ -423,6 +438,7 @@ def get_context_data(self, **kwargs):
         return context
 
     @transaction.atomic()
+    # Saving a new scoreset calls this method.
     def save_forms(self, forms: Dict[str, Any]) -> Dict[str, Any]:
         """Called by form_valid when all forms are ready to be saved."""
         forms = super().save_forms(forms=forms)
@@ -516,16 +532,12 @@ def post(self, request, *args, **kwargs):
         """
         # Store reference to object that will be created later
         self.object: ScoreSet = self.get_object()
-
         forms = self.get_form()
         valid = True
-
         if self.object.private:
             target_form: TargetGeneForm = forms.pop("target_gene_form")
             scoreset_form: ScoreSetForm = forms.pop("scoreset_form")
-
             valid &= target_form.is_valid()
-
             if not self.object.get_target().match_sequence(
                 sequence=target_form.get_targetseq()
             ):
@@ -541,7 +553,6 @@ def post(self, request, *args, **kwargs):
             valid &= scoreset_form.is_valid(
                 targetseq=target_form.get_targetseq()
             )
-
             # Check that if AA sequence, dataset defined pro variants only,
             # but only if new files have been uploaded.
             if (
@@ -558,20 +569,22 @@ def post(self, request, *args, **kwargs):
 
             # Check remaining forms which do not need special treatment
             valid &= all(form.is_valid() for _, form in forms.items())
-
             # Put forms back into forms dictionary just in case
             forms["scoreset_form"] = scoreset_form
             forms["target_gene_form"] = target_form
         else:
             scoreset_form: ScoreSetForm = forms.pop("scoreset_form")
             valid &= scoreset_form.is_valid()
+            # Without this one, the forms will be empty so that users can't edit public score set.
+            forms["scoreset_form"] = scoreset_form
 
         if valid:
             return self.form_valid(forms)
         else:
             return self.form_invalid(forms)
 
     @transaction.atomic()
+    # Save editing result calls this method. ss_form links to scoreset count_data.
     def save_forms(self, forms: Dict[str, Any]) -> Dict[str, Any]:
         """Called by form_valid when all forms are ready to be saved."""
         forms = super().save_forms(forms=forms)
diff --git a/docker-compose-dev.yml b/docker-compose-dev.yml
@@ -21,7 +21,7 @@ services:
       - DJANGO_SETTINGS_MODULE=settings.development
 
   database:
-    image: mavedb/postgres:dev
+    image: postgres:9.6
     build:
       context: docker/postgres
     volumes:
diff --git a/docker-compose-prod.yml b/docker-compose-prod.yml
@@ -16,7 +16,7 @@ services:
       - DJANGO_SETTINGS_MODULE=settings.production
 
   database:
-    image: mavedb/postgres:prod
+    image: postgres:9.6
     build:
       context: docker/postgres
     restart: unless-stopped
diff --git a/main/management/commands/addpmid.py b/main/management/commands/addpmid.py
@@ -9,7 +9,7 @@
 class Command(BaseCommand):
     def add_arguments(self, parser):
         parser.add_argument("--urn", type=str, help="Dataset URN")
-        parser.add_argument("--pmid", type=str, help="PubMed identifier")
+        parser.add_argument("--pmid", type=str, help="PubMed ID")
 
     def handle(self, *args, **kwargs):
         urn = kwargs.get("urn", None)
diff --git a/manager/tests/test_forms.py b/manager/tests/test_forms.py
@@ -37,8 +37,7 @@ def test_field_validation(self):
             f"{urn} is not a valid urn." in form.errors[urn_field_name]
         )
         self.assertTrue(
-            f"{pmid} is not a valid PubMed identifier."
-            in form.errors[pmid_field_name]
+            f"{pmid} is not a valid PubMed ID." in form.errors[pmid_field_name]
         )
 
         # Fields are valid
diff --git a/metadata/migrations/0007_auto_20210825_1634.py b/metadata/migrations/0007_auto_20210825_1634.py
diff --git a/metadata/models.py b/metadata/models.py
diff --git a/metadata/validators.py b/metadata/validators.py
diff --git a/search/forms.py b/search/forms.py
diff --git a/variant/validators/variant.py b/variant/validators/variant.py

Original file line number	Diff line number	Diff line change
`@@ -6,5 +6,5 @@`
`6`	`6`	`"md_privacy": "",`
`7`	`7`	`"md_terms": "",`
`8`	`8`	`"md_usage_guide": "",`
`9`		`- "version": "2.0.2"`
	`9`	`+ "version": "2.0.3"`
`10`	`10`	`}`