Rename GRCh36 to NCBI36

Not sure how this came to be, but NCBI36 was incorrectly named GRCh36.
Changing this, however, breaks the sort order in assembly lists. So we
now sort on the UCSC alias (hg18).

Fixes #8

CHANGES.rst

@@ -19,6 +19,8 @@ Release date to be decided.
   <https://git.lumc.nl/mutalyzer/mutalyzer/issues/30>`_).
 - Fix importing transcript mappings from UCSC database (`GitLab#9
   <https://git.lumc.nl/mutalyzer/mutalyzer/issues/9>`_).
+- Rename GRCh36 to NCBI36 (`GitLab#8
+  <https://git.lumc.nl/mutalyzer/mutalyzer/issues/8>`_).
 
 
 Version 2.0.3

extras/assemblies/GRCh36.json → extras/assemblies/NCBI36.json

 {
-  "name": "GRCh36",
+  "name": "NCBI36",
   "alias": "hg18",
   "taxonomy_id": 9606,
   "taxonomy_common_name": "Homo sapiens",

migrations/versions/2e062969eb54_rename_grch36_assembly_to_ncbi36.py

+"""Rename GRCh36 assembly to NCBI36
+
+Revision ID: 2e062969eb54
+Revises: 402ff01b0d5d
+Create Date: 2014-10-22 13:09:17.336650
+
+"""
+
+from __future__ import unicode_literals
+
+# revision identifiers, used by Alembic.
+revision = '2e062969eb54'
+down_revision = u'402ff01b0d5d'
+
+from alembic import op
+from sqlalchemy import sql
+import sqlalchemy as sa
+
+
+def upgrade():
+    ### commands auto generated by Alembic - please adjust! ###
+    assemblies = sql.table('assemblies',
+                           sql.column('name', sa.String(30)))
+    # https://alembic.readthedocs.org/en/latest/ops.html#alembic.operations.Operations.execute
+    op.execute(assemblies.update().where(assemblies.c.name == op.inline_literal('GRCh36')).values({'name': op.inline_literal('NCBI36')}))
+    ### end Alembic commands ###
+
+
+def downgrade():
+    ### commands auto generated by Alembic - please adjust! ###
+    assemblies = sql.table('assemblies',
+                           sql.column('name', sa.String(30)))
+    # https://alembic.readthedocs.org/en/latest/ops.html#alembic.operations.Operations.execute
+    op.execute(assemblies.update().where(assemblies.c.name == op.inline_literal('NCBI36')).values({'name': op.inline_literal('GRCh36')}))
+    ### end Alembic commands ###

mutalyzer/db/models.py

@@ -267,6 +267,9 @@ class Assembly(db.Base):
     #: NCBI taxonomy name (e.g., ``Homo sapiens``, ``Mus musculus``).
     taxonomy_common_name = Column(String(50), nullable=False)
 
+    #: Criteria to order assemblies by in user-visible lists.
+    order_by_criteria = taxonomy_common_name.asc(), alias.asc()
+
     def __init__(self, name, taxonomy_id, taxonomy_common_name, alias=None):
         self.name = name
         self.taxonomy_id = taxonomy_id

mutalyzer/entrypoints/admin.py

@@ -77,8 +77,7 @@ def list_assemblies():
     List genome assemblies.
     """
     assemblies = Assembly.query \
-        .order_by(Assembly.taxonomy_common_name.asc(),
-                  Assembly.name.asc()) \
+        .order_by(*Assembly.order_by_criteria) \
         .all()
 
     for assembly in assemblies:

mutalyzer/website/views.py

@@ -397,8 +397,7 @@ def position_converter():
                         code=301)
 
     assemblies = Assembly.query \
-        .order_by(Assembly.taxonomy_common_name.asc(),
-                  Assembly.name.asc()) \
+        .order_by(*Assembly.order_by_criteria) \
         .all()
 
     assembly_name_or_alias = request.args.get('assembly_name_or_alias',
@@ -518,8 +517,7 @@ def reference_loader():
     Reference sequence loader form.
     """
     assemblies = Assembly.query \
-        .order_by(Assembly.taxonomy_common_name.asc(),
-                  Assembly.name.asc()) \
+        .order_by(*Assembly.order_by_criteria) \
         .all()
 
     return render_template('reference-loader.html',
@@ -580,8 +578,7 @@ def reference_loader_submit():
                       % (method, unicode(request.form), request.remote_addr))
 
     assemblies = Assembly.query \
-        .order_by(Assembly.taxonomy_common_name.asc(),
-                  Assembly.name.asc()) \
+        .order_by(*Assembly.order_by_criteria) \
         .all()
 
     retriever = Retriever.GenBankRetriever(output)
@@ -749,8 +746,7 @@ def batch_jobs():
     job_type = request.args.get('job_type', 'name-checker')
 
     assemblies = Assembly.query \
-        .order_by(Assembly.taxonomy_common_name.asc(),
-                  Assembly.name.asc()) \
+        .order_by(*Assembly.order_by_criteria) \
         .all()
     assembly_name_or_alias = request.args.get('assembly_name_or_alias',
                                               settings.DEFAULT_ASSEMBLY)
@@ -776,8 +772,7 @@ def batch_jobs_submit():
     batch_file = request.files.get('file')
 
     assemblies = Assembly.query \
-        .order_by(Assembly.taxonomy_common_name.asc(),
-                  Assembly.name.asc()) \
+        .order_by(*Assembly.order_by_criteria) \
         .all()
     assembly_name_or_alias = request.form.get('assembly_name_or_alias',
                                               settings.DEFAULT_ASSEMBLY)