From 8543a5bdfece649a6ef659172f04fbd0e4507733 Mon Sep 17 00:00:00 2001
From: Martijn Vermaat <martijn@vermaat.name>
Date: Wed, 22 Oct 2014 13:17:30 +0200
Subject: [PATCH] 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 | 2 ++
.../assemblies/{GRCh36.json => NCBI36.json} | 2 +-
...69eb54_rename_grch36_assembly_to_ncbi36.py | 35 +++++++++++++++++++
mutalyzer/db/models.py | 3 ++
mutalyzer/entrypoints/admin.py | 3 +-
mutalyzer/website/views.py | 15 +++-----
6 files changed, 47 insertions(+), 13 deletions(-)
rename extras/assemblies/{GRCh36.json => NCBI36.json} (99%)
create mode 100644 migrations/versions/2e062969eb54_rename_grch36_assembly_to_ncbi36.py
diff --git a/CHANGES.rst b/CHANGES.rst
index e938eed4..e5ed45f8 100644
--- a/CHANGES.rst
+++ b/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
diff --git a/extras/assemblies/GRCh36.json b/extras/assemblies/NCBI36.json
similarity index 99%
rename from extras/assemblies/GRCh36.json
rename to extras/assemblies/NCBI36.json
index ca0459f6..1b9adb97 100644
--- a/extras/assemblies/GRCh36.json
+++ b/extras/assemblies/NCBI36.json
@@ -1,5 +1,5 @@
{
- "name": "GRCh36",
+ "name": "NCBI36",
"alias": "hg18",
"taxonomy_id": 9606,
"taxonomy_common_name": "Homo sapiens",
diff --git a/migrations/versions/2e062969eb54_rename_grch36_assembly_to_ncbi36.py b/migrations/versions/2e062969eb54_rename_grch36_assembly_to_ncbi36.py
new file mode 100644
index 00000000..279e8d62
--- /dev/null
+++ b/migrations/versions/2e062969eb54_rename_grch36_assembly_to_ncbi36.py
@@ -0,0 +1,35 @@
+"""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 ###
diff --git a/mutalyzer/db/models.py b/mutalyzer/db/models.py
index faa0754c..309fbc55 100644
--- a/mutalyzer/db/models.py
+++ b/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
diff --git a/mutalyzer/entrypoints/admin.py b/mutalyzer/entrypoints/admin.py
index e7c74178..c4308b23 100644
--- a/mutalyzer/entrypoints/admin.py
+++ b/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:
diff --git a/mutalyzer/website/views.py b/mutalyzer/website/views.py
index 84b5cf85..a84aaf13 100644
--- a/mutalyzer/website/views.py
+++ b/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)
--
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