diff --git a/doc/config.rst b/doc/config.rst
index bb7d27e4ee76bfdd687c33db0955961cb16ef83f..8d4192f0fd0777d778e37405099adf45336f9464 100644
--- a/doc/config.rst
+++ b/doc/config.rst
@@ -236,13 +236,13 @@ DEFAULT_ASSEMBLY
`Default value:` ``hg19``
PROTEIN_LINK_EXPIRATION
- Expiration time for cached transcript->protein links from the NCBI (in
+ Expiration time for cached transcript<->protein links from the NCBI (in
seconds).
`Default value:` `60 * 60 * 24 * 30` (30 days)
NEGATIVE_PROTEIN_LINK_EXPIRATION
- Expiration time for cached negative transcript->protein links from the NCBI
+ Expiration time for cached negative transcript<->protein links from the NCBI
(in seconds).
`Default value:` `60 * 60 * 24 * 5` (5 days)
diff --git a/migrations/versions/3492d2ee8884_transcript_protein_links_have_nullable_.py b/migrations/versions/3492d2ee8884_transcript_protein_links_have_nullable_.py
new file mode 100644
index 0000000000000000000000000000000000000000..607953558f4c5293a0a5118ebf78908956be8053
--- /dev/null
+++ b/migrations/versions/3492d2ee8884_transcript_protein_links_have_nullable_.py
@@ -0,0 +1,59 @@
+"""Transcript protein links have nullable transcript and unique protein
+
+Revision ID: 3492d2ee8884
+Revises: 4bafcc5086dd
+Create Date: 2015-09-25 15:11:45.562392
+
+"""
+
+from __future__ import unicode_literals
+
+# revision identifiers, used by Alembic.
+revision = '3492d2ee8884'
+down_revision = u'4bafcc5086dd'
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# We are adding a unique constraint here, so actually we should first make
+# sure there are no duplicate entries. However, this is highly unlikely, so we
+# don't bother prepping the migration for that.
+#
+# http://skien.cc/blog/2014/01/31/adding-unique-contraints-after-the-fact-in-sqlalchemy/
+
+
+# We want to be compatible with at least SQLite and PostgreSQL. This means
+# using `batch_alter_table` for operations yielding an ALTER TABLE statement.
+# However, we also have indices on the table and this causes problems with
+# `batch_alter_table` (it seems indices are copied too, under the same name,
+# which is invalid). To work around this, we wrap the batch operations in drop
+# and create statements for the indices.
+#
+# http://alembic.readthedocs.org/en/latest/batch.html
+
+
+def upgrade():
+ ### commands auto generated by Alembic - please adjust! ###
+ op.drop_index('ix_transcript_protein_links_transcript_accession', table_name='transcript_protein_links')
+ op.drop_index('ix_transcript_protein_links_protein_accession', table_name='transcript_protein_links')
+ with op.batch_alter_table('transcript_protein_links') as batch_op:
+ batch_op.alter_column('transcript_accession',
+ existing_type=sa.VARCHAR(length=20),
+ nullable=True)
+ op.create_index(op.f('ix_transcript_protein_links_transcript_accession'), 'transcript_protein_links', ['transcript_accession'], unique=True)
+ op.create_index(op.f('ix_transcript_protein_links_protein_accession'), 'transcript_protein_links', ['protein_accession'], unique=True)
+ ### end Alembic commands ###
+
+
+def downgrade():
+ ### commands auto generated by Alembic - please adjust! ###
+ op.drop_index(op.f('ix_transcript_protein_links_transcript_accession'), table_name='transcript_protein_links')
+ op.drop_index(op.f('ix_transcript_protein_links_protein_accession'), table_name='transcript_protein_links')
+ with op.batch_alter_table('transcript_protein_links') as batch_op:
+ batch_op.alter_column('transcript_accession',
+ existing_type=sa.VARCHAR(length=20),
+ nullable=False)
+ op.create_index('ix_transcript_protein_links_transcript_accession', 'transcript_protein_links', ['transcript_accession'], unique=True)
+ op.create_index('ix_transcript_protein_links_protein_accession', 'transcript_protein_links', ['protein_accession'], unique=False)
+ ### end Alembic commands ###
diff --git a/mutalyzer/config/default_settings.py b/mutalyzer/config/default_settings.py
index f985e8ce1179987f07f9d63a71b13ef707090a64..be79de5c8f37a38f8b87c9e268a2bfb8d98d023a 100644
--- a/mutalyzer/config/default_settings.py
+++ b/mutalyzer/config/default_settings.py
@@ -65,10 +65,10 @@ LRG_PREFIX_URL = 'ftp://ftp.ebi.ac.uk/pub/databases/lrgex/SCHEMA_1_7_ARCHIVE/'
# Allow for this fraction of errors in batch jobs.
BATCH_JOBS_ERROR_THRESHOLD = 0.05
-# Expiration time for transcript->protein links from the NCBI (in seconds).
+# Expiration time for transcript<->protein links from the NCBI (in seconds).
PROTEIN_LINK_EXPIRATION = 60 * 60 * 24 * 30
-# Expiration time for negative transcript->protein links from the NCBI (in
+# Expiration time for negative transcript<->protein links from the NCBI (in
# seconds).
NEGATIVE_PROTEIN_LINK_EXPIRATION = 60 * 60 * 24 * 5
diff --git a/mutalyzer/db/models.py b/mutalyzer/db/models.py
index 87a87c88d31faa169a5a2d45df9e6bc8d52970a4..62877968e7fbdd1b5fb2d457f590efc44d01fe10 100644
--- a/mutalyzer/db/models.py
+++ b/mutalyzer/db/models.py
@@ -224,19 +224,23 @@ class TranscriptProteinLink(db.Base):
id = Column(Integer, primary_key=True)
#: Accession number for the transcript, not including the version number
- #: (e.g., ``NM_018195`, ``XM_005270562``, ``NR_015380``).
- transcript_accession = Column(String(20), nullable=False, index=True,
+ #: (e.g., ``NM_018195`, ``XM_005270562``, ``NR_015380``). If `NULL`, the
+ #: record states that no transcript is linked to the protein.
+ transcript_accession = Column(String(20), nullable=True, index=True,
unique=True)
#: Accession number for the protein, not including the version number
#: (e.g., ``NP_060665``, ``XP_005258635``). If `NULL`, the record states
- #: that no protein is linked to the transcript by the NCBI.
- protein_accession = Column(String(20), index=True)
+ #: that no protein is linked to the transcript.
+ protein_accession = Column(String(20), nullable=True, index=True,
+ unique=True)
#: Date and time of creation.
added = Column(DateTime)
- def __init__(self, transcript_accession, protein_accession=None):
+ def __init__(self, transcript_accession=None, protein_accession=None):
+ if transcript_accession is None and protein_accession is None:
+ raise ValueError('Link must have a transcript or protein')
self.transcript_accession = transcript_accession
self.protein_accession = protein_accession
self.added = datetime.now()
diff --git a/mutalyzer/db/queries.py b/mutalyzer/db/queries.py
index 7c54d137fa19e5ff0b8459a3df305ec4241c9d2e..ab4e814e5718737c46fac971d066b65e6c5206cc 100644
--- a/mutalyzer/db/queries.py
+++ b/mutalyzer/db/queries.py
@@ -12,6 +12,7 @@ from __future__ import unicode_literals
from datetime import datetime, timedelta
from sqlalchemy import and_, or_
+import sqlalchemy.exc
from mutalyzer.config import settings
from mutalyzer.db import session
@@ -55,12 +56,17 @@ def pop_batch_queue_item(batch_job):
return item, flags
-def get_transcript_protein_link(transcript_accession):
+def get_transcript_protein_link(accession, reverse=False):
"""
Get a cached link between a transcript and a protein that is not expired
according to the configuration settings `PROTEIN_LINK_EXPIRATION` and
`NEGATIVE_PROTEIN_LINK_EXPIRATION`.
+ :arg str accession: Accession number to lookup link for.
+ :arg bool reverse: If `True`, `accession` is assumed to be a protein
+ accession number, otherwise `accession` is assumed to be a transcript
+ accession number.
+
Note that the link may be negative, i.e., the knowledge that no link
exists can also be cached. In that case, the `protein_accession` field of
the resulting `TranscriptProteinLink` object is `None`.
@@ -72,31 +78,57 @@ def get_transcript_protein_link(transcript_accession):
negative_link_datetime = datetime.now() - \
timedelta(seconds=settings.NEGATIVE_PROTEIN_LINK_EXPIRATION)
+ # Query column must have `accession`, other column has the value we're
+ # probably interested in.
+ query_column = TranscriptProteinLink.transcript_accession
+ other_column = TranscriptProteinLink.protein_accession
+
+ if reverse:
+ # Lookup by protein accession instead of transcript accession.
+ query_column, other_column = other_column, query_column
+
return TranscriptProteinLink.query \
- .filter_by(transcript_accession=transcript_accession) \
- .filter(or_(
- and_(TranscriptProteinLink.protein_accession != None,
- TranscriptProteinLink.added >= link_datetime),
- and_(TranscriptProteinLink.protein_accession == None,
- TranscriptProteinLink.added >= negative_link_datetime))) \
+ .filter_by(transcript_accession=accession) \
+ .filter(
+ query_column == accession,
+ or_(
+ and_(other_column.isnot(None),
+ TranscriptProteinLink.added >= link_datetime),
+ and_(other_column.is_(None),
+ TranscriptProteinLink.added >= negative_link_datetime))
+ ) \
.first()
-def update_transcript_protein_link(transcript_accession,
+def update_transcript_protein_link(transcript_accession=None,
protein_accession=None):
"""
Update cached link between a transcript and a protein, or create it if it
doesn't exist yet.
"""
- link = TranscriptProteinLink.query \
- .filter_by(transcript_accession=transcript_accession) \
- .first()
+ if transcript_accession is None and protein_accession is None:
+ raise ValueError('Link must have a transcript or protein')
+
+ # Filter clauses to find links for either of the given accession numbers.
+ clauses = []
+ if transcript_accession is not None:
+ clauses.append(TranscriptProteinLink.transcript_accession ==
+ transcript_accession)
+ if protein_accession is not None:
+ clauses.append(TranscriptProteinLink.protein_accession ==
+ protein_accession)
+
+ # Delete any related existing links.
+ links = TranscriptProteinLink.query.filter(or_(*clauses))
+ session.delete(links)
+ session.commit()
- if link is not None:
- link.protein_accession = protein_accession
- link.added = datetime.now()
- else:
- link = TranscriptProteinLink(transcript_accession, protein_accession)
+ # There is a race condition here between deleting old links and adding the
+ # new one. It's extremely unlikely to go wrong, and we can safely ignore
+ # it anyway.
+ link = TranscriptProteinLink(transcript_accession, protein_accession)
+ try:
session.add(link)
-
- session.commit()
+ session.commit()
+ except sqlalchemy.exc.IntegrityError:
+ session.rollback()