Update dpxdt for better sorting, contig sorting

Also handle travis build issue--we don't want to DL and build pysensembl
hammerlab · Dec 12, 2014 · 6bbc174 · 6bbc174
1 parent 64c7e07
commit 6bbc174
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Showing 12 changed files with 9 additions and 7 deletions.
diff --git a/cycledash/static/js/examine/components/Downloads.js b/cycledash/static/js/examine/components/Downloads.js
@@ -14,6 +14,6 @@ var Downloads = React.createClass({
         link = `/runs/${ this.props.run_id }/download?${ queryString }`;
     return <a className='download-vcf' href={ link }>Download VCF</a>;
   }
-})
+});
 
 module.exports = Downloads;
diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh
@@ -2,7 +2,7 @@
 # Install all deps & build everything for the Python & JS tests.
 set -o errexit
 
-pip install -r <(grep -v 'pysam\|dpxdt' requirements.txt)
+pip install -r <(grep -v 'pysam\|dpxdt\|pyensembl' requirements.txt)
 npm install
 make initenv
 

diff --git a/tests/pdifftests/examine-filter.png b/tests/pdifftests/examine-filter.png
diff --git a/tests/pdifftests/examine-sorted.png b/tests/pdifftests/examine-sorted.png
diff --git a/tests/pdifftests/examine-tooltip.png b/tests/pdifftests/examine-tooltip.png
diff --git a/tests/pdifftests/examine.png b/tests/pdifftests/examine.png
diff --git a/tests/pdifftests/runs-info.png b/tests/pdifftests/runs-info.png
diff --git a/tests/pdifftests/runs.png b/tests/pdifftests/runs.png
diff --git a/tests/pdifftests/validated-run-with-filter.png b/tests/pdifftests/validated-run-with-filter.png
diff --git a/tests/pdifftests/validated-run.png b/tests/pdifftests/validated-run.png
diff --git a/tests/python/test.py b/tests/python/test.py
@@ -1,7 +1,7 @@
 import nose
 
 from cycledash.helpers import underscorize
-from workers.relational_vcfs import vcf_to_csv
+from common.relational_vcf import vcf_to_csv
 
 
 def test_underscorize():

diff --git a/workers/gene_annotator.py b/workers/gene_annotator.py
@@ -18,21 +18,23 @@
 """
 from contextlib import contextmanager
 import csv
-from pyensembl import EnsemblRelease
-from sqlalchemy import select, update, Table, Column
+from sqlalchemy import select, Table, Column
 from sqlalchemy.types import Text, Integer
 
 from workers.shared import (worker, DATABASE_URI, TEMPORARY_DIR,
                             initialize_database, temp_csv,
                             update_extant_columns)
 
+import os
+if not os.environ.get('TRAVIS'):
+    from pyensembl import EnsemblRelease
+
 
 # TODO(tavi) Handle inconsistent states and retries.
 @worker.task
 def annotate(vcf_ids):
     if vcf_ids == False:
-        return  # An error must have occurred earlier 
-
+        return  # An error must have occurred earlier.
     for vcf_id in vcf_ids:
         _annotate_one(vcf_id)