Fix index file syntax and fix linting problems

galaxyproject · Dec 8, 2017 · 6ca896f · 6ca896f
1 parent 0ac77ad
commit 6ca896f
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Showing 5 changed files with 11 additions and 6 deletions.
diff --git a/lib/galaxy/datatypes/tabular.py b/lib/galaxy/datatypes/tabular.py
@@ -27,7 +27,6 @@
 )
 from galaxy.util import compression_utils
 from galaxy.util.checkers import is_gzip
-
 from . import dataproviders
 
 if sys.version_info > (3,):
@@ -764,7 +763,7 @@ def set_meta(self, dataset, **kwd):
             index_file = dataset.metadata.spec['tabix_index'].param.new_file(dataset=dataset)
 
         try:
-            pysam.tabix_index(dataset.file_name, index=index_file, preset='vcf')
+            pysam.tabix_index(dataset.file_name, index=index_file.file_name, preset='vcf')
         except Exception as e:
             raise Exception('Error setting VCF.gz metadata: %s' % (str(e)))
         dataset.metadata.tabix_index = index_file

diff --git a/test/unit/datatypes/test_bcf.py b/test/unit/datatypes/test_bcf.py
@@ -2,7 +2,6 @@
     Bcf,
     BcfUncompressed
 )
-
 from .util import (
     get_dataset,
     get_input_files,

diff --git a/test/unit/datatypes/test_cram.py b/test/unit/datatypes/test_cram.py
@@ -1,5 +1,6 @@
+import os
+import pysam
 from galaxy.datatypes.binary import CRAM
-
 from .util import (
     get_dataset,
     get_input_files,
@@ -9,5 +10,9 @@
 def test_cram():
     c = CRAM()
     with get_input_files('2.cram') as input_files, get_dataset(input_files[0], index_attr='cram_index') as dataset:
+        assert os.path.exists(dataset.metadata.cram_index.file_name) is False
+        c.set_index_file(dataset=dataset, index_file=dataset.metadata.cram_index)
+        assert os.path.exists(dataset.metadata.cram_index.file_name) is True
         c.set_meta(dataset)
+        pysam.AlignmentFile(dataset.file_name, index_filename=dataset.metadata.cram_index.file_name)
     assert dataset.metadata.cram_version == '3.0'
diff --git a/test/unit/datatypes/test_vcf.py b/test/unit/datatypes/test_vcf.py
@@ -25,5 +25,5 @@ def test_vcf_gz_set_meta():
     vcf_gz = VcfGz()
     with get_input_files('1.vcf.gz') as input_files, get_dataset(input_files[0], index_attr='tabix_index') as dataset:
         vcf_gz.set_meta(dataset)
-        f = pysam.VariantFile(dataset.file_name, index_filename=dataset.metadata.tabix_index)
+        f = pysam.VariantFile(dataset.file_name, index_filename=dataset.metadata.tabix_index.file_name)
         assert isinstance(f.index, pysam.libcbcf.TabixIndex) is True
diff --git a/test/unit/datatypes/util.py b/test/unit/datatypes/util.py
@@ -15,7 +15,9 @@ def get_dataset(file, index_attr='bam_index', dataset_id=1, has_data=True):
     dataset.metadata = Bunch()
     with get_input_files(file) as input_files, get_tmp_path() as index_path:
         dataset.file_name = input_files[0]
-        setattr(dataset.metadata, index_attr, index_path)
+        index = Bunch()
+        index.file_name = index_path
+        setattr(dataset.metadata, index_attr, index)
         yield dataset