Fix get_bam and get_primary_bam functions

docs/CHANGELOG.rst

@@ -9,6 +9,11 @@ All notable changes to this project are documented in this file.
 Unreleased
 ==========
 
+Fixed
+-----
+* Fix ``get_bam`` and ``get_primary_bam`` functions
+* Fix imports and line breaks for linting
+
 
 ==================
 3.0.0 - 2018-02-21

resdk/query.py

@@ -145,9 +145,9 @@ def __getitem__(self, index):
         # pylint: disable=protected-access
         if not isinstance(index, (slice,) + six.integer_types):
             raise TypeError
-        if ((not isinstance(index, slice) and index < 0) or
-                (isinstance(index, slice) and index.start is not None and index.start < 0) or
-                (isinstance(index, slice) and index.stop is not None and index.stop < 0)):
+        if ((not isinstance(index, slice) and index < 0)
+                or (isinstance(index, slice) and index.start is not None and index.start < 0)
+                or (isinstance(index, slice) and index.stop is not None and index.stop < 0)):
             raise ValueError("Negative indexing is not supported.")
         if isinstance(index, slice) and index.step is not None:
             raise ValueError("`step` parameter in slice is not supported")

resdk/resolwe.py

@@ -9,6 +9,7 @@
 
 """
 from __future__ import absolute_import, division, print_function
+from six.moves.urllib.parse import urljoin
 
 import copy
 import logging
@@ -23,7 +24,6 @@
 import yaml
 # Needed because we mock requests in test_resolwe.py
 from requests.exceptions import ConnectionError  # pylint: disable=redefined-builtin
-from six.moves.urllib.parse import urljoin  # pylint: disable=import-error
 
 from .exceptions import ValidationError, handle_http_exception
 from .query import ResolweQuery
@@ -344,8 +344,8 @@ def run(self, slug=None, input={}, descriptor=None,  # pylint: disable=redefined
         :return: data object that was just created
         :rtype: Data object
         """
-        if ((descriptor and not descriptor_schema) or
-                (not descriptor and descriptor_schema)):
+        if ((descriptor and not descriptor_schema)
+                or (not descriptor and descriptor_schema)):
             raise ValueError("Set both or neither descriptor and descriptor_schema.")
 
         if src is not None:

resdk/resources/base.py

@@ -138,10 +138,10 @@ def __setattr__(self, name, value):
         more comprehensive check is called before save.
 
         """
-        if (hasattr(self, '_original_values') and
-                name in self._original_values and
-                name in self.READ_ONLY_FIELDS and
-                value != self._original_values[name]):
+        if (hasattr(self, '_original_values')
+                and name in self._original_values
+                and name in self.READ_ONLY_FIELDS
+                and value != self._original_values[name]):
             raise ValueError("Can not change read only field {}".format(name))
 
         super(BaseResource, self).__setattr__(name, value)

resdk/resources/data.py

@@ -1,11 +1,11 @@
 """Data resource."""
 from __future__ import absolute_import, division, print_function, unicode_literals
+from six.moves.urllib.parse import urljoin
 
 import json
 import logging
 
 import requests
-from six.moves.urllib.parse import urljoin  # pylint: disable=import-error
 
 from .base import BaseResolweResource
 from .descriptor import DescriptorSchema
@@ -210,9 +210,9 @@ def put_in_download_list(elm, fname):
             field_name = 'output.{}'.format(field_name)
 
         for ann_field_name, ann in self.annotation.items():
-            if (ann_field_name.startswith('output') and
-                    (field_name is None or field_name == ann_field_name) and
-                    ann['value'] is not None):
+            if (ann_field_name.startswith('output')
+                    and (field_name is None or field_name == ann_field_name)
+                    and ann['value'] is not None):
                 if ann['type'].startswith('basic:{}:'.format(field_type)):
                     put_in_download_list(ann['value'], ann_field_name)
                 elif ann['type'].startswith('list:basic:{}:'.format(field_type)):

resdk/resources/sample.py

@@ -19,7 +19,7 @@ def get_reads(self):
 
     def get_bam(self):
         """Return ``bam`` object on the sample."""
-        return self.data.get(type='data:alignment:bam:')
+        return self.data.get(type='data:alignment:bam')
 
     def get_primary_bam(self, fallback_to_bam=False):
         """Return ``primary bam`` object on the sample.
@@ -30,7 +30,7 @@ def get_primary_bam(self, fallback_to_bam=False):
 
         """
         try:
-            return self.data.get(type='data:alignment:bam:primary:')
+            return self.data.get(type='data:alignment:bam:primary')
         except LookupError:
             if fallback_to_bam:
                 return self.get_bam()
@@ -39,11 +39,11 @@ def get_primary_bam(self, fallback_to_bam=False):
 
     def get_macs(self):
         """Return list of ``bed`` objects on the sample."""
-        return self.data.filter(type='data:chipseq:macs14:')
+        return self.data.filter(type='data:chipseq:macs14')
 
     def get_cuffquant(self):
         """Return ``cuffquant`` object on the sample."""
-        return self.data.get(type='data:cufflinks:cuffquant:')
+        return self.data.get(type='data:cufflinks:cuffquant')
 
 
 class Sample(SampleUtilsMixin, BaseCollection):

resdk/scripts/reads.py

@@ -73,8 +73,8 @@ def upload_reads():
             print("\nERROR: Incorrect file path(s).\n")
             exit(1)
     else:
-        if (all(os.path.isfile(file) for file in args.r1) and
-                all(os.path.isfile(file) for file in args.r2)):
+        if (all(os.path.isfile(file) for file in args.r1)
+                and all(os.path.isfile(file) for file in args.r2)):
             resolwe.run('upload-fastq-paired', {'src1': args.r1, 'src2': args.r2},
                         collections=args.collection)
         else:

resdk/scripts/sequp.py

@@ -243,8 +243,8 @@ def parse_annotation_file(annotation_file):
                 if exp_type:
                     descriptor['experiment_type'] = exp_type
             # Paired-end reads
-            if (annotations[sample_n]['PAIRED_END'] == 'Y' and
-                    annotations[sample_n]['FASTQ_PATH_PAIR']):
+            if (annotations[sample_n]['PAIRED_END'] == 'Y'
+                    and annotations[sample_n]['FASTQ_PATH_PAIR']):
                 rw_reads = annotations[sample_n]['FASTQ_PATH_PAIR'].split(',')
                 slug = 'upload-fastq-paired'
                 input_['src1'] = fw_reads