Fix tests

docs/tutorial-resources.rst

@@ -45,7 +45,7 @@ If you are working with ``resdk`` in an interactive session, the
 logging feature prints useful messages. It will let you know
 what is happening behind the scenes. Read more about
 :ref:`how the logging is configured in resdk<resdk_resdk_logger>`
-or about `Python logging`_ in general. 
+or about `Python logging`_ in general.
 
 .. _`Python logging`: https://docs.python.org/2/howto/logging.html
 .. _`Genialis Platform`: https://app.genialis.com
@@ -57,7 +57,7 @@ In Resolwe, meta-data is stored in the PostgreSQL database tables:
 Data, Sample, Collection, Process, DescriptorSchema, Storage,
 User, and Group. We support data management through the `REST API`_.
 Each table is represented as a REST resource with a corresponding
-endpoint. The Sample table is a special case, represented by the ``sample`` 
+endpoint. The Sample table is a special case, represented by the ``sample``
 resource. More details on samples will be given later.
 
 In ``resdk`` each REST API endpoint has a corresponding class, with
@@ -76,7 +76,7 @@ Data and Processes
 The two most important resources in Resolwe are *process* and *data*.
 A Process stores an algorithm that transforms inputs into outputs. It
 is a blueprint for one step in the analysis. A Data object is an
-instance of a Process. It is a complete record of the process step. 
+instance of a Process. It is a complete record of the process step.
 It remembers the inputs (files, arguments, parameters...), the process
 (the algorithm) and the outputs (files, images, numbers...). In
 addition, Data objects store some useful meta data, making it
@@ -87,10 +87,10 @@ easy to reproduce the dataflow and access information.
 (``mm10_chr19.fasta``) with the *Bowtie* aligner. All you have to do is
 create a Data object, setting the process and inputs. When the Data object
 is created, the platform automatically runs the given process with
-provided inputs, storing all inputs, outputs, and meta data. 
+provided inputs, storing all inputs, outputs, and meta data.
 
-You have already seen how to create and query data objects in the 
-`Download, upload, and annotations tutorial`_. 
+You have already seen how to create and query data objects in the
+`Download, upload, and annotations tutorial`_.
 You will learn the details of running processes to generate new data objects in
 the `Running processes tutorial`_. For now,
 let's just inspect the Bowtie process to learn a little more about it:
@@ -273,7 +273,7 @@ parameter is given, it will be interpreted as a unique identifier ``id`` or
 ``slug``, depending on if it is a number or string.
 
 .. code-block:: python
-   
+
     # Get a Collection object by id
     res.collection.get(128)
 
@@ -304,7 +304,7 @@ dataset using the ``process_type`` attribute:
     data.process_type
 
     # Filter data objects by type
-    res.data.filter(type='data:genome:fasta:')
+    res.data.filter(type='data:genome:fasta')
 
 The following are some examples of filtering of collections, samples and data
 objects:
@@ -336,7 +336,7 @@ objects:
     case_1 = sample_list.get(name='case_1')
 
     # select 'case_1' bam file
-    bam = case_1.data.get(type='data:alignment:bam:')
+    bam = case_1.data.get(type='data:alignment:bam')
 
     # in which collections is sample 'case_1'
     list_collections = case_1.collections
@@ -365,7 +365,7 @@ Python class attributes.
 
     # Access a resource attribute
     res.<resource>.<attribute>
-    
+
     # See a list of a resource's available attributes
     res.<resource>.__dict__.keys()
 

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

@@ -23,7 +23,7 @@
 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 six.moves.urllib.parse import urljoin  # pylint: disable=wrong-import-order
 
 from .exceptions import ValidationError, handle_http_exception
 from .query import ResolweQuery
@@ -344,8 +344,7 @@ 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

@@ -5,7 +5,7 @@
 import logging
 
 import requests
-from six.moves.urllib.parse import urljoin  # pylint: disable=import-error
+from six.moves.urllib.parse import urljoin  # pylint: disable=wrong-import-order
 
 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

resdk/tests/unit/test_relations.py

@@ -6,7 +6,7 @@
 
 import unittest
 
-from mock import MagicMock
+from mock import MagicMock, patch
 
 from resdk.resources.collection import Collection
 from resdk.resources.relation import Relation
@@ -37,7 +37,10 @@ def test_samples(self):
         relation.update()
         self.assertEqual(relation._samples, None)
 
-    def test_collection(self):
+    # I appears it is not possible to deepcopy MagicMocks so we just patch
+    # the deepcopy functionality:
+    @patch('resdk.resources.base.copy')
+    def test_collection(self, copy_mock):
         relation = Relation(id=1, resolwe=MagicMock())
         collection = Collection(id=3, resolwe=MagicMock())
         collection.id = 3  # this is overriden when initialized

resdk/tests/unit/test_resolwe.py

@@ -424,15 +424,22 @@ def test_file_processing(self, resolwe_mock, data_mock):
                     input={"src": "/path/to/file1",
                            "src_list": ["/path/to/file2", "/path/to/file3"]})
 
+    @patch('resdk.resolwe.copy')
     @patch('resdk.resolwe.Resolwe', spec=True)
-    def test_dehydrate_data(self, resolwe_mock):
+    def test_dehydrate_data(self, resolwe_mock, copy_mock):
         data_obj = Data(id=1, resolwe=MagicMock())
         data_obj.id = 1  # this is overriden when initialized
         process = self.process_mock
 
+        # I appears it is not possible to deepcopy MagicMocks so we just patch
+        # the deepcopy functionality:
+        copy_mock.deepcopy = MagicMock(return_value={"genome": data_obj})
         result = Resolwe._process_inputs(resolwe_mock, {"genome": data_obj}, process)
         self.assertEqual(result, {'genome': 1})
 
+        # I appears it is not possible to deepcopy MagicMocks so we just patch
+        # the deepcopy functionality:
+        copy_mock.deepcopy = MagicMock(return_value={"reads": data_obj})
         result = Resolwe._process_inputs(resolwe_mock, {"reads": [data_obj]}, process)
         self.assertEqual(result, {'reads': [1]})
 

setup.cfg

@@ -17,7 +17,7 @@ ignore =
 max-line-length=99
 # Ignore E127: checked by pylint
 # E127 continuation line over-indented for visual indent
-ignore=E127
+ignore=E127,W503
 
 [pydocstyle]
 match-dir = (?!tests|\.).*