PlanemoLintBear.py: Add linter bear for planemo

Added a linter bear for planemo lint
Used `planemo lint` command

Closes #1321

bears/planemo/PlanemoLintBear.py

@@ -0,0 +1,41 @@
+import os
+import shlex
+
+from coalib.bearlib.abstractions.Linter import linter
+from dependency_management.requirements.PipRequirement import PipRequirement
+from coalib.results.RESULT_SEVERITY import RESULT_SEVERITY
+from coalib.settings.Setting import typed_list
+
+
+@linter(executable='planemo',
+        output_format='regex',
+        output_regex=r'..\s(?P<severity>\w*:)(?P<message>.*)',
+        severity_map={'WARNING:': RESULT_SEVERITY.MAJOR,
+                      'CHECK:': RESULT_SEVERITY.NORMAL,
+                      'INFO:': RESULT_SEVERITY.INFO})
+class PlanemoLintBear:
+    """
+    Checks the code with pylint. This will run pylint over each file
+    separately.
+    """
+    LANGUAGES = {'xml'}
+    REQUIREMENTS = {PipRequirement('planemo', '0.36')}
+    AUTHORS = {'The coala developers'}
+    AUTHORS_EMAILS = {'[email protected]'}
+    LICENSE = 'AGPL-3.0'
+    CAN_DETECT = {'Syntax'}
+
+    @staticmethod
+    def create_arguments(filename, file, config_file,):
+        """
+        :param pylint_disable:     Disable the message, report, category or
+                                   checker with the given id(s).
+        :param pylint_enable:      Enable the message, report, category or
+                                   checker with the given id(s).
+        :param pylint_cli_options: Any command line options you wish to be
+                                   passed to pylint.
+        :param pylint_rcfile:      The rcfile for PyLint.
+        """
+        args = ('lint',)
+
+        return args + (filename,)

test-requirements.txt

@@ -6,3 +6,4 @@ pytest-timeout~=1.2
 pytest-xdist~=1.15
 requests_mock~=0.7.0
 wheel~=0.29
+planemo~=0.36

tests/planemo/PlanemoLintBearTest.py

@@ -0,0 +1,28 @@
+import os
+import re
+from queue import Queue
+from shutil import which
+from unittest.case import skipIf
+
+from bears.planemo.PlanemoLintBear import PlanemoLintBear
+from coalib.testing.LocalBearTestHelper import LocalBearTestHelper
+from coalib.settings.Section import Section
+from coalib.settings.Setting import Setting
+
+
+@skipIf(which('planemo') is None, 'Planemo is not installed')
+class PlanemoLintBearTest(LocalBearTestHelper):
+
+    def setUp(self):
+        self.section = Section('test section')
+        self.uut = PlanemoLintBear(self.section, Queue())
+        self.test_file = os.path.join(os.path.dirname(__file__),
+                                      'test_files',
+                                      'planemolint_test.xml')
+
+    def test_run(self):
+        self.check_validity(
+            self.uut,
+            [],  # Doesn't matter, planemo lint will parse the file
+            self.test_file,
+            valid=False)

tests/planemo/test_files/planemolint_test.xml

@@ -0,0 +1,66 @@
+<tool id="random_lines1" name="Select random lines" version="2.0.1">
+  <description>from a file</description>
+  <command interpreter="python">random_lines_two_pass.py "${input}" "${out_file1}" "${num_lines}"
+  #if str( $seed_source.seed_source_selector ) == "set_seed":
+      --seed "${seed_source.seed}"
+  #end if
+  </command>
+  <inputs>
+    <param name="num_lines" size="5" type="integer" value="1" label="Randomly select" help="lines"/>
+    <param format="txt" name="input" type="data" label="from"/>
+    <conditional name="seed_source">
+      <param name="seed_source_selector" type="select" label="Set a random seed">
+        <option value="no_seed" selected="True">Don't set seed</option>
+        <option value="set_seed">Set seed</option>
+      </param>
+      <when value="no_seed">
+        <!-- Do nothing here -->
+      </when>
+      <when value="set_seed">
+        <param name="seed" type="text" label="Random seed" />
+      </when>
+    </conditional>
+  </inputs>
+  <outputs>
+    <data format="input" name="out_file1" metadata_source="input"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="num_lines" value="65"/>
+      <param name="input" value="1.bed"/>
+      <param name="seed_source_selector" value="no_seed"/>
+      <output name="out_file1" file="1.bed"/>
+    </test>
+    <test>
+      <param name="num_lines" value="1"/>
+      <param name="input" value="1.bed"/>
+      <param name="seed_source_selector" value="set_seed"/>
+      <param name="seed" value="asdf"/>
+      <output name="out_file1" file="1_bed_random_lines_1_seed_asdf_out.bed"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+This tool selects N random lines from a file, with no repeats, and preserving ordering.
+
+-----
+
+**Example**
+
+Input File::
+
+    chr7  56632  56652   D17003_CTCF_R6  310  +
+    chr7  56736  56756   D17003_CTCF_R7  354  +
+    chr7  56761  56781   D17003_CTCF_R4  220  +
+    chr7  56772  56792   D17003_CTCF_R7  372  +
+    chr7  56775  56795   D17003_CTCF_R4  207  +
+
+Selecting 2 random lines might return this::
+
+    chr7  56736  56756   D17003_CTCF_R7  354  +
+    chr7  56775  56795   D17003_CTCF_R4  207  +
+
+    </help>
+</tool>