PlanemoLintBear.py: Add linter bear for planemo

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

Closes #1321

.ci/generate_bear_requirements.py

@@ -43,6 +43,7 @@
 PINNED_PACKAGES = (
    'radon',
    'click',
+   'lxml',
 )
 
 env = Environment(loader=FileSystemLoader(THIS_DIR))

bear-requirements.txt

@@ -11,10 +11,12 @@ guess-language-spirit~=0.5.2
 html-linter~=0.3.0
 isort~=4.2
 language-check~=1.0
+lxml==3.6.0
 munkres3~=1.0
 mypy-lang~=0.4.6
 nbformat~=4.1
 nltk~=3.2
+planemo~=0.36
 proselint~=0.7.0
 pycodestyle~=2.2
 pydocstyle~=1.1

bears/planemo/PlanemoLintBear.py

@@ -0,0 +1,30 @@
+
+from coalib.bearlib.abstractions.Linter import linter
+from dependency_management.requirements.PipRequirement import PipRequirement
+from coalib.results.RESULT_SEVERITY import RESULT_SEVERITY
+
+
+@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 planemo lint. This will run
+    planemo lint over each file separately.
+    """
+    LANGUAGES = {'galaxy'}
+    REQUIREMENTS = {PipRequirement('planemo', '0.36'),
+                    PipRequirement('lxml', '3.6.0')}
+    AUTHORS = {'The coala developers'}
+    AUTHORS_EMAILS = {'[email protected]'}
+    ASCIINEMA_URL = 'https://asciinema.org/a/0kiduzg55d59nxhm8wuwfvl3n'
+    LICENSE = 'AGPL-3.0'
+    CAN_DETECT = {'Syntax'}
+
+    @staticmethod
+    def create_arguments(filename, file, config_file):
+        args = ('lint',)
+        return args + (filename,)

tests/planemo/PlanemoLintBearTest.py

@@ -0,0 +1,34 @@
+import os
+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
+
+
+@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)
+        self.test_file = os.path.join(os.path.dirname(__file__),
+                                      'test_files',
+                                      'valid_planemo_test.xml')
+        self.check_validity(
+            self.uut,
+            [],  # Doesn't matter, planemo lint will parse the file
+            self.test_file,
+            valid=True)

tests/planemo/test_files/planemolint_test.xml

@@ -0,0 +1,25 @@
+
+<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>
+</tool>

tests/planemo/test_files/valid_planemo_test.xml

@@ -0,0 +1,8 @@
+
+<?xml version="1.0" encoding="UTF-8"?>
+<note>
+   <to>Tove</to>
+   <from>Jani</from>
+   <heading>Reminder</heading>
+   <body>Don't forget me this weekend!</body>
+</note>