Lint extra

planemo_ext/galaxy/tools/lint_util.py

@@ -0,0 +1,5 @@
+
+
+def is_datasource(tool_xml):
+    """Returns true if the tool is a datasource tool"""
+    return tool_xml.getroot().attrib.get('tool_type', '') == 'data_source'

planemo_ext/galaxy/tools/linters/inputs.py

@@ -1,6 +1,8 @@
+from ..lint_util import is_datasource
 
 
 def lint_inputs(tool_xml, lint_ctx):
+    datasource = is_datasource(tool_xml)
     inputs = tool_xml.findall("./inputs//param")
     num_inputs = 0
     for param in inputs:
@@ -23,10 +25,40 @@ def lint_inputs(tool_xml, lint_ctx):
             if "format" not in param_attrib:
                 lint_ctx.warn("Param input [%s] with no format specified - 'data' format will be assumed.", param_name)
         # TODO: Validate type, much more...
+
+    conditional_selects = tool_xml.findall("./inputs//conditional")
+    for conditional in conditional_selects:
+        select = conditional.find('./param[@type="select"]')
+        # Should conditionals ever not have a select?
+        if not len(select):
+            lint_ctx.info("Conditional without <param type=\"select\" />")
+            continue
+
+        select_options = select.findall('./option[@value]')
+        select_option_ids = [option.attrib['value'] for option in select_options]
+        whens = conditional.findall('./when')
+        when_ids = [when.attrib['value'] for when in whens]
+
+        for select_id in select_option_ids:
+            if select_id not in when_ids:
+                lint_ctx.warn("No <when /> block found for select option '%s'" % select_id)
+
+        for when_id in when_ids:
+            if when_id not in select_option_ids:
+                lint_ctx.warn("No <option /> block found for when block '%s'" % when_id)
+
+    if datasource:
+        for datasource_tag in ('display', 'uihints'):
+            if not any([param.tag == datasource_tag for param in inputs]):
+                lint_ctx.info("%s tag usually present in data sources" % datasource_tag)
+
     if num_inputs:
         lint_ctx.info("Found %d input parameters.", num_inputs)
     else:
-        lint_ctx.warn("Found not input parameters.")
+        if datasource:
+            lint_ctx.info("No input parameters, OK for data sources")
+        else:
+            lint_ctx.warn("Found no input parameters.")
 
 
 def lint_repeats(tool_xml, lint_ctx):

planemo_ext/galaxy/tools/linters/outputs.py

@@ -8,6 +8,10 @@ def lint_output(tool_xml, lint_ctx):
         lint_ctx.warn("Tool contains multiple output sections, behavior undefined.")
 
     num_outputs = 0
+    if len(outputs) == 0:
+        lint_ctx.warn("No outputs found")
+        return
+
     for output in list(outputs[0]):
         if output.tag not in ["data", "collection"]:
             lint_ctx.warn("Unknown element found in outputs [%s]" % output.tag)

planemo_ext/galaxy/tools/linters/tests.py

@@ -1,10 +1,14 @@
-
+from ..lint_util import is_datasource
 
 # Misspelled so as not be picked up by nosetests.
 def lint_tsts(tool_xml, lint_ctx):
     tests = tool_xml.findall("./tests/test")
-    if not tests:
+    datasource = is_datasource(tool_xml)
+
+    if not tests and not datasource:
         lint_ctx.warn("No tests found, most tools should define test cases.")
+    elif datasource:
+        lint_ctx.info("No tests found, that should be OK for data_sources.")
 
     num_valid_tests = 0
     for test in tests:
@@ -24,7 +28,7 @@ def lint_tsts(tool_xml, lint_ctx):
         else:
             num_valid_tests += 1
 
-    if num_valid_tests:
+    if num_valid_tests or datasource:
         lint_ctx.valid("%d test(s) found.", num_valid_tests)
     else:
         lint_ctx.warn("No valid test(s) found.")

planemo_ext/galaxy/tools/linters/xml_order.py

@@ -17,16 +17,37 @@
     'citations',
 ]
 
+DATASOURCE_TAG_ORDER = [
+    'description',
+    'command',
+    'inputs',
+    'request_param_translation',
+    'uihints',
+    'outputs',
+    'options',
+    'help',
+    'citations',
+]
+
 
 # Ensure the XML blocks appear in the correct order prescribed
 # by the tool author best practices.
 def lint_xml_order(tool_xml, lint_ctx):
+    tool_root = tool_xml.getroot()
+
+    if tool_root.attrib.get('tool_type', '') == 'data_source':
+        _validate_for_tags(tool_root, lint_ctx, DATASOURCE_TAG_ORDER)
+    else:
+        _validate_for_tags(tool_root, lint_ctx, TAG_ORDER)
+
+
+def _validate_for_tags(root, lint_ctx, tag_ordering):
     last_tag = None
     last_key = None
-    for elem in list(tool_xml.getroot()):
+    for elem in root:
         tag = elem.tag
-        if tag in TAG_ORDER:
-            key = TAG_ORDER.index(tag)
+        if tag in tag_ordering:
+            key = tag_ordering.index(tag)
             if last_key:
                 if last_key > key:
                     lint_ctx.warn("Best practice violation [%s] elements should come before [%s]" % (tag, last_tag))