Add --macros flag to tool_init command.

Will pull citations, requirements, stdio, and version_command out into an imported macros file. Subsequent suite definitions in the same directory generated with --macros will reuse the same file.

Fixes to lint and extensions to testing to enable this.

planemo/commands/cmd_lint.py

@@ -34,6 +34,7 @@ def cli(ctx, path, report_level="all", fail_level="warn"):
     exit = 0
     lint_args = dict(level=report_level, fail_level=fail_level)
     tools = load_tool_elements_from_path(path, load_exception_handler)
+    valid_tools = 0
     for (tool_path, tool_xml) in tools:
         if tool_xml.getroot().tag != "tool":
             if ctx.verbose:
@@ -42,6 +43,10 @@ def cli(ctx, path, report_level="all", fail_level="warn"):
         info("Linting tool %s" % tool_path)
         if not lint_xml(tool_xml, **lint_args):
             exit = 1
+        else:
+            valid_tools += 1
+    if exit == 0 and valid_tools == 0:
+        exit = 2
     sys.exit(exit)
 
 

planemo/commands/cmd_tool_init.py

@@ -4,6 +4,9 @@
 from planemo import io
 from planemo import tool_builder
 
+REUSING_MACROS_MESSAGE = ("Macros file macros.xml already exists, assuming "
+                          " it has relevant planemo-generated definitions.")
+
 
 # --input_format
 # --output_format
@@ -169,6 +172,13 @@
     help=("For use with --example_commmand, generate a tool test case from "
           "the supplied example."),
 )
+@click.option(
+    "--macros",
+    is_flag=True,
+    default=None,
+    prompt=False,
+    help="Generate a macros.xml for reuse across many tools.",
+)
 @click.command("tool_init")
 @pass_context
 def cli(ctx, **kwds):
@@ -186,6 +196,12 @@ def cli(ctx, **kwds):
     tool_description = tool_builder.build(**kwds)
     open(output, "w").write(tool_description.contents)
     io.info("Tool written to %s" % output)
+    macros = kwds["macros"]
+    macros_file = "macros.xml"
+    if macros and not os.path.exists(macros_file):
+        open(macros_file, "w").write(tool_description.macro_contents)
+    else:
+        io.info(REUSING_MACROS_MESSAGE)
     if tool_description.test_files:
         if not os.path.exists("test-data"):
             io.info("No test-data directory, creating one.")

planemo/tool_builder.py

@@ -10,6 +10,16 @@
 {%- if description %}
     <description>{{ description }}</description>
 {% endif %}
+{%- if macros %}
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+{%- if version_command %}
+    <expand macro="version_command" />
+{% endif %}
+{%- else %}
     <stdio>
         <exit_code range="1:" />
     </stdio>
@@ -24,6 +34,7 @@
 {%- if version_command %}
     <version_command>{{ version_command }}</version_command>
 {%- endif %}
+{% endif %}
     <command><![CDATA[
 {%- if command %}
         {{ command }}
@@ -62,16 +73,53 @@
         TODO: Fill in help.
 {%- endif %}
     ]]></help>
+{%- if macros %}
+    <expand macro="citations" />
+{%- else %}
 {%- if doi %}
     <citations>
 {%- for single_doi in doi %}
         <citation type="doi">{{ single_doi }}</citation>
 {%- endfor %}
     </citations>
 {%- endif %}
+{%- endif %}
 </tool>
 """
 
+MACROS_TEMPLATE = """<macros>
+    <xml name="requirements">
+        <requirements>
+{%- for requirement in requirements %}
+        {{ requirement }}
+{%- endfor %}
+            <yield/>
+{%- for container in containers %}
+        {{ container }}
+{%- endfor %}
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:" />
+        </stdio>
+    </xml>
+    <xml name="citations">
+        <citations>
+{%- for single_doi in doi %}
+            <citation type="doi">{{ single_doi }}</citation>
+{%- endfor %}
+            <yield />
+        </citations>
+    </xml>
+{%- if version_command %}
+    <xml name="version_command">
+        <version_command>{{ version_command }}</version_command>
+    </xml>
+{%- endif %}
+</macros>
+"""
+
 
 def build(**kwds):
     if Template is None:
@@ -131,16 +179,20 @@ def build(**kwds):
     kwds["tests"] = tests
 
     # Render tool content from template.
-    contents = _render_tool(kwds)
+    contents = _render(kwds)
+
+    macro_contents = None
+    if kwds["macros"]:
+        macro_contents = _render(kwds, MACROS_TEMPLATE)
 
-    return ToolDescription(contents, test_files)
+    return ToolDescription(contents, macro_contents, test_files)
 
 
-def _render_tool(kwds):
+def _render(kwds, template_str=TOOL_TEMPLATE):
     """ Apply supplied template variables to TOOL_TEMPLATE to generate
     the final tool.
     """
-    template = Template(TOOL_TEMPLATE)
+    template = Template(template_str)
     contents = template.render(**kwds)
     return contents
 
@@ -227,8 +279,9 @@ def _find_command(kwds):
 
 class ToolDescription(object):
 
-    def __init__(self, contents, test_files):
+    def __init__(self, contents, macro_contents, test_files):
         self.contents = contents
+        self.macro_contents = macro_contents
         self.test_files = test_files
 
 

tests/test_build_and_lint.py

@@ -1,28 +1,21 @@
-
+import os
 from .test_utils import CliTestCase
 
 
-INIT_COMMAND = [
-    "tool_init", "--force",
-    "--id", "seqtk_seq",
-    "--name", "Convert to FASTA (seqtk)",
-    "--requirement", "seqtk@1.0-r68",
-    "--example_command", "seqtk seq -a 2.fastq > 2.fasta",
-    "--example_input", "2.fastq",
-    "--example_output", "2.fasta",
-    "--test_case",
-    "--help_text", "The help text.",
-    "--doi", "10.1101/014043"
-]
-
-
 class BuildAndLintTestCase(CliTestCase):
 
     def test_build_and_lint(self):
         with self._isolate():
             self._check_exit_code(_init_command())
             self._check_lint(exit_code=0)
 
+    def test_build_and_lint_with_macros(self):
+        with self._isolate() as f:
+            self._check_exit_code(_init_command(macros=True))
+            self._check_lint(exit_code=0)
+            macros_file = os.path.join(f, "macros.xml")
+            assert os.path.exists(macros_file)
+
     def test_lint_fails_if_no_help(self):
         with self._isolate():
             self._check_exit_code(_init_command(help_text=False))
@@ -43,7 +36,7 @@ def _check_lint(self, exit_code=0):
         self._check_exit_code(lint_cmd, exit_code=exit_code)
 
 
-def _init_command(test_case=True, help_text=True, doi=True):
+def _init_command(test_case=True, help_text=True, doi=True, macros=False):
     command = [
         "tool_init", "--force",
         "--id", "seqtk_seq",
@@ -59,4 +52,6 @@ def _init_command(test_case=True, help_text=True, doi=True):
         command.extend(["--help_text", "The help text."])
     if doi:
         command.extend(["--doi", "10.1101/014043"])
+    if macros:
+        command.append("--macros")
     return command

tests/test_utils.py

@@ -43,6 +43,7 @@ def _check_exit_code(self, command_list, exit_code=0):
                 result.output,
             )
             raise AssertionError(message)
+        return result
 
 
 __all__ = [