Merge remote-tracking branch 'upstream/master' into serve-test

HISTORY.rst

@@ -6,11 +6,32 @@ History
 .. to_doc
 
 ---------------------
-0.75.0 (2021-07-23)
+0.75.0.dev0
 ---------------------
 
 
 
+---------------------
+0.74.8 (2021-10-10)
+---------------------
+
+* Exclude click 8.0.2. `Pull Request 1196`_
+* Add tool version numbers to autoupdate logging (thanks to `@simonbray`_).
+  `Pull Request 1188`_
+* Allow tool autoupdate without conda installation (thanks to `@simonbray`_).
+  `Pull Request 1193`_
+* use correct key execution_problem in template (thanks to `@bernt-matthias`_).
+  `Pull Request 1195`_
+
+---------------------
+0.74.7 (2021-09-21)
+---------------------
+
+* Fix documentation to include `--download_outputs` flag (thanks to
+  `@simonbray`_). `Pull Request 1184`_
+* Select refgenie config based on Galaxy version `Pull Request 1187`_
+* Extend autoupdate subcommand to workflows (thanks to `@simonbray`_). `Pull
+  Request 1151`_
 
 ---------------------
 0.74.6 (2021-07-23)
@@ -1740,6 +1761,13 @@ History
   tools - and more experimental features involving Docker and Homebrew. 7d07782_
 
 .. github_links
+.. _Pull Request 1188: https://github.com/galaxyproject/planemo/pull/1188
+.. _Pull Request 1193: https://github.com/galaxyproject/planemo/pull/1193
+.. _Pull Request 1195: https://github.com/galaxyproject/planemo/pull/1195
+.. _Pull Request 1196: https://github.com/galaxyproject/planemo/pull/1196
+.. _Pull Request 1184: https://github.com/galaxyproject/planemo/pull/1184
+.. _Pull Request 1187: https://github.com/galaxyproject/planemo/pull/1187
+.. _Pull Request 1151: https://github.com/galaxyproject/planemo/pull/1151
 .. _Pull Request 1153: https://github.com/galaxyproject/planemo/pull/1153
 .. _Pull Request 1179: https://github.com/galaxyproject/planemo/pull/1179
 .. _Pull Request 1180: https://github.com/galaxyproject/planemo/pull/1180

docs/autoupdate.rst

@@ -29,6 +29,24 @@ Formatting tools
   - A token ``@TOOL_VERSION@`` should be created which corresponds to the version number of the main requirement.
   - Optionally, a token ``@VERSION_SUFFIX@`` should be created, which should be an integer representing the number of times the XML wrapper has been updated since ``@TOOL_VERSION@`` was updated.
 
+Updating workflows
+=============================
+
+The ``autoupdate`` subcommand can also be used to automatically update workflows so that they are using the most recent Galaxy tools available.
+
+::
+
+    planemo autoupdate workflow.ga
+
+In the basic usage, a local Galaxy instance will be spun up and the workflow uploaded, refactored to include the most recent tool versions, and re-downloaded.
+
+Workflows can also be updated against an external galaxy, for example:
+
+::
+
+    planemo autoupdate workflow.ga --profile usegalaxy-eu
+
+In this case, the workflow returned will contain the most recent tool and subworkflow versions available on that Galaxy server.
 
 Implementing an autoupdate CI job
 =================================

planemo/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 
-__version__ = '0.75.0'
+__version__ = '0.75.0.dev0'
 
 
 PROJECT_NAME = "planemo"

planemo/autoupdate.py

@@ -5,6 +5,8 @@
 import re
 import xml.etree.ElementTree as ET
 
+import packaging.version
+import requests
 from galaxy.tool_util.deps import conda_util
 
 import planemo.conda
@@ -51,7 +53,11 @@ def check_conda(tool_name, ctx, **kwds):
     """
     conda_context = planemo.conda.build_conda_context(ctx, **kwds)
     if not conda_context.is_conda_installed():
-        error("Conda is not installed! Try running planemo conda_init.")
+        # check directly via Anaconda API
+        r = requests.get('https://api.anaconda.org/search', params={'name': tool_name})
+        search_results = sum([n['versions'] for n in r.json() if n['name'] == tool_name and n['owner'] in kwds['conda_ensure_channels']], [])
+        return sorted(search_results, key=lambda n: packaging.version.parse(n))[-1]
+
     target = planemo.conda.conda_util.CondaTarget(tool_name)
     search_results = conda_util.best_search_result(target, conda_context=conda_context)
     return search_results[0]['version']
@@ -62,11 +68,11 @@ def update_xml(tool_path, xml_tree, tags_to_update, wrapper_version_token, is_ma
     Write modified XML to tool_path
     """
     def update_token(xml_text, tag, token_value):
-        new_tag = '>{}<'.format(token_value).join(re.split('>.*<', tag))
+        new_tag = f'>{token_value}<'.join(re.split('>.*<', tag))
         return re.sub(tag, new_tag, xml_text)
 
     def update_requirement(xml_text, tag, requirement_value):
-        new_tag = 'version="{}"'.format(requirement_value).join(re.split('version=".*"', tag))
+        new_tag = f'version="{requirement_value}"'.join(re.split('version=".*"', tag))
         return re.sub(tag, new_tag, xml_text)
 
     with open(tool_path, 'r+', newline='') as f:
@@ -144,8 +150,7 @@ def perform_required_update(ctx, xml_files, tool_path, requirements, tokens, xml
     # finally, update each file separately
     for k, v in xml_files.items():
         update_xml(k, v, xml_to_update[k], wrapper_version_token, is_macro=(k != tool_path))
-
-    info("Tool {} updated.".format(tool_path))
+    info(f"Tool {tool_path} successfully updated.")
     return set(xml_files)
 
 
@@ -182,13 +187,31 @@ def autoupdate_tool(ctx, tool_path, modified_files=set(), **kwds):
     tokens, xml_to_update, current_main_req, updated_main_req = create_token_dict(ctx, xml_files, main_req, **kwds)
 
     if current_main_req == updated_main_req and not (modified_files & set(xml_files)):
-        info("No updates required or made to {}.".format(tool_path))
+        info(f"No updates required or made to {tool_path}.")
         return  # end here if no update needed
 
     if kwds.get('dry_run'):
-        error("Update required to {}! Tool main requirement has version {}, newest conda version is {}".format(
-              tool_path, current_main_req, updated_main_req))
+        error(f"Update required to {tool_path}! Tool main requirement has version {current_main_req}, newest conda version is {updated_main_req}")
         return
 
     else:
+        info(f"Updating {tool_path.split('/')[-1]} from version {current_main_req} to {updated_main_req}")
         return perform_required_update(ctx, xml_files, tool_path, requirements, tokens, xml_to_update, wrapper_version_token, **kwds)
+
+
+def _update_wf(config, workflow_id):
+    """
+    Recursively update a workflow, including subworkflows
+    """
+    wf = config.user_gi.workflows.show_workflow(workflow_id)
+    for step in wf['steps'].values():
+        if step['type'] == 'subworkflow':
+            # update subworkflows before the main workflow
+            _update_wf(config, step['workflow_id'])
+    config.user_gi.workflows.refactor_workflow(workflow_id, actions=[{"action_type": "upgrade_all_steps"}])
+
+
+def autoupdate_wf(ctx, config, wf):
+    workflow_id = config.workflow_id_for_runnable(wf)
+    _update_wf(config, workflow_id)
+    return config.user_gi.workflows.export_workflow_dict(workflow_id)

planemo/commands/cmd_autoupdate.py

@@ -1,9 +1,16 @@
 """Module describing the planemo ``autoupdate`` command."""
+import json
+
 import click
+from gxformat2 import from_galaxy_native
 
 from planemo import autoupdate, options
 from planemo.cli import command_function
 from planemo.config import planemo_option
+from planemo.engine import (
+    engine_context,
+    is_galaxy_engine,
+)
 from planemo.engine.test import (
     test_runnables,
 )
@@ -19,6 +26,7 @@
 )
 from planemo.runnable import (
     for_paths,
+    RunnableType
 )
 from planemo.tools import (
     is_tool_load_error,
@@ -62,7 +70,7 @@ def skip_requirements_option():
     )
 
 
-@click.command('autoupdate')
+@click.command('autoupdate')  # noqa C901
 @options.optional_tools_arg(multiple=True)
 @dry_run_option()
 @options.recursive_option()
@@ -76,29 +84,60 @@ def skip_requirements_option():
 @options.report_xunit()
 @options.fail_level_option()
 @command_function
-def cli(ctx, paths, **kwds):
+def cli(ctx, paths, **kwds):  # noqa C901
     """Auto-update tool requirements by checking against Conda and updating if newer versions are available."""
     assert_tools = kwds.get("assert_tools", True)
     recursive = kwds.get("recursive", False)
     exit_codes = []
     modified_files = set()
     tools_to_skip = [line.rstrip() for line in open(kwds['skiplist'])] if kwds['skiplist'] else []
-    for (tool_path, tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
-        if tool_path.split('/')[-1] in tools_to_skip:
-            info("Skipping tool %s" % tool_path)
-            continue
-        info("Auto-updating tool %s" % tool_path)
-        try:
-            updated = autoupdate.autoupdate_tool(ctx, tool_path, modified_files=modified_files, **kwds)
-            if updated:
-                modified_files.update(updated)
-        except Exception as e:
-            error("{} could not be updated - the following error was raised: {}".format(tool_path, e.__str__()))
-        if handle_tool_load_error(tool_path, tool_xml):
-            exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
-            continue
-        else:
-            exit_codes.append(EXIT_CODE_OK)
+    runnables = for_paths(paths)
+
+    if any(r.type in {RunnableType.galaxy_tool, RunnableType.directory} for r in runnables):
+        # update Galaxy tools
+        for (tool_path, tool_xml) in yield_tool_sources_on_paths(ctx, paths, recursive):
+            if tool_path.split('/')[-1] in tools_to_skip:
+                info("Skipping tool %s" % tool_path)
+                continue
+            info("Auto-updating tool %s" % tool_path)
+            try:
+                updated = autoupdate.autoupdate_tool(ctx, tool_path, modified_files=modified_files, **kwds)
+                if updated:
+                    modified_files.update(updated)
+            except Exception as e:
+                error(f"{tool_path} could not be updated - the following error was raised: {e.__str__()}")
+            if handle_tool_load_error(tool_path, tool_xml):
+                exit_codes.append(EXIT_CODE_GENERIC_FAILURE)
+                continue
+            else:
+                exit_codes.append(EXIT_CODE_OK)
+
+    workflows = [r for r in runnables if r.type == RunnableType.galaxy_workflow]
+    modified_workflows = []
+    if workflows:
+        assert is_galaxy_engine(**kwds)
+        if kwds.get("engine") != "external_galaxy":
+            kwds["install_most_recent_revision"] = True
+            kwds["install_resolver_dependencies"] = False
+            kwds["install_repository_dependencies"] = False
+            kwds['shed_install'] = True
+
+        with engine_context(ctx, **kwds) as galaxy_engine:
+            with galaxy_engine.ensure_runnables_served(workflows) as config:
+                for workflow in workflows:
+                    if config.updated_repos.get(workflow.path) or kwds.get("engine") == "external_galaxy":
+                        info("Auto-updating workflow %s" % workflow.path)
+                        updated_workflow = autoupdate.autoupdate_wf(ctx, config, workflow)
+                        if workflow.path.endswith(".ga"):
+                            with open(workflow.path, 'w') as f:
+                                json.dump(updated_workflow, f, indent=4, sort_keys=True)
+                        else:
+                            format2_wrapper = from_galaxy_native(updated_workflow, json_wrapper=True)
+                            with open(workflow.path, "w") as f:
+                                f.write(format2_wrapper["yaml_content"])
+                        modified_workflows.append(workflow.path)
+                    else:
+                        info("No newer tool versions were found, so the workflow was not updated.")
 
     if kwds['test']:
         if not modified_files:
@@ -108,7 +147,7 @@ def cli(ctx, paths, **kwds):
                 # only test tools in updated directories
                 modified_paths = [path for path, tool_xml in yield_tool_sources_on_paths(ctx, paths, recursive) if path in modified_files]
                 info(f"Running tests for the following auto-updated tools: {', '.join(modified_paths)}")
-                runnables = for_paths(modified_paths, temp_path=temp_path)
+                runnables = for_paths(modified_paths + modified_workflows, temp_path=temp_path)
                 kwds["engine"] = "galaxy"
                 return_value = test_runnables(ctx, runnables, original_paths=paths, **kwds)
                 exit_codes.append(return_value)