Use ephemeris to handle shed tools for workflows.

jmchilton · jmchilton · commit 1c6cfbb1b496 · 2016-06-15T15:18:52.000-04:00
diff --git a/planemo/commands/cmd_test.py b/planemo/commands/cmd_test.py
@@ -64,7 +64,6 @@ def cli(ctx, paths, **kwds):
     against that same Galaxy root - but this may not be bullet proof yet so
     please careful and do not try this against production Galaxy instances.
     """
-    kwds["for_tests"] = True
     runnables = for_paths(paths)
     enable_beta_test = any([r.type not in [RunnableType.galaxy_tool, RunnableType.directory] for r in runnables])
     enable_beta_test = enable_beta_test or not is_galaxy_engine(**kwds)
@@ -74,6 +73,7 @@ def cli(ctx, paths, **kwds):
             test_data = engine.test(runnables)
             return_value = handle_reports_and_summary(ctx, test_data.structured_data, kwds=kwds)
     else:
+        kwds["for_tests"] = True
         with galaxy_config(ctx, runnables, **kwds) as config:
             return_value = run_in_config(ctx, config, **kwds)
 
diff --git a/planemo/galaxy/activity.py b/planemo/galaxy/activity.py
@@ -81,6 +81,7 @@ def _execute(config, runnable, job_path, **kwds):
             history_id=history_id,
             inputs=job_dict,
             inputs_by="name",
+            allow_tool_state_corrections=True,
         )
         invocations_url = "%s/%s/invocations" % (
             user_gi._make_url(user_gi.workflows),
diff --git a/planemo/galaxy/config.py b/planemo/galaxy/config.py
@@ -29,6 +29,7 @@
 )
 from .workflows import (
     import_workflow,
+    install_shed_repos,
 )
 from planemo.conda import build_conda_context
 from planemo.docker import docker_host_args
@@ -610,6 +611,7 @@ def install_workflows(self):
                 self._install_workflow(runnable.path)
 
     def _install_workflow(self, path):
+        install_shed_repos(path, self.gi)
         workflow = import_workflow(path, admin_gi=self.gi, user_gi=self.user_gi)
         self._workflow_ids[path] = workflow["id"]
 
diff --git a/planemo/galaxy/workflows.py b/planemo/galaxy/workflows.py
@@ -12,9 +12,32 @@
     BioBlendImporterGalaxyInterface = None
     ImporterGalaxyInterface = object
 
+try:
+    from ephemeris import shed_install
+except ImportError:
+    shed_install = None
+
 import yaml
 
 
+def load_shed_repos(path):
+    # TODO: This is crap - doesn't have nested repositories at all.
+    if path.endswith(".ga"):
+        with open(path, "r") as f:
+            workflow = json.load(f)
+    else:
+        with open(path, "r") as f:
+            workflow = yaml.load(f)
+
+    return workflow.get("tools", [])
+
+
+def install_shed_repos(path, admin_gi):
+    tools_info = load_shed_repos(path)
+    if tools_info:
+        shed_install.install_tools(tools_info, admin_gi, path, default_install_tool_dependencies=False)
+
+
 def import_workflow(path, admin_gi, user_gi):
     """Import a workflow path to specified Galaxy instance."""
     importer = BioBlendImporterGalaxyInterface(
diff --git a/requirements.txt b/requirements.txt
@@ -8,5 +8,6 @@ jinja2
 glob2
 virtualenv
 gxformat2
+ephemeris
 galaxy-lib>=16.7.9
 cwltool>=1.0.20160511162129 ; python_version == '2.7'
diff --git a/tests/data/hello_sed_cut.txt b/tests/data/hello_sed_cut.txt
@@ -0,0 +1 @@
+Hello!
diff --git a/tests/data/shed-wf2.gxwf-test.yml b/tests/data/shed-wf2.gxwf-test.yml
@@ -0,0 +1,8 @@
+- doc: Simple test replacing some text.
+  job:
+    input1:
+      class: File
+      path: hello.txt
+  outputs:
+    wf_output_1:
+      checksum: "sha1$a8d191538209e335154750d2df575b9ddfb16fc7"
diff --git a/tests/data/shed-wf2.gxwf.yml b/tests/data/shed-wf2.gxwf.yml
@@ -0,0 +1,17 @@
+class: GalaxyWorkflow
+name: "Test Workflow Shed Stuffs"
+tools:
+  - name: text_processing
+    owner: bgruening
+inputs:
+  - id: input1
+outputs:
+  - id: wf_output_1
+    source: sed#output
+steps:
+  - tool_id: tp_sed_tool
+    label: sed
+    state:
+      infile:
+        $link: input1
+    code: "s/ World//g"

Original file line number	Diff line number	Diff line change
`@@ -81,6 +81,7 @@ def _execute(config, runnable, job_path, **kwds):`
`81`	`81`	`history_id=history_id,`
`82`	`82`	`inputs=job_dict,`
`83`	`83`	`inputs_by="name",`
	`84`	`+ allow_tool_state_corrections=True,`
`84`	`85`	`)`
`85`	`86`	`invocations_url = "%s/%s/invocations" % (`
`86`	`87`	`user_gi._make_url(user_gi.workflows),`
Original file line number	Diff line number	Diff line change
`@@ -29,6 +29,7 @@`
`29`	`29`	`)`
`30`	`30`	`from .workflows import (`
`31`	`31`	`import_workflow,`
	`32`	`+ install_shed_repos,`
`32`	`33`	`)`
`33`	`34`	`from planemo.conda import build_conda_context`
`34`	`35`	`from planemo.docker import docker_host_args`
`@@ -610,6 +611,7 @@ def install_workflows(self):`
`610`	`611`	`self._install_workflow(runnable.path)`
`611`	`612`
`612`	`613`	`def _install_workflow(self, path):`
	`614`	`+ install_shed_repos(path, self.gi)`
`613`	`615`	`workflow = import_workflow(path, admin_gi=self.gi, user_gi=self.user_gi)`
`614`	`616`	`self._workflow_ids[path] = workflow["id"]`
`615`	`617`