Merge pull request #840 from jmchilton/uri_testing_workflows

Allow URIs for workflow testing w/tests.

Author: jmchilton

planemo/galaxy/activity.py

@@ -17,6 +17,7 @@
     invocation_to_output,
     output_properties,
     output_to_cwl_json,
+    path_or_uri_to_uri,
     tool_response_to_output,
 )
 from galaxy.tools.parser import get_tool_source
@@ -179,12 +180,14 @@ def stage_in(ctx, runnable, config, user_gi, history_id, job_path, **kwds):
     def upload_func(upload_target):
 
         def _attach_file(upload_payload, uri, index=0):
-            is_path = not uri.startswith("http://") and not uri.startswith("https://") and not uri.startswith("ftp://")
-            if config.use_path_paste and is_path:
-                upload_payload["inputs"]["files_%d|url_paste" % index] = "file://%s" % os.path.abspath(uri)
+            uri = path_or_uri_to_uri(uri)
+            is_path = uri.startswith("file://")
+            if not is_path or config.use_path_paste:
+                upload_payload["inputs"]["files_%d|url_paste" % index] = uri
             else:
                 files_attached[0] = True
-                upload_payload["files_%d|file_data" % index] = attach_file(uri)
+                path = uri[len("file://"):]
+                upload_payload["files_%d|file_data" % index] = attach_file(path)
 
         if isinstance(upload_target, FileUploadTarget):
             file_path = upload_target.path

requirements.txt

@@ -13,6 +13,6 @@ virtualenv
 lxml
 gxformat2>=0.2.0
 ephemeris>=0.8
-galaxy-lib>=18.5.11
+galaxy-lib>=18.5.12
 html5lib>=0.9999999,!=0.99999999,!=0.999999999,!=1.0b10,!=1.0b09
 cwltool==1.0.20180508202931

tests/data/cat_tool_url.cwl

@@ -0,0 +1,20 @@
+#!/usr/bin/env cwl-runner
+class: CommandLineTool
+cwlVersion: 'v1.0'
+doc: "Print the contents of a file to stdout using 'cat' running in a docker container."
+hints:
+  - class: DockerRequirement
+    dockerPull: debian:wheezy
+inputs:
+  file1:
+    type: File
+    label: Input File
+    doc: "The file that will be copied using 'cat'"
+    inputBinding: {position: 1}
+outputs:
+  output_file:
+    type: File
+    outputBinding: {glob: output.txt}
+baseCommand:
+  - cat
+stdout: output.txt

tests/data/cat_tool_url_job.json

@@ -0,0 +1,6 @@
+{
+    "file1": {
+        "class": "File",
+        "path": "https://raw.githubusercontent.com/galaxyproject/planemo/master/tests/data/hello.txt"
+    }
+}

tests/data/cat_tool_url_test.yml

@@ -0,0 +1,6 @@
+- doc: Simple test
+  job: cat_tool_url_job.json
+  outputs:
+    output_file:
+      checksum: sha1$2ef7bde608ce5404e97d5f042f95f89f1c232871
+

tests/data/wf1.gxwf-job-url.yml

@@ -0,0 +1,6 @@
+{
+    "input1": {
+        "class": "File",
+        "location": "https://raw.githubusercontent.com/galaxyproject/planemo/master/tests/data/hello.txt"
+    },
+}

tests/data/wf1.gxwf-test.yml

@@ -3,3 +3,8 @@
   outputs:
     wf_output_1:
       checksum: "sha1$a0b65939670bc2c010f4d5d6a0b3e4e4590fb92b"
+- doc: concat workflow test with URL
+  job: wf1.gxwf-job-url.yml
+  outputs:
+    wf_output_1:
+      checksum: "sha1$a0b65939670bc2c010f4d5d6a0b3e4e4590fb92b"

tests/test_cmd_test.py

@@ -94,6 +94,19 @@ def test_cwltool_tool_test(self):
             self._check_exit_code(test_command, exit_code=0)
             assert_exists(os.path.join(f, "tool_test_output.json"))
 
+    @skip_if_environ("PLANEMO_SKIP_CWLTOOL_TESTS")
+    def test_cwltool_tool_url_inputs_test(self):
+        """Test testing a CWL tool with cwltool."""
+        with self._isolate() as f:
+            test_artifact = os.path.join(TEST_DATA_DIR, "cat_tool_url.cwl")
+            test_command = [
+                "test",
+                "--no-container",
+                test_artifact,
+            ]
+            self._check_exit_code(test_command, exit_code=0)
+            assert_exists(os.path.join(f, "tool_test_output.json"))
+
     @skip_if_environ("PLANEMO_SKIP_CWLTOOL_TESTS")
     @skip_unless_module("toil")
     def test_toil_tool_test(self):