Simple tests for data source responses.

- Verify a simple data source works when responding via the API.
- Verify a data source sending back a file:// parameter is blocked (GX-2017-0004/GX-2017-0003 - it is tracked different ways in the commit message and in the security issue tracker).

test/api/test_tools.py

@@ -1,5 +1,6 @@
 # Test tools API.
 import json
+import os
 
 from base import api
 from base.populators import (
@@ -78,6 +79,55 @@ class ToolsTestCase(api.ApiTestCase):
         assert f2_info["min"] is None
         assert f2_info["max"] is None
 
+    @skip_without_tool("test_data_source")
+    def test_data_source_ok_request(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.run_tool_payload(
+                tool_id="test_data_source",
+                inputs={
+                    "URL": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed",
+                    "URL_method": "get",
+                    "data_type": "bed",
+                },
+                history_id=history_id,
+            )
+            create_response = self._post("tools", data=payload)
+            self._assert_status_code_is(create_response, 200)
+            create_object = create_response.json()
+            self._assert_has_keys(create_object, "outputs")
+            assert len(create_object["outputs"]) == 1
+            output = create_object["outputs"][0]
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            output_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=output)
+            assert output_content.startswith("chr1\t147962192\t147962580")
+
+            output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output)
+            assert output_details["file_ext"] == "bed"
+
+    @skip_without_tool("test_data_source")
+    def test_data_sources_block_file_parameters(self):
+        with self.dataset_populator.test_history() as history_id:
+            payload = self.dataset_populator.run_tool_payload(
+                tool_id="test_data_source",
+                inputs={
+                    "URL": "file://%s" % os.path.join(os.getcwd(), "README.rst"),
+                    "URL_method": "get",
+                    "data_type": "bed",
+                },
+                history_id=history_id,
+            )
+            create_response = self._post("tools", data=payload)
+            self._assert_status_code_is(create_response, 200)
+            create_object = create_response.json()
+            self._assert_has_keys(create_object, "outputs")
+            assert len(create_object["outputs"]) == 1
+            output = create_object["outputs"][0]
+            self.dataset_populator.wait_for_history(history_id, assert_ok=False)
+
+            output_details = self.dataset_populator.get_history_dataset_details(history_id, dataset=output, wait=False)
+            assert output_details["state"] == "error", output_details
+            assert "has not sent back a URL parameter" in output_details["misc_info"], output_details
+
     def _show_valid_tool(self, tool_id):
         tool_show_response = self._get("tools/%s" % tool_id, data=dict(io_details=True))
         self._assert_status_code_is(tool_show_response, 200)

test/functional/tools/data_source.py

@@ -0,0 +1 @@
+../../../tools/data_source/data_source.py

test/functional/tools/samples_tool_conf.xml

@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <toolbox tool_path="${tool_conf_dir}" is_shed_conf="false">
   <tool file="upload.xml"/>
+  <tool file="test_data_source.xml"/>
   <tool file="simple_constructs.xml" />
   <tool file="color_param.xml" />
   <tool file="inheritance_simple.xml" />

test/functional/tools/test_data_source.xml

@@ -0,0 +1,33 @@
+<?xml version="1.0"?>
+<!--
+    If the value of 'URL_method' is 'get', the request will consist of the value of 'URL' coming back in
+    the initial response.  If value of 'URL_method' is 'post', any additional params coming back in the
+    initial response ( in addition to 'URL' ) will be encoded and appended to URL and a post will be performed.
+-->
+<tool name="test_data_source" id="test_data_source" tool_type="data_source" version="1.0.0">
+    <command interpreter="python">data_source.py $output $__app__.config.output_size_limit</command>
+    <inputs action="http://ratmine.mcw.edu/ratmine/begin.do" check_values="false" method="get"> 
+        <display>go to Ratmine server $GALAXY_URL</display>
+        <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=ratmine" />
+    </inputs>
+    <request_param_translation>
+        <request_param galaxy_name="URL_method" remote_name="URL_method" missing="post" />
+        <request_param galaxy_name="URL" remote_name="URL" missing="" />
+        <request_param galaxy_name="dbkey" remote_name="db" missing="?" />
+        <request_param galaxy_name="organism" remote_name="organism" missing="" />
+        <request_param galaxy_name="table" remote_name="table" missing="" />
+        <request_param galaxy_name="description" remote_name="description" missing="" />
+        <request_param galaxy_name="name" remote_name="name" missing="My Awesome Data Source Data" />
+        <request_param galaxy_name="info" remote_name="info" missing="" />
+        <request_param galaxy_name="data_type" remote_name="data_type" missing="auto" >
+            <value_translation>
+                <value galaxy_value="auto" remote_value="txt" /> <!-- intermine currently always provides 'txt', make this auto detect -->
+            </value_translation>
+        </request_param>
+    </request_param_translation>
+    <uihints minwidth="800"/>
+    <outputs>
+        <data name="output" format="txt" />
+    </outputs>
+    <options sanitize="False" refresh="True"/>
+</tool>