Test cases for renaming datasets based on tool input datasets.

Includes test cases for galaxyproject#3197 and galaxyproject#662.

test/api/test_workflows.py

@@ -214,7 +214,14 @@ def read_test_data(test_dict):
                 input_type = value["type"]
                 if input_type == "File":
                     content = read_test_data(value)
-                    hda = self.dataset_populator.new_dataset( history_id, content=content )
+                    new_dataset_kwds = {
+                        "content": content
+                    }
+                    if "name" in value:
+                        new_dataset_kwds["name"] = value["name"]
+                    if "file_type" in value:
+                        new_dataset_kwds["file_type"] = value["file_type"]
+                    hda = self.dataset_populator.new_dataset( history_id, **new_dataset_kwds )
                     label_map[key] = self._ds_entry( hda )
                     has_uploads = True
                 elif input_type == "raw":
@@ -1251,6 +1258,104 @@ def test_run_with_pja( self ):
         content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
         assert content[ "name" ] == "foo was replaced"
 
+    @skip_without_tool( "cat" )
+    def test_run_rename_based_on_input( self ):
+        history_id = self.dataset_populator.new_history()
+        self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+steps:
+  - tool_id: cat
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+    outputs:
+      out_file1:
+        rename: "#{input1 | basename} suffix"
+test_data:
+  input1:
+    value: 1.fasta
+    type: File
+    name: fasta1
+""", history_id=history_id)
+        content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
+        name = content[ "name" ]
+        assert name == "fasta1 suffix", name
+
+    @skip_without_tool( "cat" )
+    def test_run_rename_based_on_input_repeat( self ):
+        history_id = self.dataset_populator.new_history()
+        self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: input1
+  - id: input2
+steps:
+  - tool_id: cat
+    label: first_cat
+    state:
+      input1:
+        $link: input1
+      queries:
+        - input2:
+            $link: input2
+    outputs:
+      out_file1:
+        rename: "#{queries_0.input2| basename} suffix"
+test_data:
+  input1:
+    value: 1.fasta
+    type: File
+    name: fasta1
+  input2:
+    value: 1.fasta
+    type: File
+    name: fasta2
+""", history_id=history_id)
+        content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
+        name = content[ "name" ]
+        assert name == "fasta2 suffix", name
+
+    @skip_without_tool( "mapper2" )
+    def test_run_rename_based_on_input_conditional( self ):
+        history_id = self.dataset_populator.new_history()
+        self._run_jobs("""
+class: GalaxyWorkflow
+inputs:
+  - id: fasta_input
+  - id: fastq_input
+steps:
+  - tool_id: mapper2
+    state:
+      fastq_input:
+        fastq_input_selector: single
+        fastq_input1:
+          $link: fastq_input
+      reference:
+        $link: fasta_input
+    outputs:
+      out_file1:
+        # Wish it was qualified for conditionals but it doesn't seem to be. -John
+        # rename: "#{fastq_input.fastq_input1 | basename} suffix"
+        rename: "#{fastq_input1 | basename} suffix"
+test_data:
+  fasta_input:
+    value: 1.fasta
+    type: File
+    name: fasta1
+    file_type: fasta
+  fastq_input:
+    value: 1.fastqsanger
+    type: File
+    name: fastq1
+    file_type: fastqsanger
+""", history_id=history_id)
+        content = self.dataset_populator.get_history_dataset_details( history_id, wait=True, assert_ok=True )
+        name = content[ "name" ]
+        assert name == "fastq1 suffix", name
+
     @skip_without_tool( "cat1" )
     def test_run_with_runtime_pja( self ):
         workflow = self.workflow_populator.load_workflow( name="test_for_pja_runtime" )

test/functional/tools/for_workflows/mapper2.xml

@@ -0,0 +1,33 @@
+<tool id="mapper2" name="mapper2" version="0.1.0">
+    <command>
+        cp $__tool_directory__/1.bam $out_file1
+    </command>
+    <inputs>
+        <!-- Conditional input block from bwa-mem. -->
+        <conditional name="fastq_input">
+          <param name="fastq_input_selector" type="select" label="Single or Paired-end reads">
+            <option value="paired">Paired</option>
+            <option value="single">Single</option>
+            <option value="paired_collection">Paired Collection</option>
+            <option value="paired_iv">Paired Interleaved</option>
+          </param>
+          <when value="paired">
+            <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" />
+            <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" />
+          </when>
+          <when value="single">
+            <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset"/>
+          </when>
+          <when value="paired_collection">
+            <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" />
+          </when>
+          <when value="paired_iv">
+            <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" />
+          </when>
+        </conditional>
+        <param name="reference" type="data" format="fasta" label="Fasta Input"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="bam" />
+    </outputs>
+</tool>

test/functional/tools/samples_tool_conf.xml

@@ -114,6 +114,7 @@
   <tool file="for_workflows/cat_interleave.xml" />
   <tool file="for_workflows/pileup.xml" />
   <tool file="for_workflows/mapper.xml" />
+  <tool file="for_workflows/mapper2.xml" />
   <tool file="for_workflows/split.xml" />
   <tool file="for_workflows/create_input_collection.xml" />