From 9b6a9dc0c73dfc0625e55a3db4c262174bda0dff Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 13 Feb 2017 14:20:13 -0500
Subject: [PATCH] Start work on a relabelling collection operation.

I think it needs to be touched up but the basic operation seems to work so far. I think what remains to be done is:

 - Validate uniqueness of identifiers and provide nice messages if they are not unique.
 - Validate that at least the required number of lines are present in the file and provide a nice message if not.
 - Add strict mode to ensure exactly the correct number of lines is added.
 - Find where validation of identifiers happens in the API and apply same validation here - try not to let unsafe identifiers be created.
 - Consider more advanced modes - selecting a column, apply a regex replace, pick two columns for nested lists, etc.... None of this may need to be needed in the first iteration.
 - Consider another mode where a collection is labelled against an existing collection - should that be a separate tool of the same tool.
---
 config/tool_conf.xml.sample                 |  1 +
 lib/galaxy/tools/__init__.py                | 22 ++++++++-
 lib/galaxy/tools/relabel_from_file.xml      | 53 +++++++++++++++++++++
 test-data/new_labels_1.txt                  |  1 +
 test/functional/tools/samples_tool_conf.xml |  1 +
 5 files changed, 77 insertions(+), 1 deletion(-)
 create mode 100644 lib/galaxy/tools/relabel_from_file.xml
 create mode 100644 test-data/new_labels_1.txt

diff --git a/config/tool_conf.xml.sample b/config/tool_conf.xml.sample
index 3e19d92f265..2f039985374 100644
--- a/config/tool_conf.xml.sample
+++ b/config/tool_conf.xml.sample
@@ -36,6 +36,7 @@
     <tool file="${model_tools_path}/filter_failed_collection.xml" />
     <tool file="${model_tools_path}/flatten_collection.xml" />
     <tool file="${model_tools_path}/merge_collection.xml" />
+    <tool file="${model_tools_path}/relabel_from_file.xml" />
   </section>
   <section id="liftOver" name="Lift-Over">
     <tool file="extract/liftOver_wrapper.xml" />
diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
index b84709615f6..94c65ed43d2 100755
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -2506,11 +2506,31 @@ class FlattenTool( DatabaseOperationTool ):
         )
 
 
+class RelabelFromFileTool( DatabaseOperationTool ):
+    tool_type = 'relabel_from_file'
+
+    def produce_outputs( self, trans, out_data, output_collections, incoming, history ):
+        hdca = incoming[ "input" ]
+        new_labels_dataset_assoc = incoming[ "labels" ]
+        new_elements = odict()
+        log.info(new_labels_dataset_assoc)
+        new_labels_path = new_labels_dataset_assoc.file_name
+        new_labels = open(new_labels_path, "r").readlines(1024 * 1000000)
+
+        for i, dce in enumerate(hdca.collection.elements):
+            dce_object = dce.element_object
+            new_elements[new_labels[i].strip()] = dce_object.copy()
+
+        output_collections.create_collection(
+            next(iter(self.outputs.values())), "output", elements=new_elements
+        )
+
+
 # Populate tool_type to ToolClass mappings
 tool_types = {}
 for tool_class in [ Tool, SetMetadataTool, OutputParameterJSONTool,
                     DataManagerTool, DataSourceTool, AsyncDataSourceTool,
-                    UnzipCollectionTool, ZipCollectionTool, MergeCollectionTool,
+                    UnzipCollectionTool, ZipCollectionTool, MergeCollectionTool, RelabelFromFileTool,
                     DataDestinationTool ]:
     tool_types[ tool_class.tool_type ] = tool_class
 
diff --git a/lib/galaxy/tools/relabel_from_file.xml b/lib/galaxy/tools/relabel_from_file.xml
new file mode 100644
index 00000000000..f52c9e38ef9
--- /dev/null
+++ b/lib/galaxy/tools/relabel_from_file.xml
@@ -0,0 +1,53 @@
+<tool id="__RELABEL_FROM_FILE__"
+      name="Relabel List Identifiers"
+      version="1.0.0"
+      tool_type="relabel_from_file">
+    <description>from contents of a file</description>
+    <type class="RelabelFromFileTool" module="galaxy.tools" />
+    <action module="galaxy.tools.actions.model_operations"
+            class="ModelOperationToolAction"/>
+    <inputs>
+        <param type="data_collection" name="input" label="Input Collection" help="A list whose identifiers will be relabelled."/>
+        <param type="data" name="labels" format="txt" label="New Identifiers" />
+    </inputs>
+    <outputs>
+        <collection name="output" format_source="input" type_source="input" label="${on_string} (relabelled)" >
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input">
+                <collection type="list:paired">
+                    <element name="i1">
+                        <collection type="paired">
+                            <element name="forward" value="simple_line.txt" />
+                            <element name="reverse" value="simple_line_alternative.txt" />
+                        </collection>
+                    </element>
+                </collection>
+            </param>
+            <param name="labels" value="new_labels_1.txt" ftype="txt" />
+            <output_collection name="output" type="list:paired">
+              <element name="new_i1">
+                <element name="forward">
+                  <assert_contents>
+                    <has_text_matching expression="^This is a line of text.\n$" />
+                  </assert_contents>
+                </element>
+                <element name="reverse">
+                  <assert_contents>
+                    <has_text_matching expression="^This is a different line of text.\n$" />
+                  </assert_contents>
+                </element>
+              </element>
+            </output_collection>
+        </test>
+    </tests>
+    <help>
+        This tool will take an input list and a text file with new identifiers
+        and build a new list with the same datasets but these new identifiers.
+
+        This tool will create new history datasets from your collection
+        but your quota usage will not increase.
+    </help>
+</tool>
diff --git a/test-data/new_labels_1.txt b/test-data/new_labels_1.txt
new file mode 100644
index 00000000000..3fe0afa80c6
--- /dev/null
+++ b/test-data/new_labels_1.txt
@@ -0,0 +1 @@
+new_i1
\ No newline at end of file
diff --git a/test/functional/tools/samples_tool_conf.xml b/test/functional/tools/samples_tool_conf.xml
index 59f76c37d1d..35a1480f817 100644
--- a/test/functional/tools/samples_tool_conf.xml
+++ b/test/functional/tools/samples_tool_conf.xml
@@ -146,5 +146,6 @@
   <tool file="${model_tools_path}/filter_failed_collection.xml" />
   <tool file="${model_tools_path}/flatten_collection.xml" />
   <tool file="${model_tools_path}/merge_collection.xml" />
+  <tool file="${model_tools_path}/relabel_from_file.xml" />
 
 </toolbox>