From 330d71d37ce7eaa60b5c8c20ae83aeb36fec4a6c Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 18 Jan 2017 10:17:16 -0500
Subject: [PATCH] Remove tool XML modifications for requirement specifications.

Per discussion on #3117 - some people were in favor of the idea but some were opposed. I think it is still important to implement this for CWL tools and useful from a library perspective. This just removes changes to Galaxy tool XML.
---
 lib/galaxy/tools/deps/requirements.py         | 29 +-------------
 lib/galaxy/tools/xsd/galaxy.xsd               | 39 +++++++------------
 .../tools/requirement_specification_1.xml     | 18 ---------
 .../tools/requirement_specification_2.xml     | 16 --------
 4 files changed, 17 insertions(+), 85 deletions(-)
 delete mode 100644 test/functional/tools/requirement_specification_1.xml
 delete mode 100644 test/functional/tools/requirement_specification_2.xml

diff --git a/lib/galaxy/tools/deps/requirements.py b/lib/galaxy/tools/deps/requirements.py
index 2b041fc0348..92ba382e74b 100644
--- a/lib/galaxy/tools/deps/requirements.py
+++ b/lib/galaxy/tools/deps/requirements.py
@@ -210,29 +210,10 @@ def parse_requirements_from_xml( xml_root ):
 
     requirements = ToolRequirements()
     for requirement_elem in requirement_elems:
-        if "name" in requirement_elem.attrib:
-            name = requirement_elem.get( "name" )
-            spec_elems = requirement_elem.findall("specification")
-            specs = map(specification_from_element, spec_elems)
-        else:
-            name = xml_text( requirement_elem )
-            spec_uris_raw = requirement_elem.attrib.get("specification_uris", "")
-            specs = []
-            for spec_uri in spec_uris_raw.split(","):
-                if not spec_uri:
-                    continue
-                version = None
-                if "@" in spec_uri:
-                    uri, version = spec_uri.split("@", 1)
-                else:
-                    uri = spec_uri
-                uri = uri.strip()
-                if version:
-                    version = version.strip()
-                specs.append(RequirementSpecification(uri, version))
+        name = xml_text( requirement_elem )
         type = requirement_elem.get( "type", DEFAULT_REQUIREMENT_TYPE )
         version = requirement_elem.get( "version", DEFAULT_REQUIREMENT_VERSION )
-        requirement = ToolRequirement( name=name, type=type, version=version, specs=specs )
+        requirement = ToolRequirement( name=name, type=type, version=version )
         requirements.append( requirement )
 
     container_elems = []
@@ -244,12 +225,6 @@ def parse_requirements_from_xml( xml_root ):
     return requirements, containers
 
 
-def specification_from_element(specification_elem):
-    uri = specification_elem.get("uri", None)
-    version = specification_elem.get("version", None)
-    return RequirementSpecification(uri, version)
-
-
 def container_from_element(container_elem):
     identifier = xml_text(container_elem)
     type = container_elem.get("type", DEFAULT_CONTAINER_TYPE)
diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd
index 6790c324a0c..5b589306ac3 100644
--- a/lib/galaxy/tools/xsd/galaxy.xsd
+++ b/lib/galaxy/tools/xsd/galaxy.xsd
@@ -227,7 +227,7 @@ complete descriptions of the runtime of a tool.
     </xs:sequence>
   </xs:complexType>
 
-  <xs:complexType name="Requirement" mixed="true">
+  <xs:complexType name="Requirement">
     <xs:annotation>
       <xs:documentation xml:lang="en"><![CDATA[
 
@@ -276,29 +276,20 @@ resolver.
 
 ]]></xs:documentation>
     </xs:annotation>
-    <xs:sequence>
-      <xs:element name="specification" minOccurs="0" maxOccurs="unbounded" type="xs:anyType" />
-    </xs:sequence>
-    <xs:attribute name="type" type="RequirementType" use="required">
-      <xs:annotation>
-        <xs:documentation xml:lang="en"> This value defines the which type of the 3rd party module required by this tool. </xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="version" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en"> For package type requirements this value defines a specific version of the tool dependency. </xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="name" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">Name of requirement (if body of ``requirement`` element contains specification URIs).</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
-    <xs:attribute name="specification_uris" type="xs:string">
-      <xs:annotation>
-        <xs:documentation xml:lang="en">URIs and versions of requirement specification.</xs:documentation>
-      </xs:annotation>
-    </xs:attribute>
+    <xs:simpleContent>
+      <xs:extension base="xs:string">
+        <xs:attribute name="type" type="RequirementType" use="required">
+          <xs:annotation>
+            <xs:documentation xml:lang="en"> This value defines the which type of the 3rd party module required by this tool. </xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
+        <xs:attribute name="version" type="xs:string">
+          <xs:annotation>
+            <xs:documentation xml:lang="en"> For package type requirements this value defines a specific version of the tool dependency. </xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
+      </xs:extension>
+    </xs:simpleContent>
   </xs:complexType>
   <xs:complexType name="Container">
     <xs:annotation>
diff --git a/test/functional/tools/requirement_specification_1.xml b/test/functional/tools/requirement_specification_1.xml
deleted file mode 100644
index 00744e114f4..00000000000
--- a/test/functional/tools/requirement_specification_1.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<tool id="requirement_specification_1" name="requirement_specification_1" version="0.1.0" profile="16.10">
-    <command><![CDATA[
-        blastn -help > $out_file1 ;
-        echo "Moo" >> $out_file1 ;
-    ]]></command>
-    <requirements>
-        <requirement type="package" version="2.2.31" name="blast+">
-            <specification uri="https://anaconda.org/bioconda/blast" />
-            <specification uri="https://packages.debian.org/sid/ncbi-blast+" version="2.2.31-3" />
-        </requirement>
-    </requirements>
-    <inputs>
-        <param name="input1" type="data" optional="true" />
-    </inputs>
-    <outputs>
-        <data name="out_file1" format="txt" />
-    </outputs>
-</tool>
diff --git a/test/functional/tools/requirement_specification_2.xml b/test/functional/tools/requirement_specification_2.xml
deleted file mode 100644
index e3190f068cc..00000000000
--- a/test/functional/tools/requirement_specification_2.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<tool id="requirement_specification_2" name="requirement_specification_2" version="0.1.0" profile="16.01">
-    <command><![CDATA[
-        blastn -help > $out_file1 ;
-        echo "Moo" >> $out_file1 ;
-    ]]></command>
-    <requirements>
-        <!-- Demonstrate backward-compatible-ish specification_uri syntax. -->
-        <requirement type="package" version="2.2" specification_uris="https://anaconda.org/bioconda/blast@2.2.31,https://packages.debian.org/jessie/ncbi-blast+@2.2.29-3">blast+</requirement>
-    </requirements>
-    <inputs>
-        <param name="input1" type="data" optional="true" />
-    </inputs>
-    <outputs>
-        <data name="out_file1" format="txt" />
-    </outputs>
-</tool>