IMP: Add xrefs with bio.tools to XMLs (#54)

* Add xrefs with bio.tools to XMLs
qiime2 · Jun 13, 2024 · 324442b · 324442b
1 parent 3f60e53
commit 324442b
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Showing 6 changed files with 21 additions and 8 deletions.
diff --git a/q2galaxy/core/templaters/action.py b/q2galaxy/core/templaters/action.py
@@ -14,7 +14,7 @@
 from q2galaxy.core.util import XMLNode, galaxy_ui_var, rst_header
 from q2galaxy.core.templaters.common import (
     make_tool_id, make_tool_name, make_config, make_citations,
-    make_requirements)
+    make_requirements, make_xrefs)
 from q2galaxy.core.templaters.helpers import signature_to_galaxy
 
 
@@ -76,6 +76,7 @@ def make_tool(conda_meta, plugin, action, test_dir):
     tool.append(make_help(plugin, action, test_dir))
     tool.append(make_citations(plugin, action))
     tool.append(make_requirements(conda_meta, plugin.project_name))
+    tool.append(make_xrefs())
     return tool
 
 

diff --git a/q2galaxy/core/templaters/common.py b/q2galaxy/core/templaters/common.py
@@ -115,3 +115,10 @@ def make_formats_help(formats):
             help_ += f' - {format_.__name__}\n'
 
     return help_
+
+
+def make_xrefs():
+    xrefs = XMLNode('xrefs')
+    xrefs.append(
+        XMLNode('xref', 'qiime2', type='bio.tools'))
+    return xrefs
diff --git a/q2galaxy/core/templaters/export_data.py b/q2galaxy/core/templaters/export_data.py
@@ -12,7 +12,7 @@
 from q2galaxy.core.util import XMLNode, galaxy_esc, pretty_fmt_name, rst_header
 from q2galaxy.core.templaters.common import (
     make_builtin_version, make_requirements, make_tool_name_from_id,
-    make_config, make_citations, make_formats_help)
+    make_config, make_citations, make_formats_help, make_xrefs)
 
 
 def make_builtin_export(meta, tool_id):
@@ -170,6 +170,7 @@ def make_builtin_export(meta, tool_id):
     tool.append(make_citations())
     tool.append(make_requirements(meta, *[p.project_name for p in plugins]))
     tool.append(_make_help(known_formats))
+    tool.append(make_xrefs())
 
     return tool
 

diff --git a/q2galaxy/core/templaters/import_data.py b/q2galaxy/core/templaters/import_data.py
@@ -17,7 +17,8 @@
                                              make_tool_name_from_id,
                                              make_requirements,
                                              make_citations,
-                                             make_formats_help)
+                                             make_formats_help,
+                                             make_xrefs)
 
 
 def make_builtin_import(meta, tool_id):
@@ -110,6 +111,7 @@ def make_builtin_import(meta, tool_id):
     tool.append(make_citations())
     tool.append(make_requirements(meta, *[p.project_name for p in plugins]))
     tool.append(_make_help(known_formats))
+    tool.append(make_xrefs())
     return tool
 
 

diff --git a/q2galaxy/core/templaters/import_fastq_data.py b/q2galaxy/core/templaters/import_fastq_data.py
@@ -11,7 +11,8 @@
 from q2galaxy.core.templaters.common import (make_builtin_version,
                                              make_tool_name_from_id,
                                              make_requirements,
-                                             make_citations)
+                                             make_citations,
+                                             make_xrefs)
 
 
 def make_builtin_import_fastq(meta, tool_id):
@@ -33,6 +34,7 @@ def make_builtin_import_fastq(meta, tool_id):
     tool.append(_make_config())
     tool.append(make_citations())
     tool.append(make_requirements(meta, *[p.project_name for p in plugins]))
+    tool.append(make_xrefs())
     return tool
 
 

diff --git a/q2galaxy/core/util.py b/q2galaxy/core/util.py
@@ -18,10 +18,10 @@
 
 class OrderedTool(collections.OrderedDict):
     order = ["description", "macros", "edam_topics", "edam_operations",
-             "parallelism", "requirements", "code", "stdio", "version_command",
-             "command", "environment_variables", "configfiles", "inputs",
-             "request_param_translation", "outputs", "tests", "help",
-             "citations"]
+             "parallelism", "xrefs", "requirements", "code", "stdio",
+             "version_command", "command", "environment_variables",
+             "configfiles", "inputs", "request_param_translation",
+             "outputs", "tests", "help", "citations"]
     order_attr = ['name', 'argument', 'type', 'format', 'min', 'truevalue',
                   'max', 'falsevalue', 'value', 'checked', 'optional', 'label',
                   'help']