From f29601a5e014d9383830357a413b2a31e17c6f70 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 10 Jun 2024 10:31:01 +0200
Subject: [PATCH 1/3] Fix error or loading internal tool `SIFT`

Error popping up all the time:

```
Traceback (most recent call last):
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 873, in _load_tool_tag_set
    tool = self.load_tool(concrete_path, use_cached=False, tool_cache_data_dir=tool_cache_data_dir)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tool_util/toolbox/base.py", line 1100, in load_tool
    tool = self.create_tool(
           ^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 547, in create_tool
    return self._create_tool_from_source(tool_source, config_file=config_file, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 563, in _create_tool_from_source
    return create_tool_from_source(self.app, tool_source, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 355, in create_tool_from_source
    tool = ToolClass(config_file, tool_source, app, **kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 820, in __init__
    raise e
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 817, in __init__
    self.parse(tool_source, guid=guid, dynamic=dynamic)
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 1142, in parse
    self.parse_inputs(self.tool_source)
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 1427, in parse_inputs
    inputs = self.parse_input_elem(page_source, enctypes)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 1622, in parse_input_elem
    param = self.parse_param_elem(input_source, enctypes, context)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/__init__.py", line 1635, in parse_param_elem
    param = ToolParameter.build(self, input_source)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/basic.py", line 330, in build
    return parameter_types[param_type](tool, input_source)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/basic.py", line 2071, in __init__
    super().__init__(tool, input_source, trans)
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/basic.py", line 1863, in __init__
    super().__init__(tool, input_source)
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/basic.py", line 186, in __init__
    self.validators.append(validation.Validator.from_element(self, elem))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/validation.py", line 45, in from_element
    return validator_types[_type].from_element(param, elem)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/gpfs1/data/galaxy_server/galaxy/lib/galaxy/tools/parameters/validation.py", line 399, in from_element
    assert os.path.exists(filename), f"File {filename} specified by the 'filename' attribute not found"
AssertionError: File /gpfs1/data/galaxy_server/galaxy/tool-data/sift_db.loc specified by the 'filename' attribute not found
```

I think using the other validator should not cause so much trouble.
---
 tools/phenotype_association/sift.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/phenotype_association/sift.xml b/tools/phenotype_association/sift.xml
index 3654c74a053a..14ef9512c1f4 100644
--- a/tools/phenotype_association/sift.xml
+++ b/tools/phenotype_association/sift.xml
@@ -8,7 +8,7 @@
   <inputs>
     <param name="input" type="data" format="tabular" label="Dataset">
       <validator type="unspecified_build"/>
-      <validator type="dataset_metadata_in_file" filename="sift_db.loc" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/>
+      <validator type="dataset_metadata_in_data_table" table_name="sift_db" metadata_name="dbkey" metadata_column="0" message="Data is currently not available for the specified build."/>
     </param>
     <param name="chrom_col"  type="data_column" data_ref="input" label="Column with chromosome"/>
     <param name="pos_col"    type="data_column" data_ref="input" numerical="true" label="Column with position"/>

From 8938b02cbc37eea005987f7338251efc13142883 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 10 Jun 2024 10:37:31 +0200
Subject: [PATCH 2/3] add data table

---
 lib/galaxy/config/sample/tool_data_table_conf.xml.sample | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/lib/galaxy/config/sample/tool_data_table_conf.xml.sample b/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
index 6d8c50ac82c9..4f520197aa87 100644
--- a/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
@@ -110,6 +110,10 @@
         <columns>value, name, url</columns>
         <file path="tool-data/icn3d_simple_display.loc" />
     </table>
+    <table name="sift_db" comment_char="#" allow_duplicate_entries="False">
+        <columns>dbkey, path</columns>
+        <file path="tool-data/sift_db.loc" />
+    </table>
     <!-- Refgenie __dbkeys__ -->
     <table name="__dbkeys__" type="refgenie" asset="fasta" >
         <file from_config="refgenie_config_file" />

From 654c702a477f50c8158dca8750bb61831bb95a89 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 10 Jun 2024 10:52:48 +0200
Subject: [PATCH 3/3] try to fix column name

apparently data tables need a value column
---
 lib/galaxy/config/sample/tool_data_table_conf.xml.sample | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/config/sample/tool_data_table_conf.xml.sample b/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
index 4f520197aa87..244a77477e4a 100644
--- a/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
+++ b/lib/galaxy/config/sample/tool_data_table_conf.xml.sample
@@ -111,7 +111,7 @@
         <file path="tool-data/icn3d_simple_display.loc" />
     </table>
     <table name="sift_db" comment_char="#" allow_duplicate_entries="False">
-        <columns>dbkey, path</columns>
+        <columns>dbkey, value</columns>
         <file path="tool-data/sift_db.loc" />
     </table>
     <!-- Refgenie __dbkeys__ -->