From df62fe25964e3d1380cf0151b7375e545a69417e Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Fri, 10 Sep 2021 14:22:37 +0200
Subject: [PATCH] de-deprecate *not_in* validators

---
 lib/galaxy/tool_util/xsd/galaxy.xsd       | 12 +++++-------
 lib/galaxy/tools/parameters/validation.py | 12 +++++-------
 2 files changed, 10 insertions(+), 14 deletions(-)

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index b26002e41f9..9217482e4bd 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -3644,13 +3644,13 @@ parameters a ``metadata`` validator is added automatically.
 - ``dataset_metadata_in_range``: Check if a numeric metadata value is within
 a given range.
 - ``dataset_metadata_in_data_table``: Check if a metadata value is contained in a column of a data table.
+- ``dataset_metadata_not_in_data_table``: Equivalent to ``dataset_metadata_in_data_table`` with ``negate="true"``.
 
 Deprecated data validators:
 
 - ``dataset_metadata_in_file``: Use data tables with ``dataset_metadata_in_data_table``.
 Check if a metadata value is contained in a specific column of a file in the ``tool_data_path``
 (which is set in Galaxy's config).
-- ``dataset_metadata_not_in_data_table``: Use ``dataset_metadata_in_data_table`` with ``negate="true"``.
 
 ### Validators for textual inputs (``text``, ``select``, ...)
 
@@ -3672,10 +3672,7 @@ For ``text`` inputs the following validators are useful:
 - ``empty_field``: Check if the string is not empty
 - ``value_in_data_table``: Check if the value is
 contained in a column of a given data table.
-
-Deprecated:
-
-- ``value_not_in_data_table``: Use ``value_in_data_table`` with ``negate="true"``.
+- ``value_not_in_data_table``: Equivalent to ``value_in_data_table`` with ``negate="true"``.
 
 ### Validators for numeric inputs (``integer``, ``float``)
 
@@ -3736,9 +3733,10 @@ use in filenames may not contain ``..``.
             <xs:documentation xml:lang="en"><![CDATA[
 Valid values are: ``expression``, ``regex``, ``in_range``, ``length``,
 ``metadata``, ``unspecified_build``, ``no_options``, ``empty_field``,
-``dataset_metadata_in_data_table``, ``value_in_data_table``,
+``dataset_metadata_in_data_table``, ``dataset_metadata_not_in_data_table``,
+``value_in_data_table``, ``value_not_in_data_table``,
 ``dataset_ok_validator``, ``dataset_metadata_in_range``.
-Deprecated validators: ``dataset_metadata_in_file``, ``value_not_in_data_table``, ``dataset_metadata_not_in_data_table``.
+Deprecated validator: ``dataset_metadata_in_file``.
 The list of supported
 validators is in the ``validator_types`` dictionary in
 [/lib/galaxy/tools/parameters/validation.py](https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/tools/parameters/validation.py).
diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py
index 3f91097dce6..04236235cf4 100644
--- a/lib/galaxy/tools/parameters/validation.py
+++ b/lib/galaxy/tools/parameters/validation.py
@@ -816,8 +816,7 @@ class ValueInDataTableColumnValidator(Validator):
 class ValueNotInDataTableColumnValidator(ValueInDataTableColumnValidator):
     """
     Validator that checks if a value is NOT in a tool data table column.
-
-    Deprecated: use now the `negate` attribute
+    Equivalent to ValueInDataTableColumnValidator with `negate="true"`.
 
     note: this is covered in a framework test (validation_value_in_datatable)
     """
@@ -871,8 +870,7 @@ class MetadataInDataTableColumnValidator(ValueInDataTableColumnValidator):
 class MetadataNotInDataTableColumnValidator(MetadataInDataTableColumnValidator):
     """
     Validator that checks if the value for a dataset's metadata item doesn't exists in a file.
-
-    Deprecated: use now the `negate` attribute
+    Equivalent to MetadataInDataTableColumnValidator with `negate="true"`.
 
     note: this is covered in a framework test (validation_metadata_in_datatable)
     """
@@ -940,15 +938,15 @@ validator_types = dict(
     empty_dataset=DatasetEmptyValidator,
     empty_extra_files_path=DatasetExtraFilesPathEmptyValidator,
     dataset_metadata_in_data_table=MetadataInDataTableColumnValidator,
+    dataset_metadata_not_in_data_table=MetadataNotInDataTableColumnValidator,
     dataset_metadata_in_range=MetadataInRangeValidator,
     value_in_data_table=ValueInDataTableColumnValidator,
+    value_not_in_data_table=ValueNotInDataTableColumnValidator,
     dataset_ok_validator=DatasetOkValidator,
 )
 
 deprecated_validator_types = dict(
-    dataset_metadata_in_file=MetadataInFileColumnValidator,
-    dataset_metadata_not_in_data_table=MetadataNotInDataTableColumnValidator,
-    value_not_in_data_table=ValueNotInDataTableColumnValidator,
+    dataset_metadata_in_file=MetadataInFileColumnValidator
 )
 validator_types.update(deprecated_validator_types)