From d512049a4aa98c0cc82e5376703e6eebd7734697 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Wed, 9 Dec 2020 21:52:43 +0100
Subject: [PATCH] more specific functional tool tests involving
 fasta_indexes.loc

rename entries such that they are suffixed by the column name
(execpt for dbkey).
this makes tests more specific, because this ensures that always
the correct column is used.
---
 lib/galaxy_test/api/test_tools.py             |  4 +--
 test/functional/tool-data/fasta_indexes.loc   |  4 +--
 .../tools/dbkey_filter_collection.xml         | 16 +++++-----
 test/functional/tools/dbkey_filter_input.xml  |  6 ++--
 .../tools/dbkey_filter_multi_input.xml        |  6 ++--
 test/functional/tools/dbkey_output_action.xml |  2 +-
 .../functional/tools/filter_static_regexp.xml | 32 +++++++++----------
 test/functional/tools/remove_value.xml        |  8 ++---
 test/functional/tools/select_from_dataset.xml | 20 ++++++------
 9 files changed, 49 insertions(+), 49 deletions(-)

diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py
index e8c5d8f9e00..6a81373ebb4 100644
--- a/lib/galaxy_test/api/test_tools.py
+++ b/lib/galaxy_test/api/test_tools.py
@@ -1217,7 +1217,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         tool_test_dicts = [{
             "inputs": {
                 "input": ["simple_line.txt"],
-                "index": ["hg18"],
+                "index": ["hg18_value"],
             },
             "outputs": {},
             "required_files": [['simple_line.txt', {'value': 'simple_line.txt', 'dbkey': 'hg18'}]],
@@ -1235,7 +1235,7 @@ class ToolsTestCase(ApiTestCase, TestsTools):
         tool_test_dicts = [{
             "inputs": {
                 "input": ["simple_line.txt"],
-                "index": ["hg18"],
+                "index": ["hg18_value"],
             },
             "outputs": {},
             "required_files": [['simple_line.txt', {'value': 'simple_line.txt', 'dbkey': 'hgnot18'}]],
diff --git a/test/functional/tool-data/fasta_indexes.loc b/test/functional/tool-data/fasta_indexes.loc
index 3383ed89752..57f11daa9a9 100644
--- a/test/functional/tool-data/fasta_indexes.loc
+++ b/test/functional/tool-data/fasta_indexes.loc
@@ -1,2 +1,2 @@
-hg19	hg19	hg19	hg19
-hg18	hg18	hg18	hg18
\ No newline at end of file
+hg19_value	hg19	hg19_name	hg19_path
+hg18_value	hg18	hg18_name	hg18_path
diff --git a/test/functional/tools/dbkey_filter_collection.xml b/test/functional/tools/dbkey_filter_collection.xml
index eeb5937336e..ed8b5a13d8f 100644
--- a/test/functional/tools/dbkey_filter_collection.xml
+++ b/test/functional/tools/dbkey_filter_collection.xml
@@ -31,9 +31,9 @@
                     <element name="e2" value="simple_line_alternative.txt" dbkey="hg19"/>
                 </collection>
             </param>
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output">
-                <assert_contents><has_text text="hg19" /></assert_contents>
+                <assert_contents><has_text text="hg19_value" /></assert_contents>
             </output>
         </test>
         <!-- can choose any dbkey if none specified in reference -->
@@ -44,10 +44,10 @@
                     <element name="e2" value="simple_line_alternative.txt"/>
                 </collection>
             </param>
-            <param name="index" value="hg18" />
+            <param name="index" value="hg18_value" />
             <output name="output">
                 <assert_contents>
-                    <has_text text="hg18" /></assert_contents>
+                    <has_text text="hg18_value" /></assert_contents>
             </output>
         </test>
         <!-- can choose any dbkey specified in reference -->
@@ -58,9 +58,9 @@
                     <element name="e2" value="simple_line_alternative.txt" dbkey="hg18"/>
                 </collection>
             </param>
-            <param name="index" value="hg18" />
+            <param name="index" value="hg18_value" />
             <output name="output">
-                <assert_contents><has_text text="hg18" /></assert_contents>
+                <assert_contents><has_text text="hg18_value" /></assert_contents>
             </output>
         </test>
         <!-- cant choose a dkkey different from reference -->
@@ -71,9 +71,9 @@
                     <element name="e2" value="simple_line_alternative.txt" dbkey="hg19"/>
                 </collection>
             </param>
-            <param name="index" value="hg18" />
+            <param name="index" value="hg18_value" />
             <output name="output">
-                <assert_contents><not_has_text text="hg18" /></assert_contents>
+                <assert_contents><not_has_text text="hg18_value" /></assert_contents>
             </output>
         </test>
     </tests>
diff --git a/test/functional/tools/dbkey_filter_input.xml b/test/functional/tools/dbkey_filter_input.xml
index ae04f6fc58f..8bf19cdd574 100644
--- a/test/functional/tools/dbkey_filter_input.xml
+++ b/test/functional/tools/dbkey_filter_input.xml
@@ -21,19 +21,19 @@ cat '$inputs' > '$output'
         <!-- can choose a dbkey if it matches input -->
         <test>
             <param name="inputs" value="simple_line.txt" dbkey="hg19" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line.txt" />
         </test>
         <!-- choose any dbkey if not specified in reference -->
         <test>
             <param name="inputs" value="simple_line.txt" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line.txt" />
         </test>
         <!-- cant choose a dkkey different from reference -->
         <test expect_failure="true">
             <param name="inputs" value="simple_line.txt" dbkey="hg18" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line.txt" />
         </test>
     </tests>
diff --git a/test/functional/tools/dbkey_filter_multi_input.xml b/test/functional/tools/dbkey_filter_multi_input.xml
index df04926938d..9463440c2af 100644
--- a/test/functional/tools/dbkey_filter_multi_input.xml
+++ b/test/functional/tools/dbkey_filter_multi_input.xml
@@ -23,19 +23,19 @@
         <!-- can choose a dbkey if it matches input -->
         <test>
             <param name="inputs" value="simple_line.txt,simple_line.txt" dbkey="hg19" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line_x2.txt"/>
         </test>
         <!-- can choose any dbkey if none specified in reference -->
         <test>
             <param name="inputs" value="simple_line.txt,simple_line.txt" />
-            <param name="index" value="hg19" />
+            <param name="index" value="hg19_value" />
             <output name="output" file="simple_line_x2.txt"/>
         </test>
         <!-- can choose any dbkey none specified in reference -->
         <test expect_failure="true">
             <param name="inputs" value="simple_line.txt,simple_line.txt" dbkey="hg19"/>
-            <param name="index" value="hg18" />
+            <param name="index" value="hg18_value" />
             <output name="output" file="simple_line_x2.txt"/>
         </test>
     </tests>
diff --git a/test/functional/tools/dbkey_output_action.xml b/test/functional/tools/dbkey_output_action.xml
index 128e43d721f..1d29a0b4e65 100644
--- a/test/functional/tools/dbkey_output_action.xml
+++ b/test/functional/tools/dbkey_output_action.xml
@@ -26,7 +26,7 @@ echo foo > '$mapped_reads'
     <tests>
         <test>
             <param name="input" value="simple_line.txt" dbkey="hg18" />
-            <param name="index" value="hg18"/>
+            <param name="index" value="hg18_value"/>
             <output name="mapped_reads">
                 <metadata name="dbkey" value="hg18" />
                 <assert_contents>
diff --git a/test/functional/tools/filter_static_regexp.xml b/test/functional/tools/filter_static_regexp.xml
index ebfcd0756e8..090f8835e8d 100644
--- a/test/functional/tools/filter_static_regexp.xml
+++ b/test/functional/tools/filter_static_regexp.xml
@@ -45,10 +45,10 @@ echo $index_regexp_keep >> '$output' &&
     <tests>
         <!-- can choose a dbkey if it matches input -->
         <test>
-            <param name="index_static" value="hg19" />
-            <param name="index_static_keep" value="hg19" />
-            <param name="index_regexp" value="hg19" />
-            <param name="index_regexp_keep" value="hg19" />
+            <param name="index_static" value="hg19_value" />
+            <param name="index_static_keep" value="hg19_value" />
+            <param name="index_regexp" value="hg19_value" />
+            <param name="index_regexp_keep" value="hg19_value" />
             <output name="output">
                 <assert_contents>
                     <has_text text="hg19" />    
@@ -60,24 +60,24 @@ echo $index_regexp_keep >> '$output' &&
         <!-- Does this make sense - if no dbkey is defined there is no option
              available? -->
         <test expect_failure="true">
-            <param name="index_static" value="hg18" />
-            <param name="index_static_keep" value="hg19" />
-            <param name="index_regexp" value="hg19" />
-            <param name="index_regexp_keep" value="hg19" />
+            <param name="index_static" value="hg18_value" />
+            <param name="index_static_keep" value="hg19_value" />
+            <param name="index_regexp" value="hg19_value" />
+            <param name="index_regexp_keep" value="hg19_value" />
             <output name="output"/>
         </test>
         <test expect_failure="true">
-            <param name="index_static" value="hg19" />
-            <param name="index_static_keep" value="hg18" />
-            <param name="index_regexp" value="hg19" />
-            <param name="index_regexp_keep" value="hg19" />
+            <param name="index_static" value="hg19_value" />
+            <param name="index_static_keep" value="hg18_value" />
+            <param name="index_regexp" value="hg19_value" />
+            <param name="index_regexp_keep" value="hg19_value" />
             <output name="output"/>
         </test>
         <test expect_failure="true">
-            <param name="index_static" value="hg19" />
-            <param name="index_static_keep" value="hg19" />
-            <param name="index_regexp" value="hg18" />
-            <param name="index_regexp_keep" value="hg19" />
+            <param name="index_static" value="hg19_value" />
+            <param name="index_static_keep" value="hg19_value" />
+            <param name="index_regexp" value="hg18_value" />
+            <param name="index_regexp_keep" value="hg19_value" />
             <output name="output"/>
         </test>
         <test expect_failure="true">
diff --git a/test/functional/tools/remove_value.xml b/test/functional/tools/remove_value.xml
index 5671e27e278..b01e01a24f5 100644
--- a/test/functional/tools/remove_value.xml
+++ b/test/functional/tools/remove_value.xml
@@ -6,8 +6,8 @@ echo $choose_value > '$out_file'
         <param name="choose_value" type="select">
             <options from_data_table="test_fasta_indexes">
                 <!-- contains hg18 and hg19 -->
-                <filter type="remove_value" value="hg18"/>
-                <filter type="remove_value" value="hg20"/>
+                <filter type="remove_value" value="hg18_value"/>
+                <filter type="remove_value" value="hg20_value"/>
                 <!-- This doesn't work as we don't have the remaining values like name and path
                 <filter type="add_value" value="hg20"/>
                 -->
@@ -21,12 +21,12 @@ echo $choose_value > '$out_file'
         <test>
             <output name="out_file">
                 <assert_contents>
-                    <has_line line="hg19" />
+                    <has_line line="hg19_value" />
                 </assert_contents>
             </output>
         </test>
         <test expect_failure="true">
-            <param name="choose_value" value="hg18"/>
+            <param name="choose_value" value="hg18_value"/>
         </test>
     </tests>
 </tool>
diff --git a/test/functional/tools/select_from_dataset.xml b/test/functional/tools/select_from_dataset.xml
index 3a67ac01db8..14c89aa1877 100644
--- a/test/functional/tools/select_from_dataset.xml
+++ b/test/functional/tools/select_from_dataset.xml
@@ -5,7 +5,7 @@ echo select_single '$select_single' > '$output' &&
 echo select_multiple '$select_multiple' >> '$output' &&
 echo select_collection '$select_collection' >> '$output'
     ]]></command>
-	<inputs>
+    <inputs>
         <param name="single" type="data" format="tabular" label="single"/>
         <param name="select_single" type="select" label="select_single">
             <options from_dataset="single">
@@ -22,14 +22,14 @@ echo select_collection '$select_collection' >> '$output'
                 <validator type="no_options" message="No data is available in single" />
             </options>
         </param>
-		<param name="collection" type="data_collection" format="tabular" collection_type="list" label="collection"/>
+        <param name="collection" type="data_collection" format="tabular" collection_type="list" label="collection"/>
         <param name="select_collection" type="select" multiple="true" label="select_collection">
             <options from_dataset="collection">
                 <column name="name" index="0"/>
                 <column name="value" index="0"/>
                 <validator type="no_options" message="No data is available in single" />
             </options>
-		</param>
+        </param>
     </inputs>
 
     <outputs>
@@ -39,16 +39,16 @@ echo select_collection '$select_collection' >> '$output'
     <tests>
         <test>
             <param name="single" value="1.tabular" />
-			<param name="select_single" value="chr10" />
+            <param name="select_single" value="chr10" />
             <param name="multiple" value="1.tabular,2.tabular" />
             <param name="select_multiple" value="chr10,7" />
-			<param name="collection">
-			    <collection type="list">
-					<element name="1" value="1.tabular" />
-					<element name="2" value="2.tabular" />
+            <param name="collection">
+                <collection type="list">
+                    <element name="1" value="1.tabular" />
+                    <element name="2" value="2.tabular" />
                 </collection>
-	        </param>
-			<param name="select_collection" value="chr10,7" />
+            </param>
+            <param name="select_collection" value="chr10,7" />
             <output name="output">
                 <assert_contents>
                     <has_text text="select_single chr10" />