fix + paired end xlsx example

usegalaxy-eu · Dec 7, 2024 · 5d47b99 · 5d47b99
1 parent ed08d89
commit 5d47b99
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/ena_upload/ena_upload.py b/ena_upload/ena_upload.py
@@ -222,8 +222,8 @@ def generate_stream(schema, targets, Template, center, tool):
             targets.rename(columns={'file_format': 'file_type'}, inplace=True)
         file_attrib = ['file_name', 'file_type', 'file_checksum']
         other_attrib = ['alias', 'experiment_alias']
-        run_groups = targets[other_attrib].groupby(targets['alias'])
-        run_groups = run_groups.experiment_alias.unique()
+        # Create groups with alias as index
+        run_groups = targets[other_attrib].groupby('alias')['experiment_alias'].first().to_dict()
         file_groups = targets[file_attrib].groupby(targets['alias'])
 
         # param in generate() determined by the setup in template

diff --git a/ena_upload/templates/ENA_template_runs.xml b/ena_upload/templates/ENA_template_runs.xml
@@ -18,7 +18,7 @@ def mandatorytest(row, column, index):
         <EXPERIMENT_REF refname="${experiment_alias}"/>
         <DATA_BLOCK>
             <FILES>
-                <py:for each="index, row in file_groups.get_group((alias,)).iterrows()">
+                <py:for each="index, row in file_groups.get_group(alias).iterrows()">
                 <py:if test="mandatorytest(row, 'file_type', index)">
                 <xi:include href="ENA_template_FILE.xml" />
                 </py:if>

diff --git a/example_tables/ENA_excel_example_ERC000033.xlsx b/example_tables/ENA_excel_example_ERC000033.xlsx