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Handle new order of UNITS in ENA checklists #124

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Merged
bedroesb merged 1 commit into from
Mar 6, 2026
Merged

Handle new order of UNITS in ENA checklists #124

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6 changes: 3 additions & 3 deletions ena_upload/templates/ENA_template_samples_ERC000026.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -63,10 +63,10 @@ def mandatorytest(row, column, index):
<VALUE>${row['disease_site']}</VALUE>
</SAMPLE_ATTRIBUTE>
</py:if>
<py:if test="attributetest(row, 'sample_type')">
<py:if test="attributetest(row, 'sample type')">
<SAMPLE_ATTRIBUTE>
<TAG>sample_type</TAG>
<VALUE>${row['sample_type']}</VALUE>
<TAG>sample type</TAG>
<VALUE>${row['sample type']}</VALUE>
</SAMPLE_ATTRIBUTE>
</py:if>
<py:if test="attributetest(row, 'donor_id')">
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30 changes: 15 additions & 15 deletions ena_upload/templates/ENA_template_samples_ERC000046.xml
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Expand Up @@ -33,10 +33,10 @@ def mandatorytest(row, column, index):
<DESCRIPTION>${row.sample_description}</DESCRIPTION>
</py:if>
<SAMPLE_ATTRIBUTES>
<py:if test="attributetest(row, 'project_name')">
<py:if test="attributetest(row, 'project name')">
<SAMPLE_ATTRIBUTE>
<TAG>project_name</TAG>
<VALUE>${row['project_name']}</VALUE>
<TAG>project name</TAG>
<VALUE>${row['project name']}</VALUE>
</SAMPLE_ATTRIBUTE>
</py:if>
<py:if test="mandatorytest(row, 'subject_id', index)">
Expand All @@ -57,28 +57,28 @@ def mandatorytest(row, column, index):
<VALUE>${row['phenotype']}</VALUE>
</SAMPLE_ATTRIBUTE>
</py:if>
<py:if test="mandatorytest(row, 'sample_type', index)">
<py:if test="mandatorytest(row, 'sample type', index)">
<SAMPLE_ATTRIBUTE>
<TAG>sample_type</TAG>
<VALUE>${row['sample_type']}</VALUE>
<TAG>sample type</TAG>
<VALUE>${row['sample type']}</VALUE>
</SAMPLE_ATTRIBUTE>
</py:if>
<py:if test="mandatorytest(row, 'ppcg_id', index)">
<py:if test="mandatorytest(row, 'PPCG ID', index)">
<SAMPLE_ATTRIBUTE>
<TAG>ppcg_id</TAG>
<VALUE>${row['ppcg_id']}</VALUE>
<TAG>PPCG ID</TAG>
<VALUE>${row['PPCG ID']}</VALUE>
</SAMPLE_ATTRIBUTE>
</py:if>
<py:if test="mandatorytest(row, 'ppcg_sample_id', index)">
<py:if test="mandatorytest(row, 'PPCG sample ID', index)">
<SAMPLE_ATTRIBUTE>
<TAG>ppcg_sample_id</TAG>
<VALUE>${row['ppcg_sample_id']}</VALUE>
<TAG>PPCG sample ID</TAG>
<VALUE>${row['PPCG sample ID']}</VALUE>
</SAMPLE_ATTRIBUTE>
</py:if>
<py:if test="mandatorytest(row, 'pipelineuuid', index)">
<py:if test="mandatorytest(row, 'Pipeline/UUID', index)">
<SAMPLE_ATTRIBUTE>
<TAG>pipelineuuid</TAG>
<VALUE>${row['pipelineuuid']}</VALUE>
<TAG>Pipeline/UUID</TAG>
<VALUE>${row['Pipeline/UUID']}</VALUE>
</SAMPLE_ATTRIBUTE>
</py:if>
<py:if test="mandatorytest(row, 'preservation', index)">
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1 change: 0 additions & 1 deletion ena_upload/templates/ENA_template_samples_ERC000056.xml
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Expand Up @@ -1287,7 +1287,6 @@ def mandatorytest(row, column, index):
<SAMPLE_ATTRIBUTE>
<TAG>nucleic acid extraction kit</TAG>
<VALUE>${row['nucleic acid extraction kit']}</VALUE>
<UNITS>ppm</UNITS>
</SAMPLE_ATTRIBUTE>
</py:if>
<py:if test="attributetest(row, 'sample pooling')">
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