Merge pull request #78 from usegalaxy-eu/checklist_update

Automatic update of ENA Sample Checklists
usegalaxy-eu · Apr 10, 2023 · 07a4018 · 07a4018
2 parents 7605d87 + 26c67b6
commit 07a4018
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Showing 11 changed files with 94 additions and 32 deletions.
diff --git a/ena_upload/templates/ENA_template_samples_ERC000011.xml b/ena_upload/templates/ENA_template_samples_ERC000011.xml
@@ -52,12 +52,6 @@ def attributetest(row, column):
                 <VALUE>${row['tissue_type']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'collection_date')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>collection_date</TAG>
-                <VALUE>${row['collection_date']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'isolation_source')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>isolation_source</TAG>
@@ -76,6 +70,12 @@ def attributetest(row, column):
                 <VALUE>${row['collected_by']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="attributetest(row, 'collection date')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'geographic location (country and/or sea)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (country and/or sea)</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000027.xml b/ena_upload/templates/ENA_template_samples_ERC000027.xml
@@ -22,10 +22,6 @@ def attributetest(row, column):
         </SAMPLE_NAME>
         <DESCRIPTION>${row.sample_description}</DESCRIPTION>
         <SAMPLE_ATTRIBUTES>
-            <SAMPLE_ATTRIBUTE>
-                <TAG>Event Date/Time</TAG>
-                <VALUE>${row['Event Date/Time']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
             <SAMPLE_ATTRIBUTE>
                 <TAG>Latitude Start</TAG>
                 <VALUE>${row['Latitude Start']}</VALUE>
@@ -224,6 +220,16 @@ def attributetest(row, column):
                 <TAG>environmental package</TAG>
                 <VALUE>${row['environmental package']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            <py:if test="attributetest(row, 'geographic location (country and/or sea)')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <SAMPLE_ATTRIBUTE>
                 <TAG>broad-scale environmental context</TAG>
                 <VALUE>${row['broad-scale environmental context']}</VALUE>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000030.xml b/ena_upload/templates/ENA_template_samples_ERC000030.xml
@@ -28,10 +28,12 @@ def attributetest(row, column):
                 <VALUE>${row['Event Label']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="attributetest(row, 'Event Date/Time Start')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>Event Date/Time Start</TAG>
                 <VALUE>${row['Event Date/Time Start']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'Event Date/Time End')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>Event Date/Time End</TAG>
@@ -109,6 +111,18 @@ def attributetest(row, column):
                 <TAG>environmental package</TAG>
                 <VALUE>${row['environmental package']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            <py:if test="attributetest(row, 'collection date')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'geographic location (country and/or sea)')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <SAMPLE_ATTRIBUTE>
                 <TAG>broad-scale environmental context</TAG>
                 <VALUE>${row['broad-scale environmental context']}</VALUE>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000034.xml b/ena_upload/templates/ENA_template_samples_ERC000034.xml
@@ -26,6 +26,18 @@ def attributetest(row, column):
                 <TAG>tissue_type</TAG>
                 <VALUE>${row['tissue_type']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            <py:if test="attributetest(row, 'collection date')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'geographic location (country and/or sea)')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <SAMPLE_ATTRIBUTE>
                 <TAG>sex</TAG>
                 <VALUE>${row['sex']}</VALUE>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000035.xml b/ena_upload/templates/ENA_template_samples_ERC000035.xml
@@ -58,6 +58,18 @@ def attributetest(row, column):
                 <VALUE>${row['protocol']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="attributetest(row, 'collection date')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'geographic location (country and/or sea)')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'sampling time point')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>sampling time point</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000038.xml b/ena_upload/templates/ENA_template_samples_ERC000038.xml
@@ -22,10 +22,6 @@ def attributetest(row, column):
         </SAMPLE_NAME>
         <DESCRIPTION>${row.sample_description}</DESCRIPTION>
         <SAMPLE_ATTRIBUTES>
-            <SAMPLE_ATTRIBUTE>
-                <TAG>Event Date/Time</TAG>
-                <VALUE>${row['Event Date/Time']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
             <SAMPLE_ATTRIBUTE>
                 <TAG>Latitude Start</TAG>
                 <VALUE>${row['Latitude Start']}</VALUE>
@@ -51,6 +47,16 @@ def attributetest(row, column):
                 <TAG>Protocol Label</TAG>
                 <VALUE>${row['Protocol Label']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            <py:if test="attributetest(row, 'geographic location (country and/or sea)')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <SAMPLE_ATTRIBUTE>
                 <TAG>broad-scale environmental context</TAG>
                 <VALUE>${row['broad-scale environmental context']}</VALUE>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000041.xml b/ena_upload/templates/ENA_template_samples_ERC000041.xml
@@ -59,18 +59,18 @@ def attributetest(row, column):
                 <UNITS>ng/µl</UNITS>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'collection_date')">
-            <SAMPLE_ATTRIBUTE>
-                <TAG>collection_date</TAG>
-                <VALUE>${row['collection_date']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'isolation_source')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>isolation_source</TAG>
                 <VALUE>${row['isolation_source']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="attributetest(row, 'collection date')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'geographic location (country and/or sea)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (country and/or sea)</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000044.xml b/ena_upload/templates/ENA_template_samples_ERC000044.xml
@@ -52,14 +52,14 @@ def attributetest(row, column):
                 <VALUE>${row['country of travel']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <SAMPLE_ATTRIBUTE>
-                <TAG>collection_date</TAG>
-                <VALUE>${row['collection_date']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
             <SAMPLE_ATTRIBUTE>
                 <TAG>collected_by</TAG>
                 <VALUE>${row['collected_by']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (country and/or sea)</TAG>
                 <VALUE>${row['geographic location (country and/or sea)']}</VALUE>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000045.xml b/ena_upload/templates/ENA_template_samples_ERC000045.xml
@@ -22,10 +22,6 @@ def attributetest(row, column):
         </SAMPLE_NAME>
         <DESCRIPTION>${row.sample_description}</DESCRIPTION>
         <SAMPLE_ATTRIBUTES>
-            <SAMPLE_ATTRIBUTE>
-                <TAG>collection_date</TAG>
-                <VALUE>${row['collection_date']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
             <SAMPLE_ATTRIBUTE>
                 <TAG>isolation_source</TAG>
                 <VALUE>${row['isolation_source']}</VALUE>
@@ -36,6 +32,10 @@ def attributetest(row, column):
                 <VALUE>${row['collected_by']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
             <py:if test="attributetest(row, 'geographic location (country and/or sea)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (country and/or sea)</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000048.xml b/ena_upload/templates/ENA_template_samples_ERC000048.xml
@@ -244,14 +244,14 @@ def attributetest(row, column):
                 <VALUE>${row['WGA amplification kit']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <SAMPLE_ATTRIBUTE>
-                <TAG>collection_date</TAG>
-                <VALUE>${row['collection_date']}</VALUE>
-            </SAMPLE_ATTRIBUTE>
             <SAMPLE_ATTRIBUTE>
                 <TAG>isolation_source</TAG>
                 <VALUE>${row['isolation_source']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
             <py:if test="attributetest(row, 'altitude')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>altitude</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000051.xml b/ena_upload/templates/ENA_template_samples_ERC000051.xml
@@ -22,6 +22,18 @@ def attributetest(row, column):
         </SAMPLE_NAME>
         <DESCRIPTION>${row.sample_description}</DESCRIPTION>
         <SAMPLE_ATTRIBUTES>
+            <py:if test="attributetest(row, 'collection date')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>collection date</TAG>
+                <VALUE>${row['collection date']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'geographic location (country and/or sea)')">
+            <SAMPLE_ATTRIBUTE>
+                <TAG>geographic location (country and/or sea)</TAG>
+                <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
+            </SAMPLE_ATTRIBUTE>
+            </py:if>
             <SAMPLE_ATTRIBUTE>
                 <TAG>sample origin</TAG>
                 <VALUE>${row['sample origin']}</VALUE>