Merge pull request #81 from usegalaxy-eu/checklist_update

Automatic update of ENA Sample Checklists
usegalaxy-eu · Jun 5, 2023 · 455c38d · 455c38d
2 parents 87f9478 + 94c4a2d
commit 455c38d
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diff --git a/ena_upload/templates/ENA_template_samples_ERC000011.xml b/ena_upload/templates/ENA_template_samples_ERC000011.xml
@@ -70,18 +70,14 @@ 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>
                 <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
             </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'geographic location (region and locality)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (region and locality)</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000027.xml b/ena_upload/templates/ENA_template_samples_ERC000027.xml
@@ -224,12 +224,10 @@ def attributetest(row, column):
                 <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
@@ -111,18 +111,14 @@ 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_ERC000032.xml b/ena_upload/templates/ENA_template_samples_ERC000032.xml
@@ -160,12 +160,10 @@ def attributetest(row, column):
                 <VALUE>${row['illness symptoms']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'collection date')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>collection date</TAG>
                 <VALUE>${row['collection date']}</VALUE>
             </SAMPLE_ATTRIBUTE>
-            </py:if>
             <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_ERC000033.xml b/ena_upload/templates/ENA_template_samples_ERC000033.xml
@@ -64,12 +64,10 @@ def attributetest(row, column):
                 <VALUE>${row['illness symptoms']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'collection date')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>collection date</TAG>
                 <VALUE>${row['collection date']}</VALUE>
             </SAMPLE_ATTRIBUTE>
-            </py:if>
             <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_ERC000034.xml b/ena_upload/templates/ENA_template_samples_ERC000034.xml
@@ -26,18 +26,14 @@ 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
@@ -58,18 +58,14 @@ 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
@@ -51,12 +51,10 @@ def attributetest(row, column):
                 <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_ERC000039.xml b/ena_upload/templates/ENA_template_samples_ERC000039.xml
@@ -56,12 +56,10 @@ def attributetest(row, column):
                 <VALUE>${row['country of travel']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
-            <py:if test="attributetest(row, 'collection date')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>collection date</TAG>
                 <VALUE>${row['collection date']}</VALUE>
             </SAMPLE_ATTRIBUTE>
-            </py:if>
             <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_ERC000041.xml b/ena_upload/templates/ENA_template_samples_ERC000041.xml
@@ -65,18 +65,14 @@ def attributetest(row, column):
                 <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>
                 <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
             </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'geographic location (region and locality)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (region and locality)</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000043.xml b/ena_upload/templates/ENA_template_samples_ERC000043.xml
@@ -35,18 +35,14 @@ 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>
                 <VALUE>${row['geographic location (country and/or sea)']}</VALUE>
             </SAMPLE_ATTRIBUTE>
-            </py:if>
             <py:if test="attributetest(row, 'geographic location (latitude)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000045.xml b/ena_upload/templates/ENA_template_samples_ERC000045.xml
@@ -36,12 +36,10 @@ def attributetest(row, column):
                 <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>
             <py:if test="attributetest(row, 'geographic location (region and locality)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (region and locality)</TAG>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000051.xml b/ena_upload/templates/ENA_template_samples_ERC000051.xml
@@ -22,18 +22,14 @@ 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>

diff --git a/ena_upload/templates/ENA_template_samples_ERC000052.xml b/ena_upload/templates/ENA_template_samples_ERC000052.xml
@@ -57,18 +57,14 @@ def attributetest(row, column):
                 <TAG>reference host genome for decontamination</TAG>
                 <VALUE>${row['reference host genome for decontamination']}</VALUE>
             </SAMPLE_ATTRIBUTE>
-            <py:if test="attributetest(row, 'collection date')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>collection date</TAG>
                 <VALUE>${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>
             <py:if test="attributetest(row, 'geographic location (latitude)')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>geographic location (latitude)</TAG>