From cde0b9b546b30cbe271633bd05ea1a90d2ef3ef2 Mon Sep 17 00:00:00 2001
From: bedroesb <bedroesb@users.noreply.github.com>
Date: Mon, 23 Jan 2023 13:09:30 +0000
Subject: [PATCH] Update ENA Sample Checklists

---
 .../templates/ENA_template_PLATFORM.xml       |  8 ++++++
 .../ENA_template_samples_ERC000047.xml        |  2 ++
 .../ENA_template_samples_ERC000048.xml        |  8 ++++++
 ena_upload/templates/SRA.common.xsd           | 28 +++++++++++++++++++
 4 files changed, 46 insertions(+)

diff --git a/ena_upload/templates/ENA_template_PLATFORM.xml b/ena_upload/templates/ENA_template_PLATFORM.xml
index 53ec5ef..acfd8d8 100644
--- a/ena_upload/templates/ENA_template_PLATFORM.xml
+++ b/ena_upload/templates/ENA_template_PLATFORM.xml
@@ -101,4 +101,12 @@
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'dnbseq-g400 fast'">DNBSEQ-G400 FAST</INSTRUMENT_MODEL>
     <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
 </DNBSEQ>
+<ELEMENT py:when="row.platform.lower().strip() == 'element'" py:choose="">
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'element aviti'">Element AVITI</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
+</ELEMENT>
+<ULTIMA py:when="row.platform.lower().strip() == 'ultima'" py:choose="">
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'ug 100'">UG 100</INSTRUMENT_MODEL>
+    <INSTRUMENT_MODEL py:when="row.instrument_model.lower().strip() == 'unspecified'">unspecified</INSTRUMENT_MODEL>
+</ULTIMA>
 </PLATFORM>
\ No newline at end of file
diff --git a/ena_upload/templates/ENA_template_samples_ERC000047.xml b/ena_upload/templates/ENA_template_samples_ERC000047.xml
index 9b47660..71018dc 100644
--- a/ena_upload/templates/ENA_template_samples_ERC000047.xml
+++ b/ena_upload/templates/ENA_template_samples_ERC000047.xml
@@ -116,10 +116,12 @@ def attributetest(row, column):
                 <VALUE>${row['number of standard tRNAs extracted']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="attributetest(row, 'assembly software')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>assembly software</TAG>
                 <VALUE>${row['assembly software']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'feature prediction')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>feature prediction</TAG>
diff --git a/ena_upload/templates/ENA_template_samples_ERC000048.xml b/ena_upload/templates/ENA_template_samples_ERC000048.xml
index 2cd3ddc..341ef35 100644
--- a/ena_upload/templates/ENA_template_samples_ERC000048.xml
+++ b/ena_upload/templates/ENA_template_samples_ERC000048.xml
@@ -116,10 +116,12 @@ def attributetest(row, column):
                 <VALUE>${row['number of standard tRNAs extracted']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="attributetest(row, 'assembly software')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>assembly software</TAG>
                 <VALUE>${row['assembly software']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'feature prediction')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>feature prediction</TAG>
@@ -156,15 +158,19 @@ def attributetest(row, column):
                 <VALUE>${row['tRNA extraction software']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="attributetest(row, 'completeness score')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>completeness score</TAG>
                 <VALUE>${row['completeness score']}</VALUE>
                 <UNITS>%</UNITS>
             </SAMPLE_ATTRIBUTE>
+            </py:if>
+            <py:if test="attributetest(row, 'completeness software')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>completeness software</TAG>
                 <VALUE>${row['completeness software']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'completeness approach')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>completeness approach</TAG>
@@ -202,10 +208,12 @@ def attributetest(row, column):
                 <VALUE>${row['assembly quality']}</VALUE>
             </SAMPLE_ATTRIBUTE>
             </py:if>
+            <py:if test="attributetest(row, 'taxonomic identity marker')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>taxonomic identity marker</TAG>
                 <VALUE>${row['taxonomic identity marker']}</VALUE>
             </SAMPLE_ATTRIBUTE>
+            </py:if>
             <py:if test="attributetest(row, 'taxonomic classification')">
             <SAMPLE_ATTRIBUTE>
                 <TAG>taxonomic classification</TAG>
diff --git a/ena_upload/templates/SRA.common.xsd b/ena_upload/templates/SRA.common.xsd
index c53631a..019f62c 100644
--- a/ena_upload/templates/SRA.common.xsd
+++ b/ena_upload/templates/SRA.common.xsd
@@ -675,6 +675,20 @@
                     </xs:sequence>
                 </xs:complexType>
             </xs:element>
+            <xs:element name="ELEMENT">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="INSTRUMENT_MODEL" maxOccurs="1" minOccurs="1" type="com:typeElementModel"/>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
+            <xs:element name="ULTIMA">
+                <xs:complexType>
+                    <xs:sequence>
+                        <xs:element name="INSTRUMENT_MODEL" maxOccurs="1" minOccurs="1" type="com:typeUltimaModel"/>
+                    </xs:sequence>
+                </xs:complexType>
+            </xs:element>
         </xs:choice>
 
     </xs:complexType>
@@ -1040,6 +1054,20 @@
         </xs:restriction>
     </xs:simpleType>
 
+    <xs:simpleType name="typeElementModel">
+        <xs:restriction base="xs:string">
+            <xs:enumeration value="Element AVITI"/>
+            <xs:enumeration value="unspecified"/>
+        </xs:restriction>
+    </xs:simpleType>
+
+    <xs:simpleType name="typeUltimaModel">
+        <xs:restriction base="xs:string">
+            <xs:enumeration value="UG 100"/>
+            <xs:enumeration value="unspecified"/>
+        </xs:restriction>
+    </xs:simpleType>
+
     <!-- STRING ENUMERATIONS END -->
 
 </xs:schema>