From 04ab343e57c7a23451164843d1922622c5f4f9f5 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 17 Jul 2020 12:05:53 +0100
Subject: Preparing for EBI submission

---
 scripts/submit_ebi/example/project-submission.xml |  3 +-
 scripts/submit_ebi/example/project.xml            |  3 +-
 scripts/submit_ebi/example/sample-submission.xml  |  8 +++
 scripts/submit_ebi/example/sample.xml             | 68 +++++++++++++++++++++++
 4 files changed, 80 insertions(+), 2 deletions(-)
 create mode 100644 scripts/submit_ebi/example/sample-submission.xml
 create mode 100644 scripts/submit_ebi/example/sample.xml

(limited to 'scripts')

diff --git a/scripts/submit_ebi/example/project-submission.xml b/scripts/submit_ebi/example/project-submission.xml
index 2d3ddc1..1abb827 100644
--- a/scripts/submit_ebi/example/project-submission.xml
+++ b/scripts/submit_ebi/example/project-submission.xml
@@ -1,3 +1,4 @@
+<?xml version="1.0" encoding="UTF-8"?>
 <SUBMISSION>
    <ACTIONS>
       <ACTION>
@@ -6,6 +7,6 @@
       <ACTION>
          <HOLD HoldUntilDate="2020-10-10"/>
       </ACTION>
-   </ACTIONS>
+  </ACTIONS>
 </SUBMISSION>
 
diff --git a/scripts/submit_ebi/example/project.xml b/scripts/submit_ebi/example/project.xml
index 90704ab..6a817e7 100644
--- a/scripts/submit_ebi/example/project.xml
+++ b/scripts/submit_ebi/example/project.xml
@@ -1,7 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
 <PROJECT_SET>
    <PROJECT alias="PubSeq01">
       <TITLE>Testing PubSeq Sample uploads</TITLE>
-      <DESCRIPTION>This study aimed to allow for uploading sequences from PubSeq</DESCRIPTION>
+      <DESCRIPTION>This is a test to allow for uploading sequences from PubSeq</DESCRIPTION>
       <SUBMISSION_PROJECT>
          <SEQUENCING_PROJECT/>
       </SUBMISSION_PROJECT>
diff --git a/scripts/submit_ebi/example/sample-submission.xml b/scripts/submit_ebi/example/sample-submission.xml
new file mode 100644
index 0000000..9d13512
--- /dev/null
+++ b/scripts/submit_ebi/example/sample-submission.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SUBMISSION>
+   <ACTIONS>
+      <ACTION>
+         <ADD/>
+      </ACTION>
+   </ACTIONS>
+</SUBMISSION>
diff --git a/scripts/submit_ebi/example/sample.xml b/scripts/submit_ebi/example/sample.xml
new file mode 100644
index 0000000..694c471
--- /dev/null
+++ b/scripts/submit_ebi/example/sample.xml
@@ -0,0 +1,68 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<SAMPLE_SET>
+  <SAMPLE alias="PubSeqSam0001" center_name="PubSeq01">
+    <TITLE>human gastric microbiota, mucosal</TITLE>
+    <SAMPLE_NAME>
+      <TAXON_ID>1284369</TAXON_ID>
+      <SCIENTIFIC_NAME>stomach metagenome</SCIENTIFIC_NAME>
+      <COMMON_NAME></COMMON_NAME>
+    </SAMPLE_NAME>
+    <SAMPLE_ATTRIBUTES>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>investigation type</TAG>
+        <VALUE>mimarks-survey</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>sequencing method</TAG>
+        <VALUE>pyrosequencing</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>collection date</TAG>
+        <VALUE>2010</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>host body site</TAG>
+        <VALUE>Mucosa of stomach</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>human-associated environmental package</TAG>
+        <VALUE>human-associated</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>geographic location (latitude)</TAG>
+        <VALUE>1.81</VALUE>
+     <UNITS>DD</UNITS>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>geographic location (longitude)</TAG>
+        <VALUE>-78.76</VALUE>
+     <UNITS>DD</UNITS>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+     <TAG>geographic location (country and/or sea)</TAG>
+     <VALUE>Colombia</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>geographic location (region and locality)</TAG>
+        <VALUE>Tumaco</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>environment (biome)</TAG>
+        <VALUE>coast</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>environment (feature)</TAG>
+        <VALUE>human-associated habitat</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>environment (material)</TAG>
+        <VALUE>gastric biopsy</VALUE>
+      </SAMPLE_ATTRIBUTE>
+      <SAMPLE_ATTRIBUTE>
+        <TAG>ENA-CHECKLIST</TAG>
+        <VALUE>ERC000011</VALUE>
+      </SAMPLE_ATTRIBUTE>
+    </SAMPLE_ATTRIBUTES>
+  </SAMPLE>
+</SAMPLE_SET>
+
-- 
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