From 75c50cb92a65216d07d394586f97d6d28706819c Mon Sep 17 00:00:00 2001
From: Thomas Sell <thomas.sell@charite.de>
Date: Thu, 26 Oct 2023 14:28:22 +0200
Subject: [PATCH] finalise ontology update

---
 .../isatab-somatic/cookiecutter.json            |   4 ++++
 .../.s_{{cookiecutter.s_file_name}}.txt.swp     | Bin 0 -> 12288 bytes
 .../i_Investigation.txt                         |   2 +-
 3 files changed, 5 insertions(+), 1 deletion(-)
 create mode 100644 cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/.s_{{cookiecutter.s_file_name}}.txt.swp

diff --git a/cubi_isa_templates/isatab-somatic/cookiecutter.json b/cubi_isa_templates/isatab-somatic/cookiecutter.json
index 1de41f1..9eda586 100644
--- a/cubi_isa_templates/isatab-somatic/cookiecutter.json
+++ b/cubi_isa_templates/isatab-somatic/cookiecutter.json
@@ -23,6 +23,10 @@
     "exome sequencing",
     "genome sequencing"
   ],
+  "_measurement_type_terms": {
+    "exome sequencing": "http://purl.obolibrary.org/obo/OBI_0002118",
+	"genome sequencing": "http://purl.obolibrary.org/obo/OBI_0002117"
+  },
   "lib_kit": [
     "Agilent SureSelect Human All Exon V8",
     "Agilent SureSelect Human All Exon V7",
diff --git a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/.s_{{cookiecutter.s_file_name}}.txt.swp b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/.s_{{cookiecutter.s_file_name}}.txt.swp
new file mode 100644
index 0000000000000000000000000000000000000000..906d8121c8679f7f25e4bc361ce1eb3877f31ba0
GIT binary patch
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literal 0
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diff --git a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt
index 06c780c..a389e54 100644
--- a/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt
+++ b/cubi_isa_templates/isatab-somatic/{{cookiecutter.__output_dir}}/i_Investigation.txt
@@ -60,7 +60,7 @@ Study Factor Type Term Source REF
 STUDY ASSAYS
 Study Assay File Name	a_{{cookiecutter.s_file_name}}_{{cookiecutter.__assay_name}}.txt{% if cookiecutter.is_triplet == True %}	a_{{cookiecutter.s_file_name}}_transcriptome_profiling.txt{% endif %}
 Study Assay Measurement Type	{{cookiecutter.measurement_type}}{% if cookiecutter.is_triplet == True %}	transcriptome profiling{% endif %}
-Study Assay Measurement Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0002118{% if cookiecutter.is_triplet == True %}	http://purl.obolibrary.org/obo/OBI_0000424{% endif %}
+Study Assay Measurement Type Term Accession Number	{{cookiecutter._measurement_type_terms[cookiecutter.measurement_type]}}{% if cookiecutter.is_triplet == True %}	http://purl.obolibrary.org/obo/OBI_0000424{% endif %}
 Study Assay Measurement Type Term Source REF	OBI{% if cookiecutter.is_triplet == True %}	OBI{% endif %}
 Study Assay Technology Type	nucleotide sequencing{% if cookiecutter.is_triplet == True %}	nucleotide sequencing{% endif %}
 Study Assay Technology Type Term Accession Number	http://purl.obolibrary.org/obo/OBI_0000626{% if cookiecutter.is_triplet == True %}	http://purl.obolibrary.org/obo/OBI_0000626{% endif %}