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authorlltommy2020-04-07 19:51:49 +0200
committerlltommy2020-04-07 19:51:49 +0200
commit40df65dec296b81650987c8ee4f832b703ab8f74 (patch)
tree7c66d6c8c3e836d08cd6a9361982385e7ffa0b1c
parent9b1c125f91469074c7586a1278d89b85919e3eae (diff)
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adding dummy metadata qc to the project
-rw-r--r--bh20sequploader/qc_metadata.py13
-rw-r--r--example/dummyschema.yaml16
-rw-r--r--example/metadata.json0
-rw-r--r--example/metadata.yaml17
4 files changed, 46 insertions, 0 deletions
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
new file mode 100644
index 0000000..0632777
--- /dev/null
+++ b/bh20sequploader/qc_metadata.py
@@ -0,0 +1,13 @@
+import yamale
+
+## NOTE: this is just a DUMMY. Everything about this can and will change
+def qc_metadata(metadatafile):
+ print("Start metadata validation...")
+ schema = yamale.make_schema('../example/dummyschema.yaml')
+ data = yamale.make_data(metadatafile)
+ # Validate data against the schema. Throws a ValueError if data is invalid.
+ yamale.validate(schema, data)
+ print("...complete!")
+
+#qc_metadata("../example/metadata.yaml")
+
diff --git a/example/dummyschema.yaml b/example/dummyschema.yaml
new file mode 100644
index 0000000..e428324
--- /dev/null
+++ b/example/dummyschema.yaml
@@ -0,0 +1,16 @@
+#sampleInformation: include('sampleInformation')
+#InstituteInformation: include('InstituteInformation')
+---
+sampleInformation:
+ location : str()
+ host : str()
+ sequenceTechnology: str()
+ assemblyMethod: str()
+
+InstituteInformation:
+ OriginatingLab: str()
+ SubmittingLab: str()
+
+VirusDetail:
+ VirusName: str()
+ AccessionId: str()
diff --git a/example/metadata.json b/example/metadata.json
deleted file mode 100644
index e69de29..0000000
--- a/example/metadata.json
+++ /dev/null
diff --git a/example/metadata.yaml b/example/metadata.yaml
new file mode 100644
index 0000000..587d0be
--- /dev/null
+++ b/example/metadata.yaml
@@ -0,0 +1,17 @@
+sampleInformation:
+ location: "USA"
+ host : "Homo Sapiens"
+ sequenceTechnology: "Sanger"
+ assemblyMethod: "CLC Genomics"
+
+InstituteInformation:
+ OriginatingLab: "Erik's kitchen"
+ SubmittingLab: "National Institute for Viral Disease Control and Prevention, China CDC"
+
+SubmitterInformation:
+ Submitter: "National Institute for Viral Disease Control and Prevention, China CDC"
+ submissionDate: "04-04-2020"
+
+VirusDetail:
+ VirusName: "hCoV-19/USA/identifer/2020"
+ AccessionId: "EPI_ISL_Random"