Merge branch 'submission-rewrite-ick4' into dev

CDCgov · Nov 15, 2024 · c3b51f9 · c3b51f9
2 parents ab6ccf4 + 0e8da6c
commit c3b51f9
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Showing 44 changed files with 8,877 additions and 36,352 deletions.
diff --git a/assets/metadata_template.xlsx b/assets/metadata_template.xlsx
diff --git a/assets/sample_annotations/bacteria/BX248355.gff b/assets/sample_annotations/bacteria/BX248355.gff
diff --git a/assets/sample_annotations/bacteria/BX248355.gff3 b/assets/sample_annotations/bacteria/BX248355.gff3
diff --git a/assets/sample_annotations/bacteria/CP014051.gff b/assets/sample_annotations/bacteria/CP014051.gff
diff --git a/assets/sample_annotations/bacteria/CP040557.gff b/assets/sample_annotations/bacteria/CP040557.gff
diff --git a/assets/sample_annotations/bacteria/CP040557.gff3 b/assets/sample_annotations/bacteria/CP040557.gff3
diff --git a/assets/sample_annotations/bacteria/old/BX248355.gff b/assets/sample_annotations/bacteria/old/BX248355.gff
diff --git a/assets/sample_annotations/bacteria/old/CP014051.gff b/assets/sample_annotations/bacteria/old/CP014051.gff
diff --git a/assets/sample_annotations/bacteria/old/CP040557.gff b/assets/sample_annotations/bacteria/old/CP040557.gff
diff --git a/...sample_fastas/Cdiphtheriae/BX248355.fasta → assets/sample_fastas/bacteria/BX248355.fasta b/...sample_fastas/Cdiphtheriae/BX248355.fasta → assets/sample_fastas/bacteria/BX248355.fasta
diff --git a/...sample_fastas/Cdiphtheriae/CP014051.fasta → assets/sample_fastas/bacteria/CP014051.fasta b/...sample_fastas/Cdiphtheriae/CP014051.fasta → assets/sample_fastas/bacteria/CP014051.fasta
diff --git a/...sample_fastas/Cdiphtheriae/CP040557.fasta → assets/sample_fastas/bacteria/CP040557.fasta b/...sample_fastas/Cdiphtheriae/CP040557.fasta → assets/sample_fastas/bacteria/CP040557.fasta
diff --git a/assets/sample_fastqs/Cdiphtheriae/CP040557.fasta b/assets/sample_fastqs/Cdiphtheriae/CP040557.fasta
diff --git a/..._fastqs/Cdiphtheriae/BX248355_R1.fastq.gz → ...mple_fastqs/bacteria/BX248355_R1.fastq.gz b/..._fastqs/Cdiphtheriae/BX248355_R1.fastq.gz → ...mple_fastqs/bacteria/BX248355_R1.fastq.gz
diff --git a/..._fastqs/Cdiphtheriae/BX248355_R2.fastq.gz → ...mple_fastqs/bacteria/BX248355_R2.fastq.gz b/..._fastqs/Cdiphtheriae/BX248355_R2.fastq.gz → ...mple_fastqs/bacteria/BX248355_R2.fastq.gz
diff --git a/..._fastqs/Cdiphtheriae/CP040557_R1.fastq.gz → ...mple_fastqs/bacteria/CP040557_R1.fastq.gz b/..._fastqs/Cdiphtheriae/CP040557_R1.fastq.gz → ...mple_fastqs/bacteria/CP040557_R1.fastq.gz
diff --git a/..._fastqs/Cdiphtheriae/CP040557_R2.fastq.gz → ...mple_fastqs/bacteria/CP040557_R2.fastq.gz b/..._fastqs/Cdiphtheriae/CP040557_R2.fastq.gz → ...mple_fastqs/bacteria/CP040557_R2.fastq.gz
diff --git a/assets/sample_metadata/Cdiphtheriae_test_metadata.xlsx b/assets/sample_metadata/Cdiphtheriae_test_metadata.xlsx
diff --git a/assets/sample_metadata/bacteria_test_metadata.xlsx b/assets/sample_metadata/bacteria_test_metadata.xlsx
diff --git a/assets/sample_metadata/mpxv_test_metadata.xlsx b/assets/sample_metadata/mpxv_test_metadata.xlsx
diff --git a/assets/sample_metadata/mpxv_user_provided_annotations_metadata.xlsx b/assets/sample_metadata/mpxv_user_provided_annotations_metadata.xlsx
diff --git a/assets/sample_metadata/rsv_test_metadata.xlsx b/assets/sample_metadata/rsv_test_metadata.xlsx
diff --git a/assets/sample_metadata/varv_test_metadata.xlsx b/assets/sample_metadata/varv_test_metadata.xlsx
diff --git a/bin/config_files/submission_config.yaml b/bin/config_files/submission_config.yaml
@@ -0,0 +1,30 @@
+---
+NCBI_username: username 
+NCBI_password: password
+NCBI_ftp_host: 'ftp-private.ncbi.nlm.nih.gov'
+NCBI_sftp_host: 'sftp-private.ncbi.nlm.nih.gov'
+NCBI_API_URL: 'https://submit.ncbi.nlm.nih.gov/api/2.0/files/FILE_ID/?format=attachment'
+table2asn_email: 'gb-admin@ncbi.nlm.nih.gov'
+BioSample_package: "Pathogen.cl.1.0"
+Role: owner
+Type: institute
+Org_ID: 30206
+Submitting_Org: CDC
+Submitting_Org_Dept: DHCPP-PRB
+Street: 1600 Clifton Rd
+City: Atlanta
+State: GA
+Postal_code: 30329
+Country: USA
+Email: test@cdc.gov
+Phone: ""
+Specified_Release_Date: ""
+Submitter:
+  '@email': test9@cdc.gov
+  '@alt_email': test@cdc.gov
+  Name:
+    First: John
+    Last: Doe
+GISAID_client-id: TEST-EA76875B00C3
+GISAID_username: username
+GISAID_password: password
diff --git a/bin/submission.py b/bin/submission.py
diff --git a/bin/submission_create.py b/bin/submission_create.py
diff --git a/bin/submission_new.py b/bin/submission_new.py
diff --git a/bin/submission_process.py b/bin/submission_process.py
diff --git a/bin/submission_report.py b/bin/submission_report.py
diff --git a/bin/submission_submit.py b/bin/submission_submit.py