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Merge pull request #37 from CDCgov/fix_template_metadata
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update template metadata with required fields for flu
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@rchau88
rchau88 authored Feb 23, 2024
2 parents 0304732 + c2645d4 commit 081ee66
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Showing 3 changed files with 20 additions and 27 deletions.
9 changes: 1 addition & 8 deletions docker-compose.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,18 +6,11 @@ x-data-volumes:
source: $HOME/Github/Testings/seqsender
target: /data

x-seqsender-code:
&seqsender-code
type: bind
source: $HOME/Github/seqsender
target: /seqsender

services:
seqsender:
container_name: seqsender
image: cdcgov/seqsender-dev:latest
image: cdcgov/seqsender:latest
restart: always
volumes:
- *data-volume
- *seqsender-code
command: tail -f /dev/null
4 changes: 2 additions & 2 deletions process.py
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Original file line number Diff line number Diff line change
Expand Up @@ -86,18 +86,18 @@ def get_config(config_file, database):
if type(config_dict) is dict:
try:
config_dict = config_dict['Submission']
return config_dict
except:
print("Error: there is no Submission information in the config file.", file=sys.stderr)
sys.exit(1)
else:
# Check if each database has portal information listed in the config file
for d in range(len(database)):
if submission_portals[d] not in config_dict.keys():
print("\n"+"Error: " + database[d] + " is listed as one of the submitting databases in the command.", file=sys.stderr)
print("\n"+"Error: " + database[d] + " is listed as one of the submitting databases.", file=sys.stderr)
print("Error: However, there is no " + submission_portals[d] + " submission information provided in the config file.", file=sys.stderr)
print("Error: Either remove " + database[d] + " from the submitting databases or update your config file."+"\n", file=sys.stderr)
sys.exit(1)
return config_dict
else:
print("Error: Config file is incorrect. File must has a valid yaml format.", file=sys.stderr)
sys.exit(1)
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34 changes: 17 additions & 17 deletions template/FLU/flu_gisaid_metadata.csv
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Original file line number Diff line number Diff line change
@@ -1,17 +1,17 @@
sequence_name,organism, collection_date,authors,gs-Isolate_Name,gs-seq_id,gs-segment,gs-Subtype,gs-Lineage,gs-Passage_History,gs-Location,gs-province,gs-sub_province,gs-Location_Additional_info,gs-Host,gs-Host_Additional_info,gs-Submitting_Sample_Id,gs-Originating_Lab_Id,gs-Originating_Sample_Id,gs-Antigen_Character,gs-Adamantanes_Resistance_geno,gs-Oseltamivir_Resistance_geno,gs-Zanamivir_Resistance_geno,gs-Peramivir_Resistance_geno,gs-Other_Resistance_geno,gs-Adamantanes_Resistance_pheno,gs-Oseltamivir_Resistance_pheno,gs-Zanamivir_Resistance_pheno,gs-Peramivir_Resistance_pheno,gs-Other_Resistance_pheno,gs-Host_Age,gs-Host_Age_Unit,gs-Host_Gender,gs-Health_Status,gs-Note,gs-PMID
XX-566912_PB2,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_PB2,PB2,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,Y,F,,,
XX-566912_PB1,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_PB1,PB1,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,Y,F,,,
XX-566912_PA,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_PA,PA,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,Y,F,,,
XX-566912_HA,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_HA,HA,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,Y,F,,,
XX-566912_NP,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_NP,NP,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,Y,F,,,
XX-566912_NA,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_NA,NA,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,Y,F,,,
XX-566912_M,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_MP,MP,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,Y,F,,,
XX-566912_NS,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_NS,NS,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,Y,F,,,
XX-566913_PB2,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_PB2,PB2,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,Y,M,,,
XX-566913_PB1,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_PB1,PB1,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,Y,M,,,
XX-566913_PA,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_PA,PA,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,Y,M,,,
XX-566913_HA,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_HA,HA,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,Y,M,,,
XX-566913_NP,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_NP,NP,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,Y,M,,,
XX-566913_NA,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_NA,NA,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,Y,M,,,
XX-566913_M,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_MP,MP,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,Y,M,,,
XX-566913_NS,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_NS,NS,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,Y,M,,,
sequence_name,organism, collection_date,authors,gs-Isolate_Name,gs-seq_id,gs-segment,gs-Subtype,gs-Lineage,gs-Passage_History,gs-Location,gs-province,gs-sub_province,gs-Location_Additional_info,gs-Host,gs-Host_Additional_info,gs-Submitting_Sample_Id,gs-Originating_Lab_Id,gs-Originating_Sample_Id,gs-Antigen_Character,gs-Adamantanes_Resistance_geno,gs-Oseltamivir_Resistance_geno,gs-Zanamivir_Resistance_geno,gs-Peramivir_Resistance_geno,gs-Other_Resistance_geno,gs-Adamantanes_Resistance_pheno,gs-Oseltamivir_Resistance_pheno,gs-Zanamivir_Resistance_pheno,gs-Peramivir_Resistance_pheno,gs-Other_Resistance_pheno,gs-Host_Age,gs-Collection_Month,gs-Collection_Year,gs-Host_Age_Unit,gs-Host_Gender,gs-Health_Status,gs-Note,gs-PMID
XX-566912_PB2,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_PB2,PB2,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,,
XX-566912_PB1,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_PB1,PB1,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,,
XX-566912_PA,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_PA,PA,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,,
XX-566912_HA,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_HA,HA,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,,
XX-566912_NP,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_NP,NP,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,,
XX-566912_NA,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_NA,NA,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,,
XX-566912_M,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_MP,MP,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,,
XX-566912_NS,Influenza A virus,12/28/2016,"Doe, John; Doe, Jane;",A/California/566912/2016,A/California/566912/2016_NS,NS,H3N2,,Original,United States,California,,,Human,,,3080,,,,,,,,,,,,,92,,,Y,F,,,
XX-566913_PB2,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_PB2,PB2,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,,
XX-566913_PB1,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_PB1,PB1,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,,
XX-566913_PA,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_PA,PA,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,,
XX-566913_HA,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_HA,HA,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,,
XX-566913_NP,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_NP,NP,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,,
XX-566913_NA,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_NA,NA,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,,
XX-566913_M,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_MP,MP,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,,
XX-566913_NS,Influenza A virus,11/10/2016,"Doe, John; Doe, Jane;",A/Texas/566913/2016,A/Texas/566913/2016_NS,NS,H3N2,,Original,United States,Texas,,,Human,,,3081,,,,,,,,,,,,,21,,,Y,M,,,

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