diff --git a/docker-compose.yaml b/docker-compose.yaml index 76d7564..99334e5 100644 --- a/docker-compose.yaml +++ b/docker-compose.yaml @@ -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 diff --git a/process.py b/process.py index 68d4152..1f3917e 100644 --- a/process.py +++ b/process.py @@ -86,7 +86,6 @@ 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) @@ -94,10 +93,11 @@ def get_config(config_file, database): # 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) diff --git a/template/FLU/flu_gisaid_metadata.csv b/template/FLU/flu_gisaid_metadata.csv index 882659f..9235634 100644 --- a/template/FLU/flu_gisaid_metadata.csv +++ b/template/FLU/flu_gisaid_metadata.csv @@ -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,,,