GitHub - superphy/VMR_backend_scripts

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Name		Name	Last commit message	Last commit date
Latest commit History 60 Commits
__pycache__		__pycache__
adding_from_Ncbi_sources		adding_from_Ncbi_sources
amr2_visualization		amr2_visualization
conversion_vmr_ncbi		conversion_vmr_ncbi
dump_backup		dump_backup
node-psql		node-psql
plugins		plugins
schema		schema
script_cathy_to_template		script_cathy_to_template
.gitignore		.gitignore
.~lock.GRDI_Harmonization-Template_v13.3.3.xlsm#		.~lock.GRDI_Harmonization-Template_v13.3.3.xlsm#
.~lock.GRDI_Harmonization-Template_v13.4.4.xlsm#		.~lock.GRDI_Harmonization-Template_v13.4.4.xlsm#
.~lock.GRDI_Master-Reference-Guide_v8.9.8.xlsx#		.~lock.GRDI_Master-Reference-Guide_v8.9.8.xlsx#
.~lock.Harmonized_Metadata_Golden-GRDI-AMR2-WP4.5_2024-12-06.xlsx#		.~lock.Harmonized_Metadata_Golden-GRDI-AMR2-WP4.5_2024-12-06.xlsx#
.~lock.P4.2_GRDI_Harmonization-Template_v9.0.0_v30Nov2024.xlsx#		.~lock.P4.2_GRDI_Harmonization-Template_v9.0.0_v30Nov2024.xlsx#
.~lock.Sample_Metada_Frozem_Stonefruit_2024_WP4.2_EG.xlsx#		.~lock.Sample_Metada_Frozem_Stonefruit_2024_WP4.2_EG.xlsx#
.~lock.WP4.2_GRDI_Harmonization-Template_v9.0.0_after_curation_v2.xlsx#		.~lock.WP4.2_GRDI_Harmonization-Template_v9.0.0_after_curation_v2.xlsx#
.~lock.WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024.xlsm#		.~lock.WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024.xlsm#
.~lock.WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024_updated_curated.xlsx#		.~lock.WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024_updated_curated.xlsx#
Baseline_Survey_Harmonized_Version_2022-04-22.xlsx		Baseline_Survey_Harmonized_Version_2022-04-22.xlsx
Baseline_Survey_Harmonized_Version_2022-04-22_Samples_corrected.xlsx		Baseline_Survey_Harmonized_Version_2022-04-22_Samples_corrected.xlsx
EColi_MBS_part1_Jan62025.sql.gz		EColi_MBS_part1_Jan62025.sql.gz
EColi_MBS_part2_Jan62025.sql.gz		EColi_MBS_part2_Jan62025.sql.gz
EColi_MBS_part3_Jan62025.sql.gz		EColi_MBS_part3_Jan62025.sql.gz
Ecoli_MBS_gene_profile_data.sql.gz		Ecoli_MBS_gene_profile_data.sql.gz
GRDI_4.2SwineDPL-JSB_v2_EG_TamberLab_NSJ.xlsx		GRDI_4.2SwineDPL-JSB_v2_EG_TamberLab_NSJ.xlsx
GRDI_Enterococcus_Chongwu_DiarraLab_NSJ.xlsx		GRDI_Enterococcus_Chongwu_DiarraLab_NSJ.xlsx
GRDI_Harmonization-Template_v11.1.1.xlsm		GRDI_Harmonization-Template_v11.1.1.xlsm
GRDI_Harmonization-Template_v13.3.3.xlsm		GRDI_Harmonization-Template_v13.3.3.xlsm
GRDI_Harmonization-Template_v13.4.4.xlsm		GRDI_Harmonization-Template_v13.4.4.xlsm
GRDI_Harmonization-Template_v5.3.2_AC_NSJ.xlsx		GRDI_Harmonization-Template_v5.3.2_AC_NSJ.xlsx
GRDI_Harmonization-Template_v5.3.2_AL_DPL_NSJ.xlsx		GRDI_Harmonization-Template_v5.3.2_AL_DPL_NSJ.xlsx
GRDI_Harmonization-Template_v5.3.2_WP4.5 GDS_NSJ.xlsx		GRDI_Harmonization-Template_v5.3.2_WP4.5 GDS_NSJ.xlsx
GRDI_Harmonization-Template_v5.3.2_WP4.5_GDS_NSJ.xlsx		GRDI_Harmonization-Template_v5.3.2_WP4.5_GDS_NSJ.xlsx
GRDI_Harmonization-Template_v5.3.2_rw_NSJ.xlsx		GRDI_Harmonization-Template_v5.3.2_rw_NSJ.xlsx
GRDI_Harmonization-Template_v6.3.2 (Hongsheng Huang)_NSJ.xlsx		GRDI_Harmonization-Template_v6.3.2 (Hongsheng Huang)_NSJ.xlsx
GRDI_Harmonization-Template_v6.3.2.xlsm		GRDI_Harmonization-Template_v6.3.2.xlsm
GRDI_Harmonization-Template_v6.3.2_Hongsheng_Huang_NSJ.xlsx		GRDI_Harmonization-Template_v6.3.2_Hongsheng_Huang_NSJ.xlsx
GRDI_Harmonization-Template_v7.6.4.xlsm		GRDI_Harmonization-Template_v7.6.4.xlsm
GRDI_Harmonization-Template_v7.6.4_gw.xlsm		GRDI_Harmonization-Template_v7.6.4_gw.xlsm
GRDI_Harmonization-Template_v7.7.5.xlsm		GRDI_Harmonization-Template_v7.7.5.xlsm
GRDI_Harmonization-Template_v7.7.5_Test.xlsm		GRDI_Harmonization-Template_v7.7.5_Test.xlsm
GRDI_Harmonization-Template_v7.7.5_gw.xlsm		GRDI_Harmonization-Template_v7.7.5_gw.xlsm
GRDI_Harmonization-Template_v8.8.7.xlsm		GRDI_Harmonization-Template_v8.8.7.xlsm
GRDI_Harmonization-Template_v8.9.8.xlsm		GRDI_Harmonization-Template_v8.9.8.xlsm
GRDI_Harmonization-Template_v8.9.9.xlsm		GRDI_Harmonization-Template_v8.9.9.xlsm
GRDI_Harmonization-Template_v8.9.9_2023_WGS_WP3.1.xlsm		GRDI_Harmonization-Template_v8.9.9_2023_WGS_WP3.1.xlsm
GRDI_Harmonization_Template2.0_2021-E_coli_Xianhua-Moussa_Diarra_lab_curatedNSJ.xlsx		GRDI_Harmonization_Template2.0_2021-E_coli_Xianhua-Moussa_Diarra_lab_curatedNSJ.xlsx
GRDI_Master-Reference-Guide_v11.1.1.xlsx		GRDI_Master-Reference-Guide_v11.1.1.xlsx
GRDI_Master-Reference-Guide_v13.3.3.xlsx		GRDI_Master-Reference-Guide_v13.3.3.xlsx
GRDI_Master-Reference-Guide_v13.4.4.xlsx		GRDI_Master-Reference-Guide_v13.4.4.xlsx
GRDI_Master-Reference-Guide_v8.9.8.xlsx		GRDI_Master-Reference-Guide_v8.9.8.xlsx
GRDI_Master-Reference-Guide_v8.9.8_old.xlsx		GRDI_Master-Reference-Guide_v8.9.8_old.xlsx
GRDI_Master-Reference-Guide_v8.9.9.xlsx		GRDI_Master-Reference-Guide_v8.9.9.xlsx
GRDI_Salmonella_JoshTang_DiarraLab_NSJ.xlsx		GRDI_Salmonella_JoshTang_DiarraLab_NSJ.xlsx
Harmonized_Metadata_Golden-GRDI-AMR2-WP4.5_2024-12-06.xlsx		Harmonized_Metadata_Golden-GRDI-AMR2-WP4.5_2024-12-06.xlsx
P4.2_GRDI_Harmonization-Template_v9.0.0_v30Nov2024.xlsx		P4.2_GRDI_Harmonization-Template_v9.0.0_v30Nov2024.xlsx
SNC_2000_Metadata171023_ANDREWSCOTT.xlsx		SNC_2000_Metadata171023_ANDREWSCOTT.xlsx
Sample_Metada_Frozem_Stonefruit_2024_WP4.2_EG.xlsx		Sample_Metada_Frozem_Stonefruit_2024_WP4.2_EG.xlsx
StoneFruitNewInsertsNov192024.sql		StoneFruitNewInsertsNov192024.sql
WP4.2-v9.0.0_Stone_Fruit.sql		WP4.2-v9.0.0_Stone_Fruit.sql
WP4.2_GRDI_Harmonization-Template_v9.0.0.xlsm		WP4.2_GRDI_Harmonization-Template_v9.0.0.xlsm
WP4.2_GRDI_Harmonization-Template_v9.0.0_GW.csv		WP4.2_GRDI_Harmonization-Template_v9.0.0_GW.csv
WP4.2_GRDI_Harmonization-Template_v9.0.0_after_curation.csv		WP4.2_GRDI_Harmonization-Template_v9.0.0_after_curation.csv
WP4.2_GRDI_Harmonization-Template_v9.0.0_after_curation.xlsx		WP4.2_GRDI_Harmonization-Template_v9.0.0_after_curation.xlsx
WP4.2_GRDI_Harmonization-Template_v9.0.0_after_curation_v2.xlsx		WP4.2_GRDI_Harmonization-Template_v9.0.0_after_curation_v2.xlsx
WP4.2_GRDI_Harmonization-Template_v9.0.0_v11Nov2024.xlsm		WP4.2_GRDI_Harmonization-Template_v9.0.0_v11Nov2024.xlsm
WP4.2_GRDI_Harmonization-Template_v9.0.0_v11Nov2024.xlsx		WP4.2_GRDI_Harmonization-Template_v9.0.0_v11Nov2024.xlsx
WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024.xlsm		WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024.xlsm
WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024_updated.csv		WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024_updated.csv
WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024_updated.xlsx		WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024_updated.xlsx
WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024_updated_curated.xlsx		WP4.2_GRDI_Harmonization-Template_v9.0.0_v31Oct2024_updated_curated.xlsx
WP4.2_GRDI_StoneFruitSamples_Insertion.sql		WP4.2_GRDI_StoneFruitSamples_Insertion.sql
WP4.2_GRDI_Stone_Fruit_SequencesP1v12Dez2024.sql		WP4.2_GRDI_Stone_Fruit_SequencesP1v12Dez2024.sql
WP4.2_GRDI_Stone_Fruit_SequencesP1v13Dez2024.sql		WP4.2_GRDI_Stone_Fruit_SequencesP1v13Dez2024.sql
WP4.2_GRDI_Stone_Fruit_SequencesP2v12Dez2024.sql		WP4.2_GRDI_Stone_Fruit_SequencesP2v12Dez2024.sql
WP4.2_GRDI_Stone_Fruit_SequencesP2v13Dez2024.sql		WP4.2_GRDI_Stone_Fruit_SequencesP2v13Dez2024.sql
WP4.2_GRDI_Stone_Fruitv12Dez2024.sql		WP4.2_GRDI_Stone_Fruitv12Dez2024.sql
added_sample_ids.txt		added_sample_ids.txt
amr_sheet_output.xls		amr_sheet_output.xls
bioinfo_Results_131_stone_fruit_irida_sequences10Dez2024.sql		bioinfo_Results_131_stone_fruit_irida_sequences10Dez2024.sql
card.json		card.json
cathy_par1.csv		cathy_par1.csv
create_dict_of_samples.py		create_dict_of_samples.py
create_dict_of_samples_one.py		create_dict_of_samples_one.py
create_ontology_dict.py		create_ontology_dict.py
enteric_template_version.xlsx		enteric_template_version.xlsx
feed_vmr_table.py		feed_vmr_table.py
fill_ontology_fields.py		fill_ontology_fields.py
filled_Antibiogram.1.0.xlsx		filled_Antibiogram.1.0.xlsx
filled_SRA_metadata_acc.xlsx		filled_SRA_metadata_acc.xlsx
foodon.owl		foodon.owl
gene_mode.py		gene_mode.py
gene_mode_old.py		gene_mode_old.py
insert_temp.py		insert_temp.py
log.txt		log.txt
metabase.db.mv.db		metabase.db.mv.db
metabase.db.trace.db		metabase.db.trace.db
output_alyssa_golden.json		output_alyssa_golden.json
outputec_first_part_updated.json.gz		outputec_first_part_updated.json.gz

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