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feat(openchallenges): add EDAM terms SQL table and update Challenge.inputDataTypes #2265

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feat(openchallenges): add EDAM terms SQL table and update Challenge.inputDataTypes #2265

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2398b47
"add" two new tables to db
vpchung Oct 22, 2023
62c4702
add placeholders to CSV dump files
vpchung Oct 22, 2023
c6aa3fa
update OpenAPI specs
vpchung Oct 22, 2023
7236d14
Merge branch 'main' into task-2256-edam
vpchung Oct 25, 2023
7d98f4a
update max char lengths
vpchung Oct 25, 2023
a8446a3
accept NULL as possible value
vpchung Oct 25, 2023
61108b6
update openapi specs
vpchung Oct 25, 2023
edf166f
remove 0 (Other) as EDAM ID/term
vpchung Oct 26, 2023
a89e0c5
Merge branch 'main' into task-2256-edam
vpchung Feb 17, 2024
089152c
update script to include EDAM terms and annots into dump
vpchung Feb 17, 2024
aaad983
set `edam_id` as PK in table
vpchung Feb 20, 2024
2052a81
remove `id` from table
vpchung Feb 20, 2024
8c0cc90
drop "id" from CSV dump
vpchung Feb 20, 2024
e47128b
update CSV dump file
vpchung Feb 20, 2024
a7b7de2
update api spec
vpchung Feb 20, 2024
e803a30
update java files
vpchung Feb 20, 2024
ccf07f3
update angular API client
vpchung Feb 20, 2024
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2 changes: 2 additions & 0 deletions apps/openchallenges/challenge-service/src/main/resources/application.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -17,4 +17,6 @@ spring:
db_contribution_roles_csv_path: ${DB_CONTRIBUTION_ROLES_CSV_PATH:src/main/resources/db/contribution_roles.csv}
db_incentives_csv_path: ${DB_INCENTIVES_CSV_PATH:src/main/resources/db/incentives.csv}
db_submission_types_csv_path: ${DB_SUBMISSION_TYPES_CSV_PATH:src/main/resources/db/submission_types.csv}
db_edam_terms_csv_path: ${DB_EDAM_TERMS_CSV_PATH:src/main/resources/db/edam_terms.csv}
db_challenge_data_edam_csv_path: ${DB_CHALLENGE_DATA_EDAM_CSV_PATH:src/main/resources/db/challenge_data_edam.csv}
db_categories_csv_path: ${DB_CATEGORIES_CSV_PATH:src/main/resources/db/categories.csv}
304 changes: 304 additions & 0 deletions apps/openchallenges/challenge-service/src/main/resources/db/challenge_data_edam.csv
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Original file line number Diff line number Diff line change
@@ -0,0 +1,304 @@
"id","challenge_id","edam_id"
"1","1","topic_3120"
vpchung marked this conversation as resolved.
Show resolved Hide resolved
"2","2","topic_2259"
"3","3","data_3861"
"4","4","topic_3958"
"5","4","topic_3518"
"6","5","data_2603"
"7","6","data_3869"
"8","7","topic_3520"
"9","8","topic_0625"
"10","8","data_3861"
"11","9","topic_3673"
"12","10","topic_3518"
"13","11","data_2603"
"14","12","topic_0625"
"15","12","topic_3384"
"16","13","topic_3369"
"17","14","data_3861"
"18","15","data_3861"
"19","16","topic_0625"
"20","16","topic_3375"
"21","17","topic_3673"
"22","18","topic_3673"
"23","19","data_2603"
"24","19","topic_0625"
"25","20","topic_3517"
"26","21","topic_3169"
"27","23","topic_3170"
"28","24","topic_3384"
"29","25","topic_3384"
"30","25","topic_0625"
"31","26","topic_0769"
"32","27","data_3861"
"33","28","data_2536"
"34","29","topic_0154"
"35","30","data_2603"
"36","31","topic_0154"
"37","32","data_2603"
"38","33","topic_3170"
"39","34","topic_3170"
"40","37","data_2603"
"41","37","topic_3520"
"42","38","topic_3673"
"43","39","topic_3676"
"44","39","topic_3170"
"45","40","topic_0154"
"46","41","topic_3384"
"47","42","data_3861"
"48","43","data_2603"
"49","44","data_3861"
"50","45","data_2603"
"51","46","data_3861"
"52","47","data_3861"
"53","48","data_3861"
"54","49","topic_3384"
"55","50","topic_3384"
"56","51","data_2603"
"57","52","topic_3174"
"58","53","topic_3174"
"59","54","data_2603"
"60","55","format_3997"
"61","56","data_3861"
"62","58","data_3861"
"63","59","topic_3120"
"64","60","topic_3120"
"65","61","topic_3120"
"66","62","topic_3676"
"67","63","topic_3120"
"68","64","topic_3120"
"69","65","topic_3120"
"70","66","topic_3120"
"71","67","topic_3120"
"72","68","topic_3120"
"73","69","topic_3120"
"74","70","topic_3120"
"75","71","topic_3120"
"76","72","topic_3120"
"77","73","topic_3673"
"78","74","topic_3120"
"79","75","topic_3120"
"80","76","topic_3120"
"81","77","topic_3120"
"82","78","topic_3120"
"83","79","topic_3120"
"84","80","data_1460"
"85","81","data_1460"
"86","82","topic_3673"
"87","83","topic_3673"
"88","84","topic_3673"
"89","85","topic_3673"
"90","86","topic_3673"
"91","87","topic_3673"
"92","88","topic_3673"
"93","89","topic_3673"
"94","90","topic_3673"
"95","91","topic_3673"
"96","92","topic_3673"
"97","93","topic_3384"
"98","94","topic_3384"
"99","95","format_3997"
"100","96","data_3861"
"101","96","topic_3384"
"102","97","data_3861"
"103","97","topic_3384"
"104","98","data_3861"
"105","98","topic_3384"
"106","99","data_3861"
"107","99","topic_3384"
"108","100","data_3861"
"109","100","topic_3384"
"110","101","data_3861"
"111","101","topic_3384"
"112","102","topic_0625"
"113","103","data_3861"
"114","103","topic_3384"
"115","104","data_3861"
"116","104","topic_3384"
"117","105","data_3861"
"118","105","topic_3384"
"119","106","data_3861"
"120","106","topic_3384"
"121","107","data_3861"
"122","107","topic_3384"
"123","108","data_3861"
"124","108","topic_3384"
"125","109","data_3861"
"126","109","topic_3384"
"127","110","data_3861"
"128","110","topic_3384"
"129","111","data_3861"
"130","111","topic_3384"
"131","112","data_3861"
"132","112","topic_3384"
"133","113","data_3861"
"134","113","topic_3384"
"135","114","data_3861"
"136","114","topic_3384"
"137","115","data_3861"
"138","115","topic_3384"
"139","116","data_3861"
"140","116","topic_3384"
"141","117","topic_3384"
"142","117","data_1460"
"143","118","data_2603"
"144","119","topic_3384"
"145","120","topic_3384"
"146","121","topic_3384"
"147","122","data_2851"
"148","123","topic_3382"
"149","124","format_1196"
"150","125","topic_0154"
"151","126","topic_0154"
"152","127","topic_0154"
"153","128","topic_0154"
"154","129","data_1460"
"155","130","data_1460"
"156","131","data_1460"
"157","132","data_1460"
"158","133","data_3861"
"159","134","data_3861"
"160","135","data_3861"
"161","136","data_3861"
"162","137","data_3861"
"163","138","data_3861"
"164","139","data_3861"
"165","140","data_3861"
"166","140","topic_3384"
"167","141","data_3861"
"168","142","format_3997"
"169","143","data_3861"
"170","144","topic_3384"
"171","145","data_2851"
"172","146","data_2851"
"173","147","topic_3174"
"174","148","topic_3375"
"175","150","topic_3673"
"176","151","data_3869"
"177","152","data_3861"
"178","153","data_3498"
"179","154","data_2603"
"180","155","topic_3384"
"181","157","data_1460"
"182","158","topic_3384"
"183","159","topic_3384"
"184","160","topic_3384"
"185","161","topic_3384"
"186","162","topic_3384"
"187","163","data_3861"
"188","165","topic_3384"
"189","166","topic_3384"
"190","167","topic_3520"
"191","168","data_2603"
"192","169","topic_3384"
"193","170","topic_3384"
"194","171","topic_3384"
"195","172","data_3861"
"196","173","data_2603"
"197","174","data_2603"
"198","175","data_2603"
"199","176","data_2603"
"200","177","data_2603"
"201","178","data_2603"
"202","179","data_2603"
"203","180","topic_3375"
"204","181","topic_3382"
"205","182","format_3997"
"206","183","data_3861"
"207","184","topic_3384"
"208","185","topic_3384"
"209","186","data_3861"
"210","187","data_3861"
"211","188","topic_3384"
"212","189","topic_3384"
"213","190","data_0906"
"214","191","data_0906"
"215","192","data_0906"
"216","193","data_0906"
"217","194","data_3861"
"218","195","data_3861"
"219","196","data_3861"
"220","197","data_3861"
"221","198","data_3861"
"222","199","data_2603"
"223","200","data_0906"
"224","201","data_2603"
"225","202","data_2603"
"226","203","topic_3934"
"227","204","data_2603"
"228","205","data_2603"
"229","206","data_0906"
"230","207","data_0906"
"231","208","data_2603"
"232","209","data_0906"
"233","210","data_2603"
"234","211","topic_0625"
"235","212","topic_0625"
"236","213","data_2979"
"237","214","data_2603"
"238","215","data_2603"
"239","216","data_2991"
"240","217","data_2991"
"241","218","data_2603"
"242","219","topic_3673"
"243","220","topic_3120"
"244","221","topic_3673"
"245","222","topic_3676"
"246","223","topic_3120"
"247","224","topic_3120"
"248","225","topic_3120"
"249","226","topic_3120"
"250","227","topic_3120"
"251","228","topic_3120"
"252","229","topic_3676"
"253","230","topic_3676"
"254","231","topic_3676"
"255","232","topic_3676"
"256","233","topic_3676"
"257","234","data_3498"
"258","235","topic_3676"
"259","236","topic_3120"
"260","237","topic_3120"
"261","238","topic_3120"
"262","239","topic_3120"
"263","240","topic_3120"
"264","241","topic_3120"
"265","242","topic_3673"
"266","243","topic_3673"
"267","244","topic_3673"
"268","245","topic_3673"
"269","246","topic_3120"
"270","247","topic_3120"
"271","248","topic_3120"
"272","249","topic_3120"
"273","250","topic_3120"
"274","251","topic_3120"
"275","252","topic_3120"
"276","253","topic_3673"
"277","254","topic_3120"
"278","255","topic_3120"
"279","256","topic_3676"
"280","257","topic_3120"
"281","258","topic_3120"
"282","259","topic_3120"
"283","260","topic_0154"
"284","261","topic_0154"
"285","262","topic_0154"
"286","263","topic_0154"
"287","264","topic_3673"
"288","264","data_2603"
"289","265","data_2603"
"290","266","topic_3384"
"291","267","topic_3120"
"292","268","topic_3120"
"293","269","data_3498"
"294","270","topic_3120"
"295","271","topic_3120"
"296","272","topic_3120"
"297","273","topic_3120"
"298","274","topic_3673"
"299","275","topic_3120"
"300","276","topic_3120"
"301","277","topic_3120"
"302","278","data_2603"
"303","279","topic_0625"
82 changes: 82 additions & 0 deletions apps/openchallenges/challenge-service/src/main/resources/db/edam_terms.csv
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@@ -0,0 +1,82 @@
"id","edam_id","name","subclass_of","created_at","updated_at"
"1","data_0006","Data","","2023-10-18 00:00:00","2023-10-25 18:34:51"
"2","data_0883 ","Structure","data_0006","2023-10-18 00:00:00","2023-10-18 00:00:00"
"3","data_0897","Protein property","data_2087 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"4","data_0906","Pretein interaction data","data_0897","2023-10-18 00:00:00","2023-10-18 00:00:00"
"5","data_1460","Protein structure","data_0883 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"6","data_1463 ","Small molecule structure","data_0883","2023-10-18 00:00:00","2023-10-18 00:00:00"
"7","data_2048 ","Report ","data_0006","2023-10-18 00:00:00","2023-10-18 00:00:00"
"8","data_2087 ","Molecular property","data_0006","2023-10-18 00:00:00","2023-10-18 00:00:00"
"9","data_2536","Mass spectrometry data","data_3108","2023-10-18 00:00:00","2023-10-18 00:00:00"
"10","data_2603","Expression data","data_0006 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"11","data_2851","Drug structure","data_1463","2023-10-18 00:00:00","2023-10-18 00:00:00"
"12","data_2979","Peptide property","data_2087 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"13","data_2991","Protein geometry data","data_0897 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"14","data_3108","Experimental measurement","data_0006","2023-10-18 00:00:00","2023-10-18 00:00:00"
"15","data_3498","Sequence variations","data_0006 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"16","data_3861","Electronic health record","data_2048 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"17","data_3869","Whole-cell model simulation algorithm","data_0006","2023-10-18 00:00:00","2023-10-18 00:00:00"
"18","format_1196","SMILES","format_2035; format_2330","2023-10-18 00:00:00","2023-10-18 00:00:00"
"19","format_1915","Format","","2023-10-18 00:00:00","2023-10-18 00:00:00"
"20","format_2035 ","Chemical formula format","format_2350 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"21","format_2330","Textual format","format_1915 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"22","format_2333","Binary format","format_1915","2023-10-18 00:00:00","2023-10-18 00:00:00"
"23","format_2350 ","Format (by type of data)","format_1915","2023-10-18 00:00:00","2023-10-18 00:00:00"
"24","format_3547","Image format","format_2350","2023-10-18 00:00:00","2023-10-18 00:00:00"
"25","format_3997","MP4","format_2333; format_3547","2023-10-18 00:00:00","2023-10-18 00:00:00"
"26","operation_0004","Operation","","2023-10-18 00:00:00","2023-10-18 00:00:00"
"27","operation_0231","Sequence editing","operation_3096; operation_2403 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"28","operation_1777","Preotein function prediction","operation_2945; operation_2423","2023-10-18 00:00:00","2023-10-18 00:00:00"
"29","operation_2403","Sequence analysis","operation_2945 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"30","operation_2409 ","Data handling","operation_0004 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"31","operation_2423 ","Prediction and recognition","operation_0004 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"32","operation_2478 ","Nucleic acid sequence analysis","operation_2403","2023-10-18 00:00:00","2023-10-18 00:00:00"
"33","operation_2945 ","Analysis","operation_0004 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"34","operation_3096 ","Editing","operation_2409 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"35","operation_3204 ","Methylation analysis","operation_2478 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"36","operation_3207","Gene methylation analysis","operation_3204 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"37","topic_0003","Topic","","2023-10-18 00:00:00","2023-10-18 00:00:00"
"38","topic_0077 ","Nucleic acids","topic_3307 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"39","topic_0078 ","Proteins ","topic_3307","2023-10-18 00:00:00","2023-10-18 00:00:00"
"40","topic_0081 ","Structure analysis","topic_3307 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"41","topic_0108","Protein expression","topic_0078","2023-10-18 00:00:00","2023-10-18 00:00:00"
"42","topic_0154","Small molecules","topic_0081 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"43","topic_0199","Genetic variation","topic_0622; topic_3321","2023-10-18 00:00:00","2023-10-18 00:00:00"
"44","topic_0610","Ecology","topic_4019; topic_3855","2023-10-18 00:00:00","2023-10-18 00:00:00"
"45","topic_0622","Genomics","topic_3391","2023-10-18 00:00:00","2023-10-18 00:00:00"
"46","topic_0625","Genotype and phenotype","topic_3053 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"47","topic_0654","DNA","topic_0077 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"48","topic_0769","Workflows","topic_3071 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"49","topic_2259","Systems biology","topic_3070","2023-10-18 00:00:00","2023-10-18 00:00:00"
"50","topic_3053 ","Genetics ","topic_3070","2023-10-18 00:00:00","2023-10-18 00:00:00"
"51","topic_3070 ","Biology ","topic_4019 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"52","topic_3071 ","Data management","topic_0003","2023-10-18 00:00:00","2023-10-18 00:00:00"
"53","topic_3120","Protein variants","topic_0108 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"54","topic_3168","Sequencing ","topic_3361 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"55","topic_3169","CHIP-seq","topic_3168; topic_3656","2023-10-18 00:00:00","2023-10-18 00:00:00"
"56","topic_3170","RNA-Seq","topic_3168","2023-10-18 00:00:00","2023-10-18 00:00:00"
"57","topic_3174","Metagenomics","topic_0610; topic_0622","2023-10-18 00:00:00","2023-10-18 00:00:00"
"58","topic_3175 ","Structural variation","topic_0654; topic_0199","2023-10-18 00:00:00","2023-10-18 00:00:00"
"59","topic_3307 ","Computational biology","topic_4019","2023-10-18 00:00:00","2023-10-18 00:00:00"
"60","topic_3314 ","Chemistry","topic_0003","2023-10-18 00:00:00","2023-10-18 00:00:00"
"61","topic_3321","Molecular genetics","topic_3307; topic_3053","2023-10-18 00:00:00","2023-10-18 00:00:00"
"62","topic_3344","Biomedical science","topic_4019","2023-10-18 00:00:00","2023-10-18 00:00:00"
"63","topic_3361","Laboratory techniques","topic_0003 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"64","topic_3369","Chemical biology","topic_3371; topic_3070","2023-10-18 00:00:00","2023-10-18 00:00:00"
"65","topic_3371","Synthetic chemistry","topic_3314 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"66","topic_3375","Drug metabolism","topic_3376","2023-10-18 00:00:00","2023-10-18 00:00:00"
"67","topic_3376","Medicines research and development","topic_3344 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"68","topic_3382","Imaging","topic_3361 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"69","topic_3384","Medical Imaging","topic_3382 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"70","topic_3391","Omics","topic_4019","2023-10-18 00:00:00","2023-10-18 00:00:00"
"71","topic_3517","GWAS study","topic_3678 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"72","topic_3518","Microarray experiment","topic_3361 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"73","topic_3520","Preoteomic experiment","topic_3361 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"74","topic_3656 ","Immunoprecipitation experiment","topic_3361 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"75","topic_3673","Whole genome sequencing","topic_3168 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"76","topic_3676","Exome sequencing","topic_3168 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"77","topic_3678 ","Experimental design and studies","topic_0003 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"78","topic_3855 ","Environmental sciences","topic_0003 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"79","topic_3934","Cytometry ","topic_3361 ","2023-10-18 00:00:00","2023-10-18 00:00:00"
"80","topic_3958","Copy number variation","topic_3175","2023-10-18 00:00:00","2023-10-18 00:00:00"
"81","topic_4019 ","Biosciences ","topic_0003 ","2023-10-18 00:00:00","2023-10-20 00:14:24"
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