From b28670d7255d85cd80e8cf88b318428388df3119 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Fri, 28 Jun 2024 11:23:38 -0600 Subject: [PATCH] Clean db files add human reads filter method (#3421) * Update CHANGELOG.md * clean db files + add human_reads_filter_method * fix db errors * modify inserts to be in the correct order --- qiita_db/support_files/patches/92.sql | 25 ++ .../support_files/patches/test_db_sql/92.sql | 13 +- qiita_db/support_files/populate_test_db.sql | 10 +- qiita_db/support_files/qiita-db-unpatched.sql | 5 +- qiita_db/support_files/qiita-db.dbs | 35 ++- qiita_db/support_files/qiita-db.html | 257 ++++++++++++------ 6 files changed, 244 insertions(+), 101 deletions(-) diff --git a/qiita_db/support_files/patches/92.sql b/qiita_db/support_files/patches/92.sql index 19d284b36..b618c3133 100644 --- a/qiita_db/support_files/patches/92.sql +++ b/qiita_db/support_files/patches/92.sql @@ -39,3 +39,28 @@ ALTER TABLE qiita.qiita_user ADD creation_timestamp timestamp without time zone DEFAULT NOW(); COMMENT ON COLUMN qiita.qiita_user.creation_timestamp IS 'The date the user account was created'; + +-- Jun 28, 2024 +-- These columns were added by mistake to qiita-db-unpatched.sql in PR: +-- https://github.com/qiita-spots/qiita/pull/3412 so adding here now + +ALTER TABLE qiita.qiita_user ADD social_orcid character varying DEFAULT NULL; +ALTER TABLE qiita.qiita_user ADD social_researchgate character varying DEFAULT NULL; +ALTER TABLE qiita.qiita_user ADD social_googlescholar character varying DEFAULT NULL; + +-- Add human_reads_filter_method so we can keep track of the available methods +-- and link them to the preparations + +CREATE TABLE qiita.human_reads_filter_method ( + human_reads_filter_method_id bigint NOT NULL, + human_reads_filter_method_method character varying NOT NULL, + CONSTRAINT pk_human_reads_filter_method_id PRIMARY KEY ( + human_reads_filter_method_id ) + ); + +ALTER TABLE qiita.prep_template + ADD human_reads_filter_method_id bigint DEFAULT NULL; +ALTER TABLE qiita.prep_template + ADD CONSTRAINT fk_human_reads_filter_method + FOREIGN KEY ( human_reads_filter_method_id ) + REFERENCES qiita.human_reads_filter_method ( human_reads_filter_method_id ); diff --git a/qiita_db/support_files/patches/test_db_sql/92.sql b/qiita_db/support_files/patches/test_db_sql/92.sql index 65266e9f0..8346b18e1 100644 --- a/qiita_db/support_files/patches/test_db_sql/92.sql +++ b/qiita_db/support_files/patches/test_db_sql/92.sql @@ -929,11 +929,16 @@ INSERT INTO qiita.slurm_resource_allocations(processing_job_id, samples, columns -- for testing: provide creation date for one of the existing users -UPDATE qiita.qiita_user SET creation_timestamp = '2015-12-03 13:52:42.751331-07' WHERE email = 'test@foo.bar'; +UPDATE qiita.qiita_user SET + social_orcid = '0000-0002-0975-9019', + social_researchgate = 'Rob-Knight', + social_googlescholar = '_e3QL94AAAAJ', + creation_timestamp = '2015-12-03 13:52:42.751331-07' +WHERE email = 'test@foo.bar'; -- Jun 20, 2024 -- Add some non-verified users to the test DB to test new admin page: /admin/purge_users/ -INSERT INTO qiita.qiita_user VALUES ('justnow@nonvalidat.ed', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'JustNow', 'NonVeriUser', '1634 Edgemont Avenue', '303-492-1984', NULL, NULL, NULL, false, NULL, NULL, NULL, NOW()); -INSERT INTO qiita.qiita_user VALUES ('ayearago@nonvalidat.ed', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Oldie', 'NonVeriUser', '172 New Lane', '102-111-1984', NULL, NULL, NULL, false, NULL, NULL, NULL, NOW() - INTERVAL '1 YEAR'); -INSERT INTO qiita.qiita_user VALUES ('3Xdays@nonvalidat.ed', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'TooLate', 'NonVeriUser', '564 C Street', '508-492-222', NULL, NULL, NULL, false, NULL, NULL, NULL, NOW() - INTERVAL '30 DAY'); +INSERT INTO qiita.qiita_user VALUES ('justnow@nonvalidat.ed', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'JustNow', 'NonVeriUser', '1634 Edgemont Avenue', '303-492-1984', NULL, NULL, NULL, false, NOW(), NULL, NULL, NULL); +INSERT INTO qiita.qiita_user VALUES ('ayearago@nonvalidat.ed', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Oldie', 'NonVeriUser', '172 New Lane', '102-111-1984', NULL, NULL, NULL, false, NOW() - INTERVAL '1 YEAR', NULL, NULL, NULL); +INSERT INTO qiita.qiita_user VALUES ('3Xdays@nonvalidat.ed', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'TooLate', 'NonVeriUser', '564 C Street', '508-492-222', NULL, NULL, NULL, false, NOW() - INTERVAL '30 DAY', NULL, NULL, NULL); diff --git a/qiita_db/support_files/populate_test_db.sql b/qiita_db/support_files/populate_test_db.sql index 1ca2edb66..ea7c4337c 100644 --- a/qiita_db/support_files/populate_test_db.sql +++ b/qiita_db/support_files/populate_test_db.sql @@ -50,10 +50,10 @@ INSERT INTO qiita.user_level VALUES (7, 'wet-lab admin', 'Can access the private -- Data for Name: qiita_user; Type: TABLE DATA; Schema: qiita; Owner: antoniog -- -INSERT INTO qiita.qiita_user VALUES ('test@foo.bar', 4, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Dude', 'Nowhere University', '123 fake st, Apt 0, Faketown, CO 80302', '111-222-3344', NULL, NULL, NULL, false, '0000-0002-0975-9019', 'Rob-Knight', '_e3QL94AAAAJ'); -INSERT INTO qiita.qiita_user VALUES ('shared@foo.bar', 4, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Shared', 'Nowhere University', '123 fake st, Apt 0, Faketown, CO 80302', '111-222-3344', NULL, NULL, NULL, false); -INSERT INTO qiita.qiita_user VALUES ('admin@foo.bar', 1, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Admin', 'Owner University', '312 noname st, Apt K, Nonexistantown, CO 80302', '222-444-6789', NULL, NULL, NULL, false); -INSERT INTO qiita.qiita_user VALUES ('demo@microbio.me', 4, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Demo', 'Qiita Dev', '1345 Colorado Avenue', '303-492-1984', NULL, NULL, NULL, false); +INSERT INTO qiita.qiita_user VALUES ('test@foo.bar', 4, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Dude', 'Nowhere University', '123 fake st, Apt 0, Faketown, CO 80302', '111-222-3344', NULL, NULL, NULL); +INSERT INTO qiita.qiita_user VALUES ('shared@foo.bar', 4, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Shared', 'Nowhere University', '123 fake st, Apt 0, Faketown, CO 80302', '111-222-3344', NULL, NULL, NULL); +INSERT INTO qiita.qiita_user VALUES ('admin@foo.bar', 1, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Admin', 'Owner University', '312 noname st, Apt K, Nonexistantown, CO 80302', '222-444-6789', NULL, NULL, NULL); +INSERT INTO qiita.qiita_user VALUES ('demo@microbio.me', 4, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Demo', 'Qiita Dev', '1345 Colorado Avenue', '303-492-1984', NULL, NULL, NULL); -- @@ -329,7 +329,7 @@ INSERT INTO qiita.processing_job_status VALUES (6, 'waiting', 'The job is waitin -- Data for Name: processing_job; Type: TABLE DATA; Schema: qiita; Owner: antoniog -- -INSERT INTO qiita.processing_job VALUES ('6d368e16-2242-4cf8-87b4-a5dc40bb890b', 'test@foo.bar', 1, '{"max_bad_run_length":3,"min_per_read_length_fraction":0.75,"sequence_max_n":0,"rev_comp_barcode":false,"rev_comp_mapping_barcodes":false,"rev_comp":false,"phred_quality_threshold":3,"barcode_type":"golay_12","max_barcode_errors":1.5,"input_data":1,"phred_offset":"auto"}', 3, NULL, NULL, NULL, NULL, false, 1284411757); +INSERT INTO qiita.processing_job VALUES ('6d368e16-2242-4cf8-87b4-a5dc40bb890b', 'test@foo.bar', 1, '{"max_bad_run_length":3,"min_per_read_length_fraction":0.75,"sequence_max_n":0,"rev_comp_barcode":false,"rev_comp_mapping_barcodes":false,"rev_comp":false,"phred_quality_threshold":3,"barcode_type":"golay_12","max_barcode_errors":1.5,"input_data":1,"phred_offset":"auto"}', 3, NULL, NULL, NULL, NULL, false, 1284411757); INSERT INTO qiita.processing_job VALUES ('4c7115e8-4c8e-424c-bf25-96c292ca1931', 'test@foo.bar', 1, '{"max_bad_run_length":3,"min_per_read_length_fraction":0.75,"sequence_max_n":0,"rev_comp_barcode":false,"rev_comp_mapping_barcodes":true,"rev_comp":false,"phred_quality_threshold":3,"barcode_type":"golay_12","max_barcode_errors":1.5,"input_data":1,"phred_offset":"auto"}', 3, NULL, NULL, NULL, NULL, false, 1287244546); INSERT INTO qiita.processing_job VALUES ('3c9991ab-6c14-4368-a48c-841e8837a79c', 'test@foo.bar', 3, '{"reference":1,"sortmerna_e_value":1,"sortmerna_max_pos":10000,"similarity":0.97,"sortmerna_coverage":0.97,"threads":1,"input_data":2}', 3, NULL, NULL, NULL, NULL, false, 1284411377); INSERT INTO qiita.processing_job VALUES ('b72369f9-a886-4193-8d3d-f7b504168e75', 'shared@foo.bar', 1, '{"max_bad_run_length":3,"min_per_read_length_fraction":0.75,"sequence_max_n":0,"rev_comp_barcode":false,"rev_comp_mapping_barcodes":true,"rev_comp":false,"phred_quality_threshold":3,"barcode_type":"golay_12","max_barcode_errors":1.5,"input_data":1,"phred_offset":"auto"}', 3, NULL, '2015-11-22 21:15:00', NULL, NULL, false, 128552986); diff --git a/qiita_db/support_files/qiita-db-unpatched.sql b/qiita_db/support_files/qiita-db-unpatched.sql index a61b4645d..1ce86de39 100644 --- a/qiita_db/support_files/qiita-db-unpatched.sql +++ b/qiita_db/support_files/qiita-db-unpatched.sql @@ -1888,10 +1888,7 @@ CREATE TABLE qiita.qiita_user ( user_verify_code character varying, pass_reset_code character varying, pass_reset_timestamp timestamp without time zone, - receive_processing_job_emails boolean DEFAULT false, - social_orcid character varying DEFAULT NULL, - social_researchgate character varying DEFAULT NULL, - social_googlescholar character varying DEFAULT NULL + receive_processing_job_emails boolean DEFAULT false ); diff --git a/qiita_db/support_files/qiita-db.dbs b/qiita_db/support_files/qiita-db.dbs index d2cb68131..cf84177af 100644 --- a/qiita_db/support_files/qiita-db.dbs +++ b/qiita_db/support_files/qiita-db.dbs @@ -735,6 +735,13 @@ + + + + + + +
@@ -1007,6 +1014,9 @@ + + + @@ -1265,6 +1275,19 @@ + + + + + + + + + + + + + @@ -1370,6 +1393,13 @@ + + + + + + + @@ -2098,6 +2128,7 @@ $function$ + @@ -2125,14 +2156,14 @@ $function$ - + - + diff --git a/qiita_db/support_files/qiita-db.html b/qiita_db/support_files/qiita-db.html index 38d3fe23b..80fb3a211 100644 --- a/qiita_db/support_files/qiita-db.html +++ b/qiita_db/support_files/qiita-db.html @@ -2,7 +2,7 @@ -Qiita Db +QiitaDB @@ -291,6 +291,11 @@ + + + + + @@ -299,7 +304,7 @@ - Qiita Db + QiitaDB (c) DbSchema Hover columns to read the comments. @@ -410,11 +415,11 @@ analysis_users ref analysis ( analysis_id ) analysis_id - + Fk fk_analysis_users_user analysis_users ref qiita_user ( email ) -Fk fk_analysis_users_user +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 368,256L 368,1224Q 368,1232 360,1232L 336,1232' ><title>Fk fk_analysis_users_user analysis_users ref qiita_user ( email ) email @@ -442,13 +447,13 @@ artifact ref software_command ( command_id ) command_id - + Fk fk_artifact_visibility artifact ref visibility ( visibility_id ) -Fk fk_artifact_visibility +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 2176,784L 2176,864' ><title>Fk fk_artifact_visibility artifact ref visibility ( visibility_id ) -visibility_id +visibility_id Fk fk_artifact_filepath_artifact @@ -825,14 +830,6 @@ <path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 640,1392L 592,1392' ><title>Fk fk_study_tags per_study_tags ref study_tags ( study_tag ) study_tag - - - Fk fk_prep_template_artifact -prep_template ref artifact ( artifact_id ) - -Fk fk_prep_template_artifact -prep_template ref artifact ( artifact_id ) -artifact_id Fk fk_prep_template_data_type @@ -866,13 +863,13 @@ prep_template_processing_job ref prep_template ( prep_template_id ) prep_template_id - + Fk fk_prep_template_processing_job_job prep_template_processing_job ref processing_job ( processing_job_id ) -Fk fk_prep_template_processing_job_job +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 2656,912L 2648,912Q 2640,912 2640,920L 2640,1032Q 2640,1040 2632,1040L 1880,1040Q 1872,1040 1872,1032L 1872,1000Q 1872,992 1864,992L 1800,992Q 1792,992 1792,984L 1792,984Q 1792,976 1784,976L 1776,976' ><title>Fk fk_prep_template_processing_job_job prep_template_processing_job ref processing_job ( processing_job_id ) -processing_job_id +processing_job_id Fk fk_prep_template @@ -898,13 +895,13 @@ preparation_artifact ref artifact ( artifact_id ) artifact_id - + Fk fk_prep_template_id preparation_artifact ref prep_template ( prep_template_id ) -Fk fk_prep_template_id +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 2640,624L 2632,624Q 2624,624 2624,632L 2624,824Q 2624,832 2616,832L 2408,832Q 2400,832 2400,840L 2400,1272Q 2400,1280 2392,1280L 2272,1280' ><title>Fk fk_prep_template_id preparation_artifact ref prep_template ( prep_template_id ) -prep_template_id +prep_template_id Fk fk_processing_job_logging @@ -921,14 +918,6 @@ <path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 1520,832L 1456,832' ><title>Fk fk_processing_job_status processing_job ref processing_job_status ( processing_job_status_id ) processing_job_status_id - - - Fk fk_processing_job -processing_job ref software_command ( command_id ) - -Fk fk_processing_job -processing_job ref software_command ( command_id ) -command_id Fk fk_processing_job_validator_c @@ -962,13 +951,13 @@ processing_job_workflow_root ref processing_job_workflow ( processing_job_workflow_id ) processing_job_workflow_id - + Fk fk_user_user_level qiita_user ref user_level ( user_level_id ) -Fk fk_user_user_level +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 288,1504L 288,1528Q 288,1536 280,1536L 272,1536' ><title>Fk fk_user_user_level qiita_user ref user_level ( user_level_id ) -user_level_id +user_level_id Fk fk_reference_sequence_filepath @@ -994,29 +983,29 @@ reference ref filepath ( tree_filepath -> filepath_id ) tree_filepath - + Fk fk_filepath_id sample_template_filepath ref filepath ( filepath_id ) -Fk fk_filepath_id +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 2896,1280L 2896,1160Q 2896,1152 2904,1152L 2928,1152' ><title>Fk fk_filepath_id sample_template_filepath ref filepath ( filepath_id ) filepath_id - + Fk fk_study_id sample_template_filepath ref study ( study_id ) -Fk fk_study_id +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 2704,1296L 2648,1296Q 2640,1296 2640,1288L 2640,1240Q 2640,1232 2632,1232L 1880,1232Q 1872,1232 1872,1240L 1872,1336Q 1872,1344 1864,1344L 360,1344Q 352,1344 352,1336L 352,872Q 352,864 344,864L 320,864' ><title>Fk fk_study_id sample_template_filepath ref study ( study_id ) study_id - + Fk fk_slurm_resource_allocations slurm_resource_allocations ref processing_job ( processing_job_id ) -Fk fk_slurm_resource_allocations +<path transform='translate(8,0)' marker-start='url(#foot1)' marker-end='url(#arrow1)' d='M 1872,784L 1776,784' ><title>Fk fk_slurm_resource_allocations slurm_resource_allocations ref processing_job ( processing_job_id ) -processing_job_id +processing_job_id Fk fk_software_software_type @@ -1090,19 +1079,19 @@ study ref timeseries_type ( timeseries_type_id ) timeseries_type_id - + Fk fk_study_artifact_artifact study_artifact ref artifact ( artifact_id ) -Fk fk_study_artifact_artifact +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 304,1104L 304,1096Q 304,1088 312,1088L 904,1088Q 912,1088 912,1096L 912,1304Q 912,1312 920,1312L 1928,1312Q 1936,1312 1936,1304L 1936,1080Q 1936,1072 1944,1072L 2104,1072Q 2112,1072 2112,1064L 2112,744Q 2112,736 2120,736L 2144,736' ><title>Fk fk_study_artifact_artifact study_artifact ref artifact ( artifact_id ) artifact_id - + Fk fk_study_artifact_study study_artifact ref study ( study_id ) -Fk fk_study_artifact_study +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 320,1136L 328,1136Q 336,1136 336,1128L 336,856Q 336,848 328,848L 320,848' ><title>Fk fk_study_artifact_study study_artifact ref study ( study_id ) study_id @@ -1146,27 +1135,27 @@ study_prep_template ref prep_template ( prep_template_id ) prep_template_id - + Fk fk_study_prep_template_study study_prep_template ref study ( study_id ) -Fk fk_study_prep_template_study +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 592,1104L 592,1080Q 592,1072 600,1072L 696,1072Q 704,1072 704,1064L 704,600Q 704,592 696,592L 632,592Q 624,592 624,584L 624,424Q 624,416 616,416L 312,416Q 304,416 304,424L 304,496' ><title>Fk fk_study_prep_template_study study_prep_template ref study ( study_id ) -study_id +study_id - + Fk fk_required_sample_info_study study_sample ref study ( study_id ) -Fk fk_required_sample_info_study +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 704,1200L 704,1112Q 704,1104 712,1104L 712,1104Q 720,1104 720,1096L 720,920Q 720,912 712,912L 392,912Q 384,912 384,920L 384,920Q 384,928 376,928L 280,928Q 272,928 272,920L 272,896' ><title>Fk fk_required_sample_info_study study_sample ref study ( study_id ) study_id - + Fk fk_email study_tags ref qiita_user ( email ) -Fk fk_email +<path transform='translate(8,0)' marker-start='url(#foot1p)' marker-end='url(#arrow1)' d='M 416,1376L 336,1376' ><title>Fk fk_email study_tags ref qiita_user ( email ) email @@ -1979,9 +1968,9 @@ * varchar varchar - + - + prep_templateTable qiita.prep_template Pk pk_prep_template ( prep_template_id ) prep_template_idprep_template_id * bigint default nextval('qiita.prep_template_prep_template_id_seq'::regclass) @@ -2015,7 +2004,9 @@ boolean default false boolean reprocess_job_idreprocess_job_id uuid default NULL -uuid +uuid human_reads_filter_method_idhuman_reads_filter_method_id +bigint default NULL +bigint @@ -2202,41 +2193,50 @@ varchar varchar - - - -qiita_userTable qiita.qiita_user +<rect class='entity' style='stroke:none;' x='48' y='1208' width='288' height='288' rx='8' ry='8' /> +<path d='M 48 1236 L 48 1216 Q 48 1208 56 1208 L 328 1208 Q 336 1208 336 1216 L 336 1236 L48 1236 ' style='fill:url(#tbg_D1BEF4);stroke:1;stroke-opacity:0.1;' /> +<rect class='entity' x='48' y='1208' width='288' height='288' rx='8' ry='8' style='fill:none;stroke:#28272C'/> +<a xlink:href='#qiita.qiita_user'><text x='157' y='1227' >qiita_user</text><title>Table qiita.qiita_user Holds all user information - Pk pk_user ( email ) emailemail + <use id='nn' x='50' y='1245' xlink:href='#nn'/><use id='pk' x='50' y='1244' xlink:href='#pk'><title>Pk pk_user ( email ) emailemail * varchar -varcharReferred by analysis_users ( email ) +<text x='320' y='1256' text-anchor='end' class='colType'>varchar</text><a xlink:href='#qiita.qiita_user.email'><use id='ref' x='324' y='1244' xlink:href='#ref'/><title>Referred by analysis_users ( email ) Referred by study_tags ( email ) - idx_user ( user_level_id ) user_level_iduser_level_id + <use id='nn' x='50' y='1261' xlink:href='#nn'/><use id='idx' x='50' y='1260' xlink:href='#idx'><title>idx_user ( user_level_id ) user_level_iduser_level_id * integer default 5 user level -integerReferences user_level ( user_level_id ) - passwordpassword +<text x='320' y='1272' text-anchor='end' class='colType'>integer</text><a xlink:href='#qiita.qiita_user.user_level_id'><use id='fk' x='324' y='1260' xlink:href='#fk'/><title>References user_level ( user_level_id ) + passwordpassword * varchar -varchar namename +<text x='320' y='1288' text-anchor='end' class='colType'>varchar</text> <a xlink:href='#qiita.qiita_user_name'><text id='qiita.qiita_user.name' x='67' y='1303'>name</text><title>name varchar -varchar affiliationaffiliation +<text x='320' y='1304' text-anchor='end' class='colType'>varchar</text> <a xlink:href='#qiita.qiita_user_affiliation'><text id='qiita.qiita_user.affiliation' x='67' y='1319'>affiliation</text><title>affiliation varchar -varchar addressaddress +<text x='320' y='1320' text-anchor='end' class='colType'>varchar</text> <a xlink:href='#qiita.qiita_user_address'><text id='qiita.qiita_user.address' x='67' y='1335'>address</text><title>address varchar -varchar phonephone +<text x='320' y='1336' text-anchor='end' class='colType'>varchar</text> <a xlink:href='#qiita.qiita_user_phone'><text id='qiita.qiita_user.phone' x='67' y='1351'>phone</text><title>phone varchar -varchar user_verify_codeuser_verify_code +<text x='320' y='1352' text-anchor='end' class='colType'>varchar</text> <a xlink:href='#qiita.qiita_user_user_verify_code'><text id='qiita.qiita_user.user_verify_code' x='67' y='1367'>user_verify_code</text><title>user_verify_code varchar Code for initial user email verification -varchar pass_reset_codepass_reset_code +<text x='320' y='1368' text-anchor='end' class='colType'>varchar</text> <a xlink:href='#qiita.qiita_user_pass_reset_code'><text id='qiita.qiita_user.pass_reset_code' x='67' y='1383'>pass_reset_code</text><title>pass_reset_code varchar Randomly generated code for password reset -varchar pass_reset_timestamppass_reset_timestamp +<text x='320' y='1384' text-anchor='end' class='colType'>varchar</text> <a xlink:href='#qiita.qiita_user_pass_reset_timestamp'><text id='qiita.qiita_user.pass_reset_timestamp' x='67' y='1399'>pass_reset_timestamp</text><title>pass_reset_timestamp timestamp(0) Time the reset code was generated -timestamp(0) receive_processing_job_emailsreceive_processing_job_emails +<text x='320' y='1400' text-anchor='end' class='colType'>timestamp(0)</text> <use id='nn' x='50' y='1405' xlink:href='#nn'/><a xlink:href='#qiita.qiita_user_receive_processing_job_emails'><text id='qiita.qiita_user.receive_processing_job_emails' x='67' y='1415'>receive_processing_job_emails</text><title>receive_processing_job_emails * boolean default false -boolean +boolean social_orcidsocial_orcid +varchar default NULL +varchar social_researchgatesocial_researchgate +varchar default NULL +varchar social_googlescholarsocial_googlescholar +varchar default NULL +varchar creation_timestampcreation_timestamp +timestamp default NOW() +The date the user account was created +timestamp @@ -2322,26 +2322,32 @@ * varchar varchar - - - -slurm_resource_allocationsTable qiita.slurm_resource_allocations - Pk pk_slurm_resource_allocations_processing_job_id ( processing_job_id ) processing_job_idprocessing_job_id +<rect class='entity' style='stroke:none;' x='1888' y='616' width='192' height='208' rx='8' ry='8' /> +<path d='M 1888 644 L 1888 624 Q 1888 616 1896 616 L 2072 616 Q 2080 616 2080 624 L 2080 644 L1888 644 ' style='fill:url(#tbg_F4DDBE);stroke:1;stroke-opacity:0.1;' /> +<rect class='entity' x='1888' y='616' width='192' height='208' rx='8' ry='8' style='fill:none;stroke:#2C2927'/> +<a xlink:href='#qiita.slurm_resource_allocations'><text x='1894' y='635' >slurm_resource_allocations</text><title>Table qiita.slurm_resource_allocations + Pk pk_slurm_resource_allocations_processing_job_id ( processing_job_id ) processing_job_idprocessing_job_id * uuid -uuidReferences processing_job ( processing_job_id ) - samplessamples +<text x='2064' y='664' text-anchor='end' class='colType'>uuid</text><a xlink:href='#qiita.slurm_resource_allocations.processing_job_id'><use id='fk' x='2068' y='652' xlink:href='#fk'/><title>References processing_job ( processing_job_id ) + samplessamples integer -integer columnscolumns +<text x='2064' y='680' text-anchor='end' class='colType'>integer</text> <a xlink:href='#qiita.slurm_resource_allocations_columns'><text id='qiita.slurm_resource_allocations.columns' x='1907' y='695'>columns</text><title>columns integer -integer input_sizeinput_size +<text x='2064' y='696' text-anchor='end' class='colType'>integer</text> <a xlink:href='#qiita.slurm_resource_allocations_input_size'><text id='qiita.slurm_resource_allocations.input_size' x='1907' y='711'>input_size</text><title>input_size bigint -bigint extra_infoextra_info +<text x='2064' y='712' text-anchor='end' class='colType'>bigint</text> <a xlink:href='#qiita.slurm_resource_allocations_extra_info'><text id='qiita.slurm_resource_allocations.extra_info' x='1907' y='727'>extra_info</text><title>extra_info varchar default null -varchar memory_usedmemory_used +<text x='2064' y='728' text-anchor='end' class='colType'>varchar</text> <a xlink:href='#qiita.slurm_resource_allocations_memory_used'><text id='qiita.slurm_resource_allocations.memory_used' x='1907' y='743'>memory_used</text><title>memory_used bigint -bigint walltime_usedwalltime_used +<text x='2064' y='744' text-anchor='end' class='colType'>bigint</text> <a xlink:href='#qiita.slurm_resource_allocations_walltime_used'><text id='qiita.slurm_resource_allocations.walltime_used' x='1907' y='759'>walltime_used</text><title>walltime_used integer -integer +integer job_startjob_start +text +text node_namenode_name +varchar default NULL +varchar node_modelnode_model +varchar default NULL +varchar @@ -2715,6 +2721,16 @@ varchar visibility_descriptionvisibility_description * varchar varchar + + + + +human_reads_filter_methodTable qiita.human_reads_filter_method + Pk pk_human_reads_filter_method_human_reads_filter_method_id ( human_reads_filter_method_id ) human_reads_filter_method_idhuman_reads_filter_method_id +* bigint +bigint human_reads_filter_method_namehuman_reads_filter_method_name +* varchar +varchar
@@ -4331,6 +4347,30 @@
+

+
Table human_reads_filter_method
 + + + + + + + + + + + + + + + + + + + + +
IdxField NameData Type
*human_reads_filter_method_id bigint
*human_reads_filter_method_name varchar
Indexes
pk_human_reads_filter_method_human_reads_filter_method_id ON human_reads_filter_method_id
+

Table investigation

Overarching investigation information.An investigation comprises one or more individual studies.

@@ -4983,6 +5023,12 @@ uuid DEFAULT NULL + +   + human_reads_filter_method_id + bigint DEFAULT NULL + + Indexes pk_prep_template ON prep_template_id @@ -5514,7 +5560,7 @@


-
Table qiita_user
 +
Table qiita_user

Holds all user information

@@ -5587,6 +5633,30 @@ + + + + + + + + + + + + + + + + + + + + + + + + @@ -5821,7 +5891,7 @@
boolean DEFAULT false
 social_orcid varchar DEFAULT NULL
 social_researchgate varchar DEFAULT NULL
 social_googlescholar varchar DEFAULT NULL
 creation_timestamp timestamp DEFAULT NOW() The date the user account was created
Indexes
pk_user ON email


-
Table slurm_resource_allocations
 +
Table slurm_resource_allocations
 @@ -5862,6 +5932,21 @@ + + + + + + + + + + + + + + +
IdxField NameData Type
walltime_used integer
 job_start text
 node_name varchar DEFAULT NULL
 node_model varchar DEFAULT NULL
Indexes
pk_slurm_resource_allocations_processing_job_id ON processing_job_id