Skip to content

Commit

Permalink
Clean db files add human reads filter method (#3421)
Browse files Browse the repository at this point in the history 
* Update CHANGELOG.md

* clean db files + add human_reads_filter_method

* fix db errors

* modify inserts to be in the correct order
  • Loading branch information
@antgonza
antgonza authored Jun 28, 2024
1 parent 751e559 commit b28670d
Show file tree
Hide file tree
Showing 6 changed files with 244 additions and 101 deletions.
25 changes: 25 additions & 0 deletions qiita_db/support_files/patches/92.sql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 );
13 changes: 9 additions & 4 deletions qiita_db/support_files/patches/test_db_sql/92.sql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 = '[email protected]';
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 = '[email protected]';

-- 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 ('[email protected]', 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 ('[email protected]', 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 ('[email protected]', 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 ('[email protected]', 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 ('[email protected]', 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 ('[email protected]', 5, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'TooLate', 'NonVeriUser', '564 C Street', '508-492-222', NULL, NULL, NULL, false, NOW() - INTERVAL '30 DAY', NULL, NULL, NULL);
10 changes: 5 additions & 5 deletions qiita_db/support_files/populate_test_db.sql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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 ('[email protected]', 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 ('[email protected]', 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 ('[email protected]', 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 ('[email protected]', 4, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Demo', 'Qiita Dev', '1345 Colorado Avenue', '303-492-1984', NULL, NULL, NULL, false);
INSERT INTO qiita.qiita_user VALUES ('[email protected]', 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 ('[email protected]', 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 ('[email protected]', 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 ('[email protected]', 4, '$2a$12$gnUi8Qg.0tvW243v889BhOBhWLIHyIJjjgaG6dxuRJkUM8nXG9Efe', 'Demo', 'Qiita Dev', '1345 Colorado Avenue', '303-492-1984', NULL, NULL, NULL);


--
Expand Down Expand Up @@ -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', '[email protected]', 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', '[email protected]', 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', '[email protected]', 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', '[email protected]', 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', '[email protected]', 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);
Expand Down
5 changes: 1 addition & 4 deletions qiita_db/support_files/qiita-db-unpatched.sql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
);


Expand Down
35 changes: 33 additions & 2 deletions qiita_db/support_files/qiita-db.dbs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -735,6 +735,13 @@
<column name="filepath_type" />
</index>
</table>
<table name="human_reads_filter_method" prior="human_reads_filter" >
<column name="human_reads_filter_method_id" type="bigint" jt="-5" mandatory="y" />
<column name="human_reads_filter_method_name" type="varchar" jt="12" mandatory="y" />
<index name="pk_human_reads_filter_method_human_reads_filter_method_id" unique="PRIMARY_KEY" >
<column name="human_reads_filter_method_id" />
</index>
</table>
<table name="investigation" >
<comment><![CDATA[Overarching investigation information.An investigation comprises one or more individual studies.]]></comment>
<column name="investigation_id" type="bigint" length="19" decimal="0" jt="-5" mandatory="y" >
Expand Down Expand Up @@ -1007,6 +1014,9 @@
<column name="reprocess_job_id" type="uuid" jt="1111" >
<defo><![CDATA[NULL]]></defo>
</column>
<column name="human_reads_filter_method_id" type="bigint" jt="-5" >
<defo><![CDATA[NULL]]></defo>
</column>
<index name="pk_prep_template" unique="PRIMARY_KEY" >
<column name="prep_template_id" />
</index>
Expand Down Expand Up @@ -1265,6 +1275,19 @@
<column name="receive_processing_job_emails" type="boolean" jt="-7" mandatory="y" >
<defo><![CDATA[false]]></defo>
</column>
<column name="social_orcid" type="varchar" jt="12" >
<defo><![CDATA[NULL]]></defo>
</column>
<column name="social_researchgate" type="varchar" jt="12" >
<defo><![CDATA[NULL]]></defo>
</column>
<column name="social_googlescholar" type="varchar" jt="12" >
<defo><![CDATA[NULL]]></defo>
</column>
<column name="creation_timestamp" type="timestamp" jt="93" >
<defo><![CDATA[NOW()]]></defo>
<comment><![CDATA[The date the user account was created]]></comment>
</column>
<index name="pk_user" unique="PRIMARY_KEY" >
<column name="email" />
</index>
Expand Down Expand Up @@ -1370,6 +1393,13 @@
</column>
<column name="memory_used" type="bigint" jt="-5" />
<column name="walltime_used" type="integer" jt="4" />
<column name="job_start" type="text" jt="12" />
<column name="node_name" type="varchar" jt="12" >
<defo><![CDATA[NULL]]></defo>
</column>
<column name="node_model" type="varchar" jt="12" >
<defo><![CDATA[NULL]]></defo>
</column>
<index name="pk_slurm_resource_allocations_processing_job_id" unique="PRIMARY_KEY" >
<column name="processing_job_id" />
</index>
Expand Down Expand Up @@ -2098,6 +2128,7 @@ $function$
<entity schema="qiita" name="environmental_package" color="C7F4BE" x="752" y="960" />
<entity schema="qiita" name="filepath" color="BED3F4" x="2944" y="1024" />
<entity schema="qiita" name="filepath_type" color="BED3F4" x="2960" y="1296" />
<entity schema="qiita" name="human_reads_filter_method" color="C1D8EE" x="2304" y="1312" />
<entity schema="qiita" name="investigation" color="C7F4BE" x="704" y="464" />
<entity schema="qiita" name="investigation_study" color="C7F4BE" x="736" y="688" />
<entity schema="qiita" name="logging" color="F4DDBE" x="1760" y="320" />
Expand Down Expand Up @@ -2125,14 +2156,14 @@ $function$
<entity schema="qiita" name="processing_job_workflow" color="F4DDBE" x="1600" y="1168" />
<entity schema="qiita" name="processing_job_workflow_root" color="F4DDBE" x="1600" y="1056" />
<entity schema="qiita" name="publication" color="F4DDBE" x="3232" y="832" />
<entity schema="qiita" name="qiita_user" color="D1BEF4" x="64" y="1232" />
<entity schema="qiita" name="qiita_user" color="D1BEF4" x="48" y="1216" />
<entity schema="qiita" name="reference" color="BED3F4" x="3248" y="1024" />
<entity schema="qiita" name="restrictions" color="BED3F4" x="2768" y="1424" />
<entity schema="qiita" name="sample_template_filepath" color="BED3F4" x="2720" y="1296" />
<entity schema="qiita" name="sample_x" color="BED3F4" x="912" y="1408" />
<entity schema="qiita" name="settings" color="F82E15" x="64" y="160" />
<entity schema="qiita" name="severity" color="F4DDBE" x="1632" y="240" />
<entity schema="qiita" name="slurm_resource_allocations" color="F4DDBE" x="1888" y="640" />
<entity schema="qiita" name="slurm_resource_allocations" color="F4DDBE" x="1888" y="624" />
<entity schema="qiita" name="software" color="F4DDBE" x="3232" y="320" />
<entity schema="qiita" name="software_artifact_type" color="BEBEF4" x="2128" y="304" />
<entity schema="qiita" name="software_command" color="F4DDBE" x="2880" y="320" />
Expand Down
Loading

0 comments on commit b28670d

Please sign in to comment.