Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Clean db files add human reads filter method #3421

Merged
merged 13 commits into from
Jun 28, 2024
Merged

Clean db files add human reads filter method #3421

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
57d1b14
Update CHANGELOG.md
antgonza Jan 29, 2024
13eafdf
fix CHANGELOG.md CONFLICT
antgonza Feb 27, 2024
ee98f64
Merge branch 'dev' of github.com:biocore/qiita into dev
antgonza Apr 16, 2024
c3ce6a4
Merge branch 'dev' of github.com:biocore/qiita into dev
antgonza Apr 21, 2024
6767990
Merge branch 'dev' of github.com:biocore/qiita into dev
antgonza Apr 23, 2024
3c1f71b
Merge branch 'dev' of github.com:biocore/qiita into dev
antgonza Apr 26, 2024
8edd0c8
Merge branch 'dev' of github.com:biocore/qiita into dev
antgonza Apr 26, 2024
5711b0c
Merge branch 'dev' of github.com:biocore/qiita into dev
antgonza May 15, 2024
9613bdb
Merge branch 'dev' of github.com:biocore/qiita into dev
antgonza May 30, 2024
bcb4433
Merge branch 'dev' of github.com:biocore/qiita into dev
antgonza Jun 28, 2024
7d42b84
clean db files + add human_reads_filter_method
antgonza Jun 28, 2024
f7324e8
fix db errors
antgonza Jun 28, 2024
e3253cd
modify inserts to be in the correct order
antgonza Jun 28, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
25 changes: 25 additions & 0 deletions qiita_db/support_files/patches/92.sql
View file
Open in desktop
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
Open in desktop
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
Open in desktop
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
Open in desktop
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
Open in desktop
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
Loading