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antgonzaantgonza
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clean db files + add human_reads_filter_method
1 parent bcb4433 commit 7d42b84

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4 files changed

+230
-92
lines changed

4 files changed

+230
-92
lines changed

‎qiita_db/support_files/patches/92.sql

Lines changed: 25 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -39,3 +39,28 @@ ALTER TABLE qiita.qiita_user
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ADD creation_timestamp timestamp without time zone DEFAULT NOW();
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COMMENT ON COLUMN qiita.qiita_user.creation_timestamp IS 'The date the user account was created';
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-- Jun 28, 2024
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-- These columns were added by mistake to qiita-db-unpatched.sql in PR:
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-- https://github.com/qiita-spots/qiita/pull/3412 so adding here now
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ALTER TABLE qiita.qiita_user ADD social_orcid character varying DEFAULT NULL;
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ALTER TABLE qiita.qiita_user ADD social_researchgate character varying DEFAULT NULL;
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ALTER TABLE qiita.qiita_user ADD social_googlescholar character varying DEFAULT NULL;
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-- Add human_reads_filter_method so we can keep track of the available methods
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-- and link them to the preparations
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CREATE TABLE qiita.human_reads_filter_method (
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human_reads_filter_method_id bigint NOT NULL,
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human_reads_filter_method_method character varying NOT NULL;
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CONSTRAINT pk_human_reads_filter_method_id PRIMARY KEY (
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human_reads_filter_method_id )
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);
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ALTER TABLE qiita.prep_template
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ADD human_reads_filter_method_id bigint DEFAULT NULL;
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ALTER TABLE qiita.prep_template
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ADD CONSTRAINT fk_human_reads_filter_method
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FOREIGN KEY ( human_reads_filter_method_id )
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REFERENCES qiita.human_reads_filter_method ( human_reads_filter_method_id );

‎qiita_db/support_files/qiita-db-unpatched.sql

Lines changed: 1 addition & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1888,10 +1888,7 @@ CREATE TABLE qiita.qiita_user (
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user_verify_code character varying,
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pass_reset_code character varying,
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pass_reset_timestamp timestamp without time zone,
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receive_processing_job_emails boolean DEFAULT false,
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social_orcid character varying DEFAULT NULL,
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social_researchgate character varying DEFAULT NULL,
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social_googlescholar character varying DEFAULT NULL
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receive_processing_job_emails boolean DEFAULT false
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);
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‎qiita_db/support_files/qiita-db.dbs

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

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