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Merged
merged 4 commits into from
Apr 16, 2024
Merged

qiita.slurm_resource_allocations #3391

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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
dc82e12
add db changes including fix #3368
antgonza Apr 16, 2024
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20 changes: 20 additions & 0 deletions qiita_db/support_files/patches/92.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,20 @@
-- Apr 16, 2024
-- Adding a new table to contain the basic slurm information to minimize
-- the number of times we need to retrieve this information

CREATE TABLE qiita.slurm_resource_allocations (
processing_job_id uuid NOT NULL,
samples integer,
columns integer,
input_size bigint,
extra_info varchar DEFAULT NULL,
memory_used bigint,
walltime_used integer,
CONSTRAINT pk_slurm_resource_allocations_processing_job_id PRIMARY KEY (
processing_job_id )
);

ALTER TABLE qiita.slurm_resource_allocations
ADD CONSTRAINT fk_slurm_resource_allocations
FOREIGN KEY ( processing_job_id )
REFERENCES qiita.processing_job ( processing_job_id );
39 changes: 37 additions & 2 deletions qiita_db/support_files/qiita-db.dbs
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Expand Up @@ -1326,6 +1326,22 @@
<column name="sample_id" />
</index>
</table>
<table name="settings" prior="base_work_dir" >
<column name="test" type="boolean" jt="-7" mandatory="y" >
<defo><![CDATA[true]]></defo>
</column>
<column name="base_data_dir" type="varchar" jt="12" mandatory="y" />
<column name="base_work_dir" type="varchar" jt="12" mandatory="y" />
<column name="current_patch" type="varchar" jt="12" mandatory="y" >
<defo><![CDATA['unpatched'::character varying]]></defo>
</column>
<column name="max_preparation_samples" type="integer" jt="4" >
<defo><![CDATA[800]]></defo>
</column>
<column name="max_artifacts_in_workflow" type="integer" jt="4" >
<defo><![CDATA[35]]></defo>
</column>
</table>
<table name="severity" >
<column name="severity_id" type="integer" length="10" decimal="0" jt="4" mandatory="y" >
<defo><![CDATA[nextval('qiita.severity_severity_id_seq'::regclass)]]></defo>
Expand All @@ -1338,6 +1354,23 @@
<column name="severity" />
</index>
</table>
<table name="slurm_resource_allocations" prior="tbl" >
<column name="processing_job_id" type="uuid" jt="1111" mandatory="y" />
<column name="samples" type="integer" jt="4" />
<column name="columns" type="integer" jt="4" />
<column name="input_size" type="bigint" jt="-5" />
<column name="extra_info" type="varchar" jt="12" >
<defo><![CDATA[null]]></defo>
</column>
<column name="memory_used" type="bigint" jt="-5" />
<column name="walltime_used" type="integer" jt="4" />
<index name="pk_slurm_resource_allocations_processing_job_id" unique="PRIMARY_KEY" >
<column name="processing_job_id" />
</index>
<fk name="fk_slurm_resource_allocations" to_schema="qiita" to_table="processing_job" >
<fk_column name="processing_job_id" pk="processing_job_id" />
</fk>
</table>
<table name="software" >
<column name="software_id" type="bigint" length="19" decimal="0" jt="-5" mandatory="y" >
<defo><![CDATA[nextval('qiita.software_software_id_seq'::regclass)]]></defo>
Expand Down Expand Up @@ -2023,14 +2056,14 @@ $function$
</schema>
<connector name="PostgreSQL" database="PostgreSQL" driver_class="org.postgresql.Driver" driver_jar="postgresql-42.2.18.jar" driver_desc="Standard" host="localhost" port="5432" instance="qiita_test" user="antoniog" />
<layout name="Qiita DB Schema" id="Layout_1647" show_column_type="y" show_relation="columns" >
<comment><![CDATA[Qiita DB Schema]]></comment>
<comment><![CDATA[Qiita DB]]></comment>
<entity schema="qiita" name="analysis" color="D1BEF4" x="720" y="48" />
<entity schema="qiita" name="analysis_artifact" color="D1BEF4" x="496" y="48" />
<entity schema="qiita" name="analysis_filepath" color="F4DDBE" x="1680" y="624" />
<entity schema="qiita" name="analysis_portal" color="D1BEF4" x="1024" y="64" />
<entity schema="qiita" name="analysis_processing_job" color="D1BEF4" x="416" y="304" />
<entity schema="qiita" name="analysis_sample" color="D1BEF4" x="752" y="272" />
<entity schema="qiita" name="analysis_users" color="D1BEF4" x="304" y="176" />
<entity schema="qiita" name="analysis_users" color="D1BEF4" x="352" y="176" />
<entity schema="qiita" name="archive_feature_value" color="D1BEF4" x="1312" y="48" />
<entity schema="qiita" name="archive_merging_scheme" color="D1BEF4" x="1616" y="48" />
<entity schema="qiita" name="artifact" color="BED3F4" x="2160" y="576" />
Expand Down Expand Up @@ -2091,7 +2124,9 @@ $function$
<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="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
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