75 lines
5.7 KiB
SQL
75 lines
5.7 KiB
SQL
-- mirri.vw_strains_202206 source
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CREATE OR REPLACE VIEW `mirri`.`vw_strains_202206` AS
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with `taxonomy` as (
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select
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`zmsmt`.`_id` AS `_id`,
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`zmsmt`.`x` AS `x`,
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`zmsmt`.`y` AS `y`,
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`zmsmt`.`idx` AS `idx`,
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`zmsmt`.`idy` AS `idy`
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from
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`mirri`.`zy_mirri_strains_mirri_taxonomy_737` `zmsmt`)
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select
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`s`.`name` AS `MIRRI Accession number`,
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`s`.`mirri_accession_number` AS `Accession number`,
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`s`.`restriction_on_use` AS `Restrictions on use`,
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`s`.`nagoya` AS `Nagoya protocol restrictions and compliance conditions`,
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`s`.`abs_url` AS `ABS related files`,
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`s`.`mta_url` AS `MTA url`,
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`s`.`mta_text` AS `MTA text`,
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`s`.`strains_from_reg_collection` AS `Strain from a Registered Collection`,
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`s`.`risk_group` AS `Risk Group`,
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`s`.`dual_use` AS `Dual use`,
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`s`.`quarantine_europe` AS `Quarantine in Europe`,
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trim(leading ';' from concat((case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 2), '¶',-(1)) = '2') then ';Algae' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 3), '¶',-(1)) = '2') then ';Archaea' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 4), '¶',-(1)) = '2') then ';Bacteria' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 5), '¶',-(1)) = '2') then ';Cyanobacteria' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 6), '¶',-(1)) = '2') then ';Filamentous Fungi' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 7), '¶',-(1)) = '2') then ';Phage' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 8), '¶',-(1)) = '2') then ';Plasmid' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 9), '¶',-(1)) = '2') then ';Virus' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 10), '¶',-(1)) = '2') then ';Yeast' else '' end),(case when (substring_index(substring_index(`s`.`type_of_organim`, '¶', 11), '¶',-(1)) = '2') then ';Microalgae' else '' end))) AS `Organism type`,
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`t`.`name` AS `Taxon name`,
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`s`.`infra_subsp_name` AS `Infrasubspecific names`,
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`s`.`comment_taxonomy` AS `Comment on taxonomy`,
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`s`.`type_description` AS `Type`,
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`s`.`status` AS `Status`,
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`s`.`history` AS `History of deposit`,
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`s`.`depositor` AS `Depositor`,
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trim(leading '//' from trim(leading '//0' from concat(substr(`s`.`deposited_date`, 7, 2), '/', substr(`s`.`deposited_date`, 5, 2), '/', substr(`s`.`deposited_date`, 1, 4)))) AS `Date of deposit`,
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`s`.`collector` AS `Collected by`,
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trim(leading '//' from trim(leading '//0' from concat(substr(`s`.`collection_date`, 7, 2), '/', substr(`s`.`collection_date`, 5, 2), '/', substr(`s`.`collection_date`, 1, 4)))) AS `Date of collection`,
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`s`.`isolator` AS `Isolated by`,
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trim(leading '//' from trim(leading '//0' from concat(substr(`s`.`isolation_date`, 7, 2), '/', substr(`s`.`isolation_date`, 5, 2), '/', substr(`s`.`isolation_date`, 1, 4)))) AS `Date of isolation`,
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trim(leading '//' from trim(leading '//0' from concat(substr(`s`.`catalogue_date`, 7, 2), '/', substr(`s`.`catalogue_date`, 5, 2), '/', substr(`s`.`catalogue_date`, 1, 4)))) AS `Date of inclusion in the catalogue`,
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`s`.`tested_growth_temp` AS `Tested temperature growth range`,
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`s`.`growth_temp` AS `Recommended growth temperature`,
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NULL AS `Recommended medium for growth`,
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trim(leading ';' from concat((case when (substring_index(substring_index(`s`.`form_supply`, '¶', 2), '¶',-(1)) = '2') then 'Agar' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 3), '¶',-(1)) = '2') then ';Cryo' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 4), '¶',-(1)) = '2') then ';Dry Ice' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 5), '¶',-(1)) = '2') then ';Liquid Culture Medium' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 6), '¶',-(1)) = '2') then ';Lyo' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 7), '¶',-(1)) = '2') then ';Oil' else '' end),(case when (substring_index(substring_index(`s`.`form_supply`, '¶', 8), '¶',-(1)) = '2') then ';Water' else '' end))) AS `Form of supply`,
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`s`.`other_denomination` AS `Other denomination`,
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`s`.`coordinates` AS `Coordinates of geographic origin`,
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`s`.`origin_id` AS `Country`,
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`s`.`locality_of_origin` AS `Geographic origin`,
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`s`.`gmo` AS `GMO`,
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NULL AS `GMO construction information`,
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`s`.`mutant` AS `Mutant information`,
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`s`.`genotype` AS `Genotype`,
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`s`.`literature_doi` AS `Literature`,
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`s`.`sexual_state` AS `Sexual state`,
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`s`.`ploidy` AS `Ploidy`,
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`s`.`interspecific_hybrid` AS `Interspecific hybrid`,
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`s`.`pathogenicity` AS `Pathogenicity`,
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`s`.`enzyme_production` AS `Enzyme production`,
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`s`.`metabolites_production` AS `Production of metabolites`,
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`s`.`applications` AS `Applications`,
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`s`.`remarks` AS `Remarks`,
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`s`.`plasmids` AS `Plasmids`,
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`s`.`plasmids_collections` AS `Plasmids collections fields`,
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`s`.`substrate_of_isolation` AS `Substrate/host of isolation`,
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`s`.`isolation_habitat` AS `Isolation habitat`,
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`s`.`ontobiotope` AS `Ontobiotope term for the isolation habitat`,
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NULL AS `Genomic sequences and accession numbers`,
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NULL AS `Literature linked to the sequence/genome`,
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NULL AS `Link to other sites`,
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NULL AS `QPS`,
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NULL AS `Axenic culture`
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from
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((`mirri`.`mirri_strains` `s`
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left join `taxonomy` `tu` on
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((`tu`.`x` = `s`.`_id`)))
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left join `mirri`.`mirri_taxonomy` `t` on
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((`t`.`_id` = `tu`.`y`))); |