From bfd13e620b378e773c84cae4404e0a3f21bd3d8c Mon Sep 17 00:00:00 2001 From: Adam Rauch Date: Sat, 1 Aug 2020 10:21:05 -0700 Subject: [PATCH] Consolidate bootstrap scripts to 0.00-18.20.sql --- ...{cds-0.00-17.30.sql => cds-0.00-18.20.sql} | 638 ++++++++++++++++- .../dbscripts/postgresql/cds-18.10-18.20.sql | 646 ------------------ 2 files changed, 627 insertions(+), 657 deletions(-) rename resources/schemas/dbscripts/postgresql/{cds-0.00-17.30.sql => cds-0.00-18.20.sql} (51%) delete mode 100644 resources/schemas/dbscripts/postgresql/cds-18.10-18.20.sql diff --git a/resources/schemas/dbscripts/postgresql/cds-0.00-17.30.sql b/resources/schemas/dbscripts/postgresql/cds-0.00-18.20.sql similarity index 51% rename from resources/schemas/dbscripts/postgresql/cds-0.00-17.30.sql rename to resources/schemas/dbscripts/postgresql/cds-0.00-18.20.sql index bb1711c80..21d490bb2 100644 --- a/resources/schemas/dbscripts/postgresql/cds-0.00-17.30.sql +++ b/resources/schemas/dbscripts/postgresql/cds-0.00-18.20.sql @@ -18,7 +18,6 @@ CREATE SCHEMA cds; - CREATE TABLE cds.Feedback ( RowId SERIAL, @@ -33,7 +32,6 @@ CREATE TABLE cds.Feedback CONSTRAINT pk_feedback PRIMARY KEY (Container, RowId) ); - CREATE TABLE cds.Sites ( Id VARCHAR(250) NOT NULL, @@ -48,7 +46,6 @@ CREATE TABLE cds.Sites CONSTRAINT pk_sites PRIMARY KEY (Container, Id) ); - CREATE TABLE cds.import_Study ( prot VARCHAR(250) NOT NULL, network VARCHAR(250), @@ -431,7 +428,6 @@ CREATE TABLE cds.import_BAMA ( CONSTRAINT PK_import_BAMA PRIMARY KEY (row_id) ); - CREATE TABLE cds.Study ( study_name VARCHAR(250) NOT NULL, container ENTITYID UNIQUE NOT NULL, @@ -624,8 +620,6 @@ CREATE TABLE cds.Properties ( CONSTRAINT PK_Properties PRIMARY KEY (RowId) ); -/* cds-15.286-15.287.sql */ - CREATE TABLE cds.GridBase ( SubjectId VARCHAR(250), Study VARCHAR(250), @@ -642,10 +636,6 @@ CREATE TABLE cds.GridBase ( CREATE INDEX IX_GridBase_Study ON cds.GridBase(Study); CREATE INDEX IX_GridBase_SubjectId ON cds.GridBase(SubjectId); - - -/* cds-15.287-15.288.sql */ - CREATE TABLE cds.import_ICSAntigen ( assay_identifier VARCHAR(250) NOT NULL REFERENCES cds.import_Assay(assay_identifier), antigen_name VARCHAR(250), @@ -1061,4 +1051,630 @@ ALTER TABLE cds.import_studyassay ADD COLUMN provenance_source VARCHAR(250); ALTER TABLE cds.import_studyassay ADD COLUMN provenance_summary TEXT; ALTER TABLE cds.studyassay ADD COLUMN provenance_source VARCHAR(250); -ALTER TABLE cds.studyassay ADD COLUMN provenance_summary TEXT; \ No newline at end of file +ALTER TABLE cds.studyassay ADD COLUMN provenance_summary TEXT; + +/* cds-18.10-18.20.sql */ + +TRUNCATE + cds.import_ics, + cds.import_els_ifng, + cds.import_bama, + cds.import_studysitepersonnel, + cds.import_studypartgrouparmsubject, + cds.import_studysitefunction, + cds.import_studyrelationship, + cds.import_studypublication, + cds.import_studyproduct, + cds.import_studypersonnel, + cds.import_studypartgrouparmvisitproduct, + cds.import_studypartgrouparmproduct, + cds.import_studydocument, + cds.import_studyassay, + cds.import_productinsert, + cds.import_studypartgrouparmvisit, + cds.import_studypartgrouparm, + cds.import_studygroups, + cds.import_nabantigen, + cds.import_icsantigen, + cds.import_elispotantigen, + cds.import_bamaantigen, + cds.import_studysubject, + cds.import_product, + cds.import_nab, + cds.import_assay, + cds.import_studyrelationshiporder, + cds.import_site, + cds.import_publication, + cds.import_personnel, + cds.import_document, + cds.import_lab, + cds.import_study +RESTART IDENTITY CASCADE; + +-- Drop FKs +ALTER TABLE cds.import_ics DROP CONSTRAINT import_ics_assay_identifier_fkey; +ALTER TABLE cds.import_ics DROP CONSTRAINT import_ics_lab_code_fkey; +ALTER TABLE cds.import_ics DROP CONSTRAINT import_ics_prot_fkey; + +ALTER TABLE cds.import_els_ifng DROP CONSTRAINT import_els_ifng_assay_identifier_fkey; +ALTER TABLE cds.import_els_ifng DROP CONSTRAINT import_els_ifng_lab_code_fkey; +ALTER TABLE cds.import_els_ifng DROP CONSTRAINT import_els_ifng_prot_fkey; + +ALTER TABLE cds.import_bama DROP CONSTRAINT import_bama_assay_identifier_fkey; +ALTER TABLE cds.import_bama DROP CONSTRAINT import_bama_lab_code_fkey; +ALTER TABLE cds.import_bama DROP CONSTRAINT import_bama_prot_fkey; + +ALTER TABLE cds.import_studysitepersonnel DROP CONSTRAINT import_studysitepersonnel_person_id_fkey; +ALTER TABLE cds.import_studysitepersonnel DROP CONSTRAINT import_studysitepersonnel_prot_fkey; +ALTER TABLE cds.import_studysitepersonnel DROP CONSTRAINT import_studysitepersonnel_site_id_fkey; + +ALTER TABLE cds.import_studypartgrouparmsubject DROP CONSTRAINT fk_armsubject_studysubject; +ALTER TABLE cds.import_studypartgrouparmsubject DROP CONSTRAINT import_studypartgrouparmsubject_prot_fkey; + +ALTER TABLE cds.import_studysitefunction DROP CONSTRAINT import_studysitefunction_prot_fkey; +ALTER TABLE cds.import_studysitefunction DROP CONSTRAINT import_studysitefunction_site_id_fkey; + +ALTER TABLE cds.import_studyrelationship DROP CONSTRAINT fk_import_study_relationship_prot; + +ALTER TABLE cds.import_studypersonnel DROP CONSTRAINT import_studypersonnel_person_id_fkey; +ALTER TABLE cds.import_studypersonnel DROP CONSTRAINT import_studypersonnel_prot_fkey; + +ALTER TABLE cds.import_studypartgrouparmvisitproduct DROP CONSTRAINT import_studypartgrouparmvisitproduct_product_id_fkey; +ALTER TABLE cds.import_studypartgrouparmvisitproduct DROP CONSTRAINT import_studypartgrouparmvisitproduct_prot_fkey; + +ALTER TABLE cds.import_studypartgrouparmproduct DROP CONSTRAINT import_studypartgrouparmproduct_product_id_fkey; +ALTER TABLE cds.import_studypartgrouparmproduct DROP CONSTRAINT import_studypartgrouparmproduct_prot_fkey; + +ALTER TABLE cds.import_productinsert DROP CONSTRAINT import_productinsert_product_id_fkey; +ALTER TABLE cds.import_productinsert DROP CONSTRAINT uq_import_productinsert; + +ALTER TABLE cds.import_product DROP CONSTRAINT import_product_product_name_key; + +ALTER TABLE cds.import_studypartgrouparmvisit DROP CONSTRAINT import_studypartgrouparmvisit_prot_fkey; + +ALTER TABLE cds.import_studypartgrouparm DROP CONSTRAINT import_studypartgrouparm_prot_fkey; + +ALTER TABLE cds.import_nabantigen DROP CONSTRAINT import_nabantigen_assay_identifier_fkey; + +ALTER TABLE cds.import_icsantigen DROP CONSTRAINT import_icsantigen_assay_identifier_fkey; + +ALTER TABLE cds.import_elispotantigen DROP CONSTRAINT import_elispotantigen_assay_identifier_fkey; + +ALTER TABLE cds.import_bamaantigen DROP CONSTRAINT import_bamaantigen_assay_identifier_fkey; + +ALTER TABLE cds.import_studysubject DROP CONSTRAINT import_studysubject_prot_fkey; + +ALTER TABLE cds.import_nab DROP CONSTRAINT import_nab_assay_identifier_fkey; +ALTER TABLE cds.import_nab DROP CONSTRAINT import_nab_lab_code_fkey; +ALTER TABLE cds.import_nab DROP CONSTRAINT import_nab_prot_fkey; + +-- Drop PKs +ALTER TABLE cds.import_studysitepersonnel DROP CONSTRAINT pk_import_studysitepersonnel; +ALTER TABLE cds.import_studypartgrouparmsubject DROP CONSTRAINT pk_import_studypartgrouparmsubject; +ALTER TABLE cds.import_studysitefunction DROP CONSTRAINT pk_import_studysitefunction; +ALTER TABLE cds.import_studyrelationship DROP CONSTRAINT pk_import_studyrelationship; +ALTER TABLE cds.import_studypublication DROP CONSTRAINT pk_import_studypublication; +ALTER TABLE cds.import_studyproduct DROP CONSTRAINT pk_import_studyproduct; +ALTER TABLE cds.import_studypersonnel DROP CONSTRAINT pk_import_studypersonnel; +ALTER TABLE cds.import_studypartgrouparmvisitproduct DROP CONSTRAINT pk_import_studypartgrouparmvisitproduct; +ALTER TABLE cds.import_studypartgrouparmproduct DROP CONSTRAINT pk_import_studypartgrouparmproduct; +ALTER TABLE cds.import_studydocument DROP CONSTRAINT pk_import_studydocument; +ALTER TABLE cds.import_studyassay DROP CONSTRAINT pk_import_studyassay; +ALTER TABLE cds.import_studypartgrouparmvisit DROP CONSTRAINT pk_import_studypartgrouparmvisit; +ALTER TABLE cds.import_studypartgrouparm DROP CONSTRAINT pk_import_studyarm; +ALTER TABLE cds.import_nabantigen DROP CONSTRAINT pk_import_nabantigen; +ALTER TABLE cds.import_icsantigen DROP CONSTRAINT pk_import_icsantigen; +ALTER TABLE cds.import_elispotantigen DROP CONSTRAINT pk_import_elispotantigen; +ALTER TABLE cds.import_bamaantigen DROP CONSTRAINT pk_import_bamaantigen; +ALTER TABLE cds.import_studysubject DROP CONSTRAINT pk_import_studysubject; +ALTER TABLE cds.import_product DROP CONSTRAINT pk_import_product; +ALTER TABLE cds.import_assay DROP CONSTRAINT pk_import_assay; +ALTER TABLE cds.import_studyrelationshiporder DROP CONSTRAINT pk_import_studyrelationshiporder; +ALTER TABLE cds.import_site DROP CONSTRAINT pk_import_site; +ALTER TABLE cds.import_publication DROP CONSTRAINT pk_import_publication; +ALTER TABLE cds.import_personnel DROP CONSTRAINT pk_import_personnel; +ALTER TABLE cds.import_document DROP CONSTRAINT pk_import_document; +ALTER TABLE cds.import_lab DROP CONSTRAINT pk_import_lab; +ALTER TABLE cds.import_study DROP CONSTRAINT pk_import_study; + + +-- Add container columns +ALTER TABLE cds.import_ics ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_els_ifng ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_bama ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studysitepersonnel ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studypartgrouparmsubject ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studysitefunction ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studyrelationship ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studypublication ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studyproduct ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studypersonnel ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studypartgrouparmvisitproduct ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studypartgrouparmproduct ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studydocument ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studyassay ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_productinsert ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studypartgrouparmvisit ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studypartgrouparm ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studygroups ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_nabantigen ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_icsantigen ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_elispotantigen ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_bamaantigen ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studysubject ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_product ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_nab ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_assay ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_studyrelationshiporder ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_site ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_publication ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_personnel ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_document ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_lab ADD COLUMN container ENTITYID NOT NULL; +ALTER TABLE cds.import_study ADD COLUMN container ENTITYID NOT NULL; + +-- Add PKs +ALTER TABLE cds.import_studysitepersonnel ADD PRIMARY KEY (container, prot, site_id, person_id); +ALTER TABLE cds.import_studypartgrouparmsubject ADD PRIMARY KEY (container, prot, subject_id, study_part, study_group, study_arm); +ALTER TABLE cds.import_studysitefunction ADD PRIMARY KEY (container, prot, site_id, site_type); +ALTER TABLE cds.import_studyrelationship ADD PRIMARY KEY (container, prot, rel_prot); +ALTER TABLE cds.import_studypublication ADD PRIMARY KEY (container, prot, publication_id); +ALTER TABLE cds.import_studyproduct ADD PRIMARY KEY (container, prot, product_id); +ALTER TABLE cds.import_studypersonnel ADD PRIMARY KEY (container, prot, person_id); +ALTER TABLE cds.import_studypartgrouparmvisitproduct ADD PRIMARY KEY (container, prot, study_part, study_group, study_arm, study_day, product_id); +ALTER TABLE cds.import_studypartgrouparmproduct ADD PRIMARY KEY (container, prot, study_part, study_group, study_arm, product_id); +ALTER TABLE cds.import_studydocument ADD PRIMARY KEY (container, prot, document_id); +ALTER TABLE cds.import_studyassay ADD PRIMARY KEY (container, prot, assay_identifier); +ALTER TABLE cds.import_studypartgrouparmvisit ADD PRIMARY KEY (container, prot, study_part, study_arm, study_group, study_day); +ALTER TABLE cds.import_studypartgrouparm ADD PRIMARY KEY (container, prot, study_part, study_group, study_arm); +ALTER TABLE cds.import_nabantigen ADD PRIMARY KEY (container, antigen_name, target_cell, antigen_type); +ALTER TABLE cds.import_icsantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); +ALTER TABLE cds.import_elispotantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); +ALTER TABLE cds.import_bamaantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); +ALTER TABLE cds.import_studysubject ADD PRIMARY KEY (container, prot, subject_id); +ALTER TABLE cds.import_product ADD PRIMARY KEY (container, product_id); +ALTER TABLE cds.import_assay ADD PRIMARY KEY (container, assay_identifier); +ALTER TABLE cds.import_studyrelationshiporder ADD PRIMARY KEY (container, relationship); +ALTER TABLE cds.import_site ADD PRIMARY KEY (container, site_id); +ALTER TABLE cds.import_publication ADD PRIMARY KEY (container, publication_id); +ALTER TABLE cds.import_personnel ADD PRIMARY KEY (container, person_id); +ALTER TABLE cds.import_document ADD PRIMARY KEY (container, document_id); +ALTER TABLE cds.import_lab ADD PRIMARY KEY (container, lab_code); +ALTER TABLE cds.import_study ADD PRIMARY KEY (container, prot); + +-- Add FKs +ALTER TABLE cds.import_ics ADD CONSTRAINT import_ics_assay_identifier_fkey + FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); +ALTER TABLE cds.import_ics ADD CONSTRAINT import_ics_lab_code_fkey + FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code); +ALTER TABLE cds.import_ics ADD CONSTRAINT import_ics_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_els_ifng ADD CONSTRAINT import_els_ifng_assay_identifier_fkey + FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); +ALTER TABLE cds.import_els_ifng ADD CONSTRAINT import_els_ifng_lab_code_fkey + FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code); +ALTER TABLE cds.import_els_ifng ADD CONSTRAINT import_els_ifng_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_bama ADD CONSTRAINT import_bama_assay_identifier_fkey + FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); +ALTER TABLE cds.import_bama ADD CONSTRAINT import_bama_lab_code_fkey + FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code); +ALTER TABLE cds.import_bama ADD CONSTRAINT import_bama_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_studysitepersonnel ADD CONSTRAINT import_studysitepersonnel_person_id_fkey + FOREIGN KEY (container, person_id) REFERENCES cds.import_personnel (container, person_id); +ALTER TABLE cds.import_studysitepersonnel ADD CONSTRAINT import_studysitepersonnel_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); +ALTER TABLE cds.import_studysitepersonnel ADD CONSTRAINT import_studysitepersonnel_site_id_fkey + FOREIGN KEY (container, site_id) REFERENCES cds.import_site (container, site_id); + +ALTER TABLE cds.import_studypartgrouparmsubject ADD CONSTRAINT fk_armsubject_studysubject + FOREIGN KEY (container, prot, subject_id) REFERENCES cds.import_studysubject (container, prot, subject_id); +ALTER TABLE cds.import_studypartgrouparmsubject ADD CONSTRAINT import_studypartgrouparmsubject_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_studysitefunction ADD CONSTRAINT import_studysitefunction_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); +ALTER TABLE cds.import_studysitefunction ADD CONSTRAINT import_studysitefunction_site_id_fkey + FOREIGN KEY (container, site_id) REFERENCES cds.import_site (container, site_id); + +ALTER TABLE cds.import_studyrelationship ADD CONSTRAINT fk_import_study_relationship_prot + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_studypersonnel ADD CONSTRAINT import_studypersonnel_person_id_fkey + FOREIGN KEY (container, person_id) REFERENCES cds.import_personnel (container, person_id); +ALTER TABLE cds.import_studypersonnel ADD CONSTRAINT import_studypersonnel_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_studypartgrouparmvisitproduct ADD CONSTRAINT import_studypartgrouparmvisitproduct_product_id_fkey + FOREIGN KEY (container, product_id) REFERENCES cds.import_product (container, product_id); +ALTER TABLE cds.import_studypartgrouparmvisitproduct ADD CONSTRAINT import_studypartgrouparmvisitproduct_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_studypartgrouparmproduct ADD CONSTRAINT import_studypartgrouparmproduct_product_id_fkey + FOREIGN KEY (container, product_id) REFERENCES cds.import_product (container, product_id); +ALTER TABLE cds.import_studypartgrouparmproduct ADD CONSTRAINT import_studypartgrouparmproduct_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_productinsert ADD CONSTRAINT import_productinsert_product_id_fkey + FOREIGN KEY (container, product_id) REFERENCES cds.import_product (container, product_id); +ALTER TABLE cds.import_productinsert ADD CONSTRAINT uq_import_productinsert + UNIQUE (container, product_id, insert_id, clade_id); + +ALTER TABLE cds.import_product ADD CONSTRAINT import_product_product_name_key + UNIQUE (container, product_name); + +ALTER TABLE cds.import_studypartgrouparmvisit ADD CONSTRAINT import_studypartgrouparmvisit_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_studypartgrouparm ADD CONSTRAINT import_studypartgrouparm_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_nabantigen ADD CONSTRAINT import_nabantigen_assay_identifier_fkey + FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); + +ALTER TABLE cds.import_icsantigen ADD CONSTRAINT import_icsantigen_assay_identifier_fkey + FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); + +ALTER TABLE cds.import_elispotantigen ADD CONSTRAINT import_elispotantigen_assay_identifier_fkey + FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); + +ALTER TABLE cds.import_bamaantigen ADD CONSTRAINT import_bamaantigen_assay_identifier_fkey + FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); + +ALTER TABLE cds.import_studysubject ADD CONSTRAINT import_studysubject_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + +ALTER TABLE cds.import_nab ADD CONSTRAINT import_nab_assay_identifier_fkey + FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); +ALTER TABLE cds.import_nab ADD CONSTRAINT import_nab_lab_code_fkey + FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code); +ALTER TABLE cds.import_nab ADD CONSTRAINT import_nab_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); + + + +-- These tables have container that is project container +TRUNCATE + cds.lab, + cds.nabantigen, + cds.icsantigen, + cds.elispotantigen, + cds.document, + cds.bamaantigen, + cds.publication, + cds.properties, + cds.product, + cds.assay +RESTART IDENTITY CASCADE; + +-- These tables have container that is subfolder (study) container +TRUNCATE + cds.facts, + cds.feedback, + cds.gridbase, + cds.sites, + cds.study, + cds.studyassay, + cds.studydocument, + cds.studygroup, + cds.studygroupvisitmap, + cds.studypartgrouparmproduct, + cds.studyproductmap, + cds.studypublication, + cds.studyrelationship, + cds.subjectproductmap, + cds.treatmentarm, + cds.treatmentarmsubjectmap, + cds.visittagalignment, + cds.visittagmap +RESTART IDENTITY CASCADE; + +-- Drop FKs +ALTER TABLE cds.nabantigen DROP CONSTRAINT nabantigen_assay_identifier_fkey; +ALTER TABLE cds.icsantigen DROP CONSTRAINT icsantigen_assay_identifier_fkey; +ALTER TABLE cds.elispotantigen DROP CONSTRAINT elispotantigen_assay_identifier_fkey; +ALTER TABLE cds.bamaantigen DROP CONSTRAINT bamaantigen_assay_identifier_fkey; + +ALTER TABLE cds.studypartgrouparmproduct DROP CONSTRAINT studypartgrouparmproduct_product_id_fkey; +ALTER TABLE cds.studypartgrouparmproduct DROP CONSTRAINT studypartgrouparmproduct_prot_fkey; +ALTER TABLE cds.studyrelationship DROP CONSTRAINT fk_study_relationship_prot; +ALTER TABLE cds.subjectproductmap DROP CONSTRAINT subjectproductmap_product_id_fkey; +ALTER TABLE cds.treatmentarmsubjectmap DROP CONSTRAINT treatmentarmsubjectmap_arm_id_fkey; +ALTER TABLE cds.visittagmap DROP CONSTRAINT visittagmap_arm_id_fkey; + +-- Drop and Add PKs +ALTER TABLE cds.lab DROP CONSTRAINT pk_lab; +ALTER TABLE cds.lab ADD PRIMARY KEY (container, lab_code); + +ALTER TABLE cds.nabantigen DROP CONSTRAINT pk_nabantigen; +ALTER TABLE cds.nabantigen ADD PRIMARY KEY (container, antigen_name, target_cell, antigen_type); + +ALTER TABLE cds.icsantigen DROP CONSTRAINT pk_icsantigens; +ALTER TABLE cds.icsantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); + +ALTER TABLE cds.elispotantigen DROP CONSTRAINT pk_elispotantigen; +ALTER TABLE cds.elispotantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); + +ALTER TABLE cds.document DROP CONSTRAINT pk_document; +ALTER TABLE cds.document ADD PRIMARY KEY (container, document_id); + +ALTER TABLE cds.bamaantigen DROP CONSTRAINT pk_bamaantigen; +ALTER TABLE cds.bamaantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); + +ALTER TABLE cds.publication DROP CONSTRAINT pk_publication; +ALTER TABLE cds.publication ADD PRIMARY KEY (container, id); + +ALTER TABLE cds.product DROP CONSTRAINT pk_product; +ALTER TABLE cds.product DROP CONSTRAINT uq_product; +ALTER TABLE cds.product DROP CONSTRAINT product_product_name_key; +ALTER TABLE cds.product ADD PRIMARY KEY (container, product_id); +ALTER TABLE cds.product ADD CONSTRAINT product_product_name_key UNIQUE (container, product_name); + +ALTER TABLE cds.assay DROP CONSTRAINT pk_assay; +ALTER TABLE cds.assay ADD PRIMARY KEY (container, assay_identifier); + +ALTER TABLE cds.study DROP CONSTRAINT pk_study; +ALTER TABLE cds.study ADD PRIMARY KEY (container, study_name); + +ALTER TABLE cds.studyassay DROP CONSTRAINT pk_studyassay; +ALTER TABLE cds.studyassay ADD PRIMARY KEY (container, prot, assay_identifier); + +ALTER TABLE cds.studydocument DROP CONSTRAINT pk_studydocument; +ALTER TABLE cds.studydocument ADD PRIMARY KEY (container, prot, document_id); + +ALTER TABLE cds.studypartgrouparmproduct DROP CONSTRAINT pk_studypartgrouparmproduct; +ALTER TABLE cds.studypartgrouparmproduct ADD PRIMARY KEY (container, prot, study_part, study_group, study_arm, product_id); + +ALTER TABLE cds.studypublication DROP CONSTRAINT pk_studypublication; +ALTER TABLE cds.studypublication ADD PRIMARY KEY (container, prot, publication_id); + +ALTER TABLE cds.studyrelationship DROP CONSTRAINT pk_studyrelationship; +ALTER TABLE cds.studyrelationship ADD PRIMARY KEY (container, prot, rel_prot); + +ALTER TABLE cds.treatmentarm DROP CONSTRAINT pk_treatmentarm; +ALTER TABLE cds.treatmentarm ADD PRIMARY KEY (container, arm_id); + +-- New fields to reference product properly +ALTER TABLE cds.studyproductmap ADD COLUMN projectContainer ENTITYID NOT NULL; +ALTER TABLE cds.studypartgrouparmproduct ADD COLUMN projectContainer ENTITYID NOT NULL; +ALTER TABLE cds.subjectproductmap ADD COLUMN projectContainer ENTITYID NOT NULL; + +-- Add FKs +ALTER TABLE cds.nabantigen ADD CONSTRAINT nabantigen_assay_identifier_fkey FOREIGN KEY (container, assay_identifier) REFERENCES + cds.assay (container, assay_identifier); + +ALTER TABLE cds.icsantigen ADD CONSTRAINT icsantigen_assay_identifier_fkey FOREIGN KEY (container, assay_identifier) REFERENCES + cds.assay (container, assay_identifier); + +ALTER TABLE cds.elispotantigen ADD CONSTRAINT elispotantigen_assay_identifier_fkey FOREIGN KEY (container, assay_identifier) REFERENCES + cds.assay (container, assay_identifier); + +ALTER TABLE cds.bamaantigen ADD CONSTRAINT bamaantigen_assay_identifier_fkey FOREIGN KEY (container, assay_identifier) REFERENCES + cds.assay (container, assay_identifier); + +ALTER TABLE cds.studypartgrouparmproduct ADD CONSTRAINT studypartgrouparmproduct_product_id_fkey FOREIGN KEY (projectContainer, product_id) REFERENCES + cds.product (container, product_id); +ALTER TABLE cds.studypartgrouparmproduct ADD CONSTRAINT studypartgrouparmproduct_prot_fkey FOREIGN KEY (container, prot) REFERENCES + cds.study (container, study_name); + +ALTER TABLE cds.studyproductmap ADD CONSTRAINT studyproductmap_product_id_fkey FOREIGN KEY (projectContainer, product_id) REFERENCES + cds.product (container, product_id); + +ALTER TABLE cds.studyrelationship ADD CONSTRAINT fk_study_relationship_prot FOREIGN KEY (container, prot) REFERENCES + cds.study (container, study_name); + +ALTER TABLE cds.subjectproductmap ADD CONSTRAINT subjectproductmap_product_id_fkey FOREIGN KEY (projectContainer, product_id) REFERENCES + cds.product (container, product_id); + +ALTER TABLE cds.treatmentarmsubjectmap ADD CONSTRAINT treatmentarmsubjectmap_arm_id_fkey FOREIGN KEY (container, arm_id) REFERENCES + cds.treatmentarm (container, arm_id); + +ALTER TABLE cds.visittagmap ADD CONSTRAINT visittagmap_arm_id_fkey FOREIGN KEY (container, arm_id) REFERENCES + cds.treatmentarm (container, arm_id); +; + +ALTER TABLE cds.import_nabantigen DROP CONSTRAINT import_nabantigen_pkey; +ALTER TABLE cds.import_nabantigen ADD PRIMARY KEY (container, assay_identifier, antigen_name, target_cell, antigen_type); + +ALTER TABLE cds.nabantigen DROP CONSTRAINT nabantigen_pkey; +ALTER TABLE cds.nabantigen ADD PRIMARY KEY (container, assay_identifier, antigen_name, target_cell, antigen_type); + +CREATE TABLE cds.import_MAbMetadata ( + container ENTITYID NOT NULL, + mab_id VARCHAR(250) NOT NULL, + mab_name_std VARCHAR(250), + mab_lanlid VARCHAR(250), + mab_hxb2_location VARCHAR(250), + mab_ab_binding_type VARCHAR(250), + mab_isotype VARCHAR(250), + mab_donorid VARCHAR(250), + mab_donor_species VARCHAR(250), + mab_donor_clade VARCHAR(250), + + CONSTRAINT PK_import_MAbMetadata PRIMARY KEY (container, mab_id) +); + +CREATE TABLE cds.MAbMetadata ( + container ENTITYID NOT NULL, + mab_id VARCHAR(250) NOT NULL, + mab_name_std VARCHAR(250), + mab_lanlid VARCHAR(250), + mab_hxb2_location VARCHAR(250), + mab_ab_binding_type VARCHAR(250), + mab_isotype VARCHAR(250), + mab_donorid VARCHAR(250), + mab_donor_species VARCHAR(250), + mab_donor_clade VARCHAR(250), + + CONSTRAINT PK_MAbMetadata PRIMARY KEY (container, mab_id) +); + +CREATE TABLE cds.import_MAbMixMetadata ( + container ENTITYID NOT NULL, + mab_mix_id VARCHAR(250) NOT NULL, + mab_mix_name_std VARCHAR(250), + mab_mix_label VARCHAR(250), + + CONSTRAINT PK_import_MAbMixMetadata PRIMARY KEY (container, mab_mix_id) +); + +CREATE TABLE cds.MAbMixMetadata ( + container ENTITYID NOT NULL, + mab_mix_id VARCHAR(250) NOT NULL, + mab_mix_name_std VARCHAR(250), + mab_mix_label VARCHAR(250), + + CONSTRAINT PK_MAbMixMetadata PRIMARY KEY (container, mab_mix_id) +); + +CREATE TABLE cds.import_MAbMix ( + container ENTITYID NOT NULL, + mab_mix_id VARCHAR(250) NOT NULL, + mab_id VARCHAR(250) NOT NULL, + + CONSTRAINT PK_import_MAbMix PRIMARY KEY (container, mab_mix_id, mab_id), + + CONSTRAINT import_MAbMix_mab_mix_id_fkey + FOREIGN KEY (container, mab_mix_id) REFERENCES cds.import_MAbMixMetadata (container, mab_mix_id), + + CONSTRAINT import_MAbMix_mab_id_fkey + FOREIGN KEY (container, mab_id) REFERENCES cds.import_MAbMetadata (container, mab_id) +); + +CREATE TABLE cds.MAbMix ( + container ENTITYID NOT NULL, + mab_mix_id VARCHAR(250) NOT NULL, + mab_id VARCHAR(250) NOT NULL, + + CONSTRAINT PK_MAbMix PRIMARY KEY (container, mab_mix_id, mab_id), + + CONSTRAINT MAbMix_mab_mix_id_fkey + FOREIGN KEY (container, mab_mix_id) REFERENCES cds.MAbMixMetadata (container, mab_mix_id), + + CONSTRAINT MAbMix_mab_id_fkey + FOREIGN KEY (container, mab_id) REFERENCES cds.MAbMetadata (container, mab_id) +); + +CREATE TABLE cds.import_NABMAb ( + row_id SERIAL, + container ENTITYID NOT NULL, + + prot VARCHAR(250) NOT NULL, + mab_mix_id VARCHAR(250) NOT NULL, + mab_name_source VARCHAR(250), + target_cell VARCHAR(250), + assay_identifier VARCHAR(250), + summary_level VARCHAR(250), + clade VARCHAR(250), + neutralization_tier VARCHAR(250), + virus_dilution VARCHAR(250), + specimen_type VARCHAR(250), + lab_code VARCHAR(250), + virus VARCHAR(250), + virus_type VARCHAR(250), + + initial_concentration NUMERIC(15,4), + specimen_concentration_id INTEGER, + mab_concentration NUMERIC(15,4), + mab_concentration_units VARCHAR(250), + min_concentration NUMERIC(15,4), + max_concentration NUMERIC(15,4), + min_well_value NUMERIC(15,4), + max_well_value NUMERIC(15,4), + mean_well_value NUMERIC(15,4), + well_std_dev NUMERIC(15,4), + percent_neutralization NUMERIC(15,4), + neutralization_plus_minus NUMERIC(15,4), + titer_ic50 NUMERIC(15,4), + titer_ic80 NUMERIC(15,4), + nab_response_ic50 BOOLEAN, + nab_response_ic80 BOOLEAN, + slope NUMERIC(15,4), + + fit_min NUMERIC(15,4), + fit_max NUMERIC(15,4), + fit_asymmetry NUMERIC(15,4), + fit_slope NUMERIC(15,4), + fit_inflection NUMERIC(15,4), + fit_error NUMERIC(15,4), + + CONSTRAINT PK_import_NABMAb PRIMARY KEY (row_id), + + CONSTRAINT import_NABMAb_mab_mix_id_fkey + FOREIGN KEY (container, mab_mix_id) REFERENCES cds.import_MAbMixMetadata (container, mab_mix_id), + + CONSTRAINT import_NABMAb_prot_fkey + FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot), + + CONSTRAINT import_NABMAb_assay_identifier_fkey + FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier), + + CONSTRAINT import_NABMAb_lab_code_fkey + FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code) +); + +ALTER TABLE cds.import_NABMAb + RENAME COLUMN nab_response_ic50 to response_ic50; +ALTER TABLE cds.import_NABMAb + RENAME COLUMN nab_response_ic80 to response_ic80; + +ALTER TABLE cds.import_NABMAb + RENAME COLUMN titer_ic50 to titer_curve_ic50; +ALTER TABLE cds.import_NABMAb + RENAME COLUMN titer_ic80 to titer_curve_ic80; + +ALTER TABLE cds.import_NABMAb ALTER COLUMN titer_curve_ic50 TYPE double precision; +ALTER TABLE cds.import_NABMAb ALTER COLUMN titer_curve_ic80 TYPE double precision; + +ALTER TABLE cds.import_NABMAb ADD COLUMN curve_id INTEGER; +ALTER TABLE cds.import_NABMAb ADD COLUMN vaccine_matched BOOLEAN; +ALTER TABLE cds.import_NABMAb ADD COLUMN titer_point_ic50 double precision; +ALTER TABLE cds.import_NABMAb ADD COLUMN titer_point_ic80 double precision; + +/* Materialize the mabgridbase query */ +DROP TABLE IF EXISTS cds.mAbGridBase; + +CREATE TABLE cds.mAbGridBase ( + mab_mix_id VARCHAR(250), + mab_mix_name_std VARCHAR(250), + study VARCHAR(250), + virus VARCHAR(250), + clade VARCHAR(250), + neutralization_tier VARCHAR(250), + tier_clade_virus VARCHAR(250), + titer_curve_ic50 NUMERIC(15,4), + titer_curve_ic50_group VARCHAR(10), + + target_cell VARCHAR(250), + lab_code VARCHAR(250), + summary_level VARCHAR(250), + + curve_id INTEGER, + + container ENTITYID, + + CONSTRAINT PK_mAbGridBase PRIMARY KEY (container, mab_mix_id, tier_clade_virus, target_cell, lab_code, summary_level, curve_id) +); + +DROP TABLE IF EXISTS cds.mAbMetaGridBase; + +CREATE TABLE cds.mAbMetaGridBase ( + mab_mix_id VARCHAR(250), + mab_mix_name_std VARCHAR(250), + mab_id VARCHAR(250), + mab_hxb2_location VARCHAR(250), + mab_isotype VARCHAR(250), + mab_donor_species VARCHAR(250), + container ENTITYID, + + CONSTRAINT PK_mAbMetaGridBase PRIMARY KEY (container, mab_mix_id, mab_id) +); + +ALTER TABLE cds.import_NABMAb + RENAME COLUMN response_ic50 to nab_response_ic50; +ALTER TABLE cds.import_NABMAb + RENAME COLUMN response_ic80 to nab_response_ic80; \ No newline at end of file diff --git a/resources/schemas/dbscripts/postgresql/cds-18.10-18.20.sql b/resources/schemas/dbscripts/postgresql/cds-18.10-18.20.sql deleted file mode 100644 index b19a552a5..000000000 --- a/resources/schemas/dbscripts/postgresql/cds-18.10-18.20.sql +++ /dev/null @@ -1,646 +0,0 @@ -/* - * Copyright (c) 2018 LabKey Corporation - * - * Licensed under the Apache License, Version 2.0 (the "License"); - * you may not use this file except in compliance with the License. - * You may obtain a copy of the License at - * - * http://www.apache.org/licenses/LICENSE-2.0 - * - * Unless required by applicable law or agreed to in writing, software - * distributed under the License is distributed on an "AS IS" BASIS, - * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. - * See the License for the specific language governing permissions and - * limitations under the License. - */ -/* cds-18.10-18.11.sql */ - -TRUNCATE - cds.import_ics, - cds.import_els_ifng, - cds.import_bama, - cds.import_studysitepersonnel, - cds.import_studypartgrouparmsubject, - cds.import_studysitefunction, - cds.import_studyrelationship, - cds.import_studypublication, - cds.import_studyproduct, - cds.import_studypersonnel, - cds.import_studypartgrouparmvisitproduct, - cds.import_studypartgrouparmproduct, - cds.import_studydocument, - cds.import_studyassay, - cds.import_productinsert, - cds.import_studypartgrouparmvisit, - cds.import_studypartgrouparm, - cds.import_studygroups, - cds.import_nabantigen, - cds.import_icsantigen, - cds.import_elispotantigen, - cds.import_bamaantigen, - cds.import_studysubject, - cds.import_product, - cds.import_nab, - cds.import_assay, - cds.import_studyrelationshiporder, - cds.import_site, - cds.import_publication, - cds.import_personnel, - cds.import_document, - cds.import_lab, - cds.import_study -RESTART IDENTITY CASCADE; - --- Drop FKs -ALTER TABLE cds.import_ics DROP CONSTRAINT import_ics_assay_identifier_fkey; -ALTER TABLE cds.import_ics DROP CONSTRAINT import_ics_lab_code_fkey; -ALTER TABLE cds.import_ics DROP CONSTRAINT import_ics_prot_fkey; - -ALTER TABLE cds.import_els_ifng DROP CONSTRAINT import_els_ifng_assay_identifier_fkey; -ALTER TABLE cds.import_els_ifng DROP CONSTRAINT import_els_ifng_lab_code_fkey; -ALTER TABLE cds.import_els_ifng DROP CONSTRAINT import_els_ifng_prot_fkey; - -ALTER TABLE cds.import_bama DROP CONSTRAINT import_bama_assay_identifier_fkey; -ALTER TABLE cds.import_bama DROP CONSTRAINT import_bama_lab_code_fkey; -ALTER TABLE cds.import_bama DROP CONSTRAINT import_bama_prot_fkey; - -ALTER TABLE cds.import_studysitepersonnel DROP CONSTRAINT import_studysitepersonnel_person_id_fkey; -ALTER TABLE cds.import_studysitepersonnel DROP CONSTRAINT import_studysitepersonnel_prot_fkey; -ALTER TABLE cds.import_studysitepersonnel DROP CONSTRAINT import_studysitepersonnel_site_id_fkey; - -ALTER TABLE cds.import_studypartgrouparmsubject DROP CONSTRAINT fk_armsubject_studysubject; -ALTER TABLE cds.import_studypartgrouparmsubject DROP CONSTRAINT import_studypartgrouparmsubject_prot_fkey; - -ALTER TABLE cds.import_studysitefunction DROP CONSTRAINT import_studysitefunction_prot_fkey; -ALTER TABLE cds.import_studysitefunction DROP CONSTRAINT import_studysitefunction_site_id_fkey; - -ALTER TABLE cds.import_studyrelationship DROP CONSTRAINT fk_import_study_relationship_prot; - -ALTER TABLE cds.import_studypersonnel DROP CONSTRAINT import_studypersonnel_person_id_fkey; -ALTER TABLE cds.import_studypersonnel DROP CONSTRAINT import_studypersonnel_prot_fkey; - -ALTER TABLE cds.import_studypartgrouparmvisitproduct DROP CONSTRAINT import_studypartgrouparmvisitproduct_product_id_fkey; -ALTER TABLE cds.import_studypartgrouparmvisitproduct DROP CONSTRAINT import_studypartgrouparmvisitproduct_prot_fkey; - -ALTER TABLE cds.import_studypartgrouparmproduct DROP CONSTRAINT import_studypartgrouparmproduct_product_id_fkey; -ALTER TABLE cds.import_studypartgrouparmproduct DROP CONSTRAINT import_studypartgrouparmproduct_prot_fkey; - -ALTER TABLE cds.import_productinsert DROP CONSTRAINT import_productinsert_product_id_fkey; -ALTER TABLE cds.import_productinsert DROP CONSTRAINT uq_import_productinsert; - -ALTER TABLE cds.import_product DROP CONSTRAINT import_product_product_name_key; - -ALTER TABLE cds.import_studypartgrouparmvisit DROP CONSTRAINT import_studypartgrouparmvisit_prot_fkey; - -ALTER TABLE cds.import_studypartgrouparm DROP CONSTRAINT import_studypartgrouparm_prot_fkey; - -ALTER TABLE cds.import_nabantigen DROP CONSTRAINT import_nabantigen_assay_identifier_fkey; - -ALTER TABLE cds.import_icsantigen DROP CONSTRAINT import_icsantigen_assay_identifier_fkey; - -ALTER TABLE cds.import_elispotantigen DROP CONSTRAINT import_elispotantigen_assay_identifier_fkey; - -ALTER TABLE cds.import_bamaantigen DROP CONSTRAINT import_bamaantigen_assay_identifier_fkey; - -ALTER TABLE cds.import_studysubject DROP CONSTRAINT import_studysubject_prot_fkey; - -ALTER TABLE cds.import_nab DROP CONSTRAINT import_nab_assay_identifier_fkey; -ALTER TABLE cds.import_nab DROP CONSTRAINT import_nab_lab_code_fkey; -ALTER TABLE cds.import_nab DROP CONSTRAINT import_nab_prot_fkey; - --- Drop PKs -ALTER TABLE cds.import_studysitepersonnel DROP CONSTRAINT pk_import_studysitepersonnel; -ALTER TABLE cds.import_studypartgrouparmsubject DROP CONSTRAINT pk_import_studypartgrouparmsubject; -ALTER TABLE cds.import_studysitefunction DROP CONSTRAINT pk_import_studysitefunction; -ALTER TABLE cds.import_studyrelationship DROP CONSTRAINT pk_import_studyrelationship; -ALTER TABLE cds.import_studypublication DROP CONSTRAINT pk_import_studypublication; -ALTER TABLE cds.import_studyproduct DROP CONSTRAINT pk_import_studyproduct; -ALTER TABLE cds.import_studypersonnel DROP CONSTRAINT pk_import_studypersonnel; -ALTER TABLE cds.import_studypartgrouparmvisitproduct DROP CONSTRAINT pk_import_studypartgrouparmvisitproduct; -ALTER TABLE cds.import_studypartgrouparmproduct DROP CONSTRAINT pk_import_studypartgrouparmproduct; -ALTER TABLE cds.import_studydocument DROP CONSTRAINT pk_import_studydocument; -ALTER TABLE cds.import_studyassay DROP CONSTRAINT pk_import_studyassay; -ALTER TABLE cds.import_studypartgrouparmvisit DROP CONSTRAINT pk_import_studypartgrouparmvisit; -ALTER TABLE cds.import_studypartgrouparm DROP CONSTRAINT pk_import_studyarm; -ALTER TABLE cds.import_nabantigen DROP CONSTRAINT pk_import_nabantigen; -ALTER TABLE cds.import_icsantigen DROP CONSTRAINT pk_import_icsantigen; -ALTER TABLE cds.import_elispotantigen DROP CONSTRAINT pk_import_elispotantigen; -ALTER TABLE cds.import_bamaantigen DROP CONSTRAINT pk_import_bamaantigen; -ALTER TABLE cds.import_studysubject DROP CONSTRAINT pk_import_studysubject; -ALTER TABLE cds.import_product DROP CONSTRAINT pk_import_product; -ALTER TABLE cds.import_assay DROP CONSTRAINT pk_import_assay; -ALTER TABLE cds.import_studyrelationshiporder DROP CONSTRAINT pk_import_studyrelationshiporder; -ALTER TABLE cds.import_site DROP CONSTRAINT pk_import_site; -ALTER TABLE cds.import_publication DROP CONSTRAINT pk_import_publication; -ALTER TABLE cds.import_personnel DROP CONSTRAINT pk_import_personnel; -ALTER TABLE cds.import_document DROP CONSTRAINT pk_import_document; -ALTER TABLE cds.import_lab DROP CONSTRAINT pk_import_lab; -ALTER TABLE cds.import_study DROP CONSTRAINT pk_import_study; - - --- Add container columns -ALTER TABLE cds.import_ics ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_els_ifng ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_bama ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studysitepersonnel ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studypartgrouparmsubject ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studysitefunction ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studyrelationship ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studypublication ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studyproduct ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studypersonnel ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studypartgrouparmvisitproduct ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studypartgrouparmproduct ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studydocument ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studyassay ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_productinsert ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studypartgrouparmvisit ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studypartgrouparm ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studygroups ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_nabantigen ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_icsantigen ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_elispotantigen ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_bamaantigen ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studysubject ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_product ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_nab ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_assay ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_studyrelationshiporder ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_site ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_publication ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_personnel ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_document ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_lab ADD COLUMN container ENTITYID NOT NULL; -ALTER TABLE cds.import_study ADD COLUMN container ENTITYID NOT NULL; - --- Add PKs -ALTER TABLE cds.import_studysitepersonnel ADD PRIMARY KEY (container, prot, site_id, person_id); -ALTER TABLE cds.import_studypartgrouparmsubject ADD PRIMARY KEY (container, prot, subject_id, study_part, study_group, study_arm); -ALTER TABLE cds.import_studysitefunction ADD PRIMARY KEY (container, prot, site_id, site_type); -ALTER TABLE cds.import_studyrelationship ADD PRIMARY KEY (container, prot, rel_prot); -ALTER TABLE cds.import_studypublication ADD PRIMARY KEY (container, prot, publication_id); -ALTER TABLE cds.import_studyproduct ADD PRIMARY KEY (container, prot, product_id); -ALTER TABLE cds.import_studypersonnel ADD PRIMARY KEY (container, prot, person_id); -ALTER TABLE cds.import_studypartgrouparmvisitproduct ADD PRIMARY KEY (container, prot, study_part, study_group, study_arm, study_day, product_id); -ALTER TABLE cds.import_studypartgrouparmproduct ADD PRIMARY KEY (container, prot, study_part, study_group, study_arm, product_id); -ALTER TABLE cds.import_studydocument ADD PRIMARY KEY (container, prot, document_id); -ALTER TABLE cds.import_studyassay ADD PRIMARY KEY (container, prot, assay_identifier); -ALTER TABLE cds.import_studypartgrouparmvisit ADD PRIMARY KEY (container, prot, study_part, study_arm, study_group, study_day); -ALTER TABLE cds.import_studypartgrouparm ADD PRIMARY KEY (container, prot, study_part, study_group, study_arm); -ALTER TABLE cds.import_nabantigen ADD PRIMARY KEY (container, antigen_name, target_cell, antigen_type); -ALTER TABLE cds.import_icsantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); -ALTER TABLE cds.import_elispotantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); -ALTER TABLE cds.import_bamaantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); -ALTER TABLE cds.import_studysubject ADD PRIMARY KEY (container, prot, subject_id); -ALTER TABLE cds.import_product ADD PRIMARY KEY (container, product_id); -ALTER TABLE cds.import_assay ADD PRIMARY KEY (container, assay_identifier); -ALTER TABLE cds.import_studyrelationshiporder ADD PRIMARY KEY (container, relationship); -ALTER TABLE cds.import_site ADD PRIMARY KEY (container, site_id); -ALTER TABLE cds.import_publication ADD PRIMARY KEY (container, publication_id); -ALTER TABLE cds.import_personnel ADD PRIMARY KEY (container, person_id); -ALTER TABLE cds.import_document ADD PRIMARY KEY (container, document_id); -ALTER TABLE cds.import_lab ADD PRIMARY KEY (container, lab_code); -ALTER TABLE cds.import_study ADD PRIMARY KEY (container, prot); - --- Add FKs -ALTER TABLE cds.import_ics ADD CONSTRAINT import_ics_assay_identifier_fkey - FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); -ALTER TABLE cds.import_ics ADD CONSTRAINT import_ics_lab_code_fkey - FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code); -ALTER TABLE cds.import_ics ADD CONSTRAINT import_ics_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_els_ifng ADD CONSTRAINT import_els_ifng_assay_identifier_fkey - FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); -ALTER TABLE cds.import_els_ifng ADD CONSTRAINT import_els_ifng_lab_code_fkey - FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code); -ALTER TABLE cds.import_els_ifng ADD CONSTRAINT import_els_ifng_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_bama ADD CONSTRAINT import_bama_assay_identifier_fkey - FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); -ALTER TABLE cds.import_bama ADD CONSTRAINT import_bama_lab_code_fkey - FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code); -ALTER TABLE cds.import_bama ADD CONSTRAINT import_bama_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_studysitepersonnel ADD CONSTRAINT import_studysitepersonnel_person_id_fkey - FOREIGN KEY (container, person_id) REFERENCES cds.import_personnel (container, person_id); -ALTER TABLE cds.import_studysitepersonnel ADD CONSTRAINT import_studysitepersonnel_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); -ALTER TABLE cds.import_studysitepersonnel ADD CONSTRAINT import_studysitepersonnel_site_id_fkey - FOREIGN KEY (container, site_id) REFERENCES cds.import_site (container, site_id); - -ALTER TABLE cds.import_studypartgrouparmsubject ADD CONSTRAINT fk_armsubject_studysubject - FOREIGN KEY (container, prot, subject_id) REFERENCES cds.import_studysubject (container, prot, subject_id); -ALTER TABLE cds.import_studypartgrouparmsubject ADD CONSTRAINT import_studypartgrouparmsubject_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_studysitefunction ADD CONSTRAINT import_studysitefunction_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); -ALTER TABLE cds.import_studysitefunction ADD CONSTRAINT import_studysitefunction_site_id_fkey - FOREIGN KEY (container, site_id) REFERENCES cds.import_site (container, site_id); - -ALTER TABLE cds.import_studyrelationship ADD CONSTRAINT fk_import_study_relationship_prot - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_studypersonnel ADD CONSTRAINT import_studypersonnel_person_id_fkey - FOREIGN KEY (container, person_id) REFERENCES cds.import_personnel (container, person_id); -ALTER TABLE cds.import_studypersonnel ADD CONSTRAINT import_studypersonnel_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_studypartgrouparmvisitproduct ADD CONSTRAINT import_studypartgrouparmvisitproduct_product_id_fkey - FOREIGN KEY (container, product_id) REFERENCES cds.import_product (container, product_id); -ALTER TABLE cds.import_studypartgrouparmvisitproduct ADD CONSTRAINT import_studypartgrouparmvisitproduct_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_studypartgrouparmproduct ADD CONSTRAINT import_studypartgrouparmproduct_product_id_fkey - FOREIGN KEY (container, product_id) REFERENCES cds.import_product (container, product_id); -ALTER TABLE cds.import_studypartgrouparmproduct ADD CONSTRAINT import_studypartgrouparmproduct_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_productinsert ADD CONSTRAINT import_productinsert_product_id_fkey - FOREIGN KEY (container, product_id) REFERENCES cds.import_product (container, product_id); -ALTER TABLE cds.import_productinsert ADD CONSTRAINT uq_import_productinsert - UNIQUE (container, product_id, insert_id, clade_id); - -ALTER TABLE cds.import_product ADD CONSTRAINT import_product_product_name_key - UNIQUE (container, product_name); - -ALTER TABLE cds.import_studypartgrouparmvisit ADD CONSTRAINT import_studypartgrouparmvisit_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_studypartgrouparm ADD CONSTRAINT import_studypartgrouparm_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_nabantigen ADD CONSTRAINT import_nabantigen_assay_identifier_fkey - FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); - -ALTER TABLE cds.import_icsantigen ADD CONSTRAINT import_icsantigen_assay_identifier_fkey - FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); - -ALTER TABLE cds.import_elispotantigen ADD CONSTRAINT import_elispotantigen_assay_identifier_fkey - FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); - -ALTER TABLE cds.import_bamaantigen ADD CONSTRAINT import_bamaantigen_assay_identifier_fkey - FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); - -ALTER TABLE cds.import_studysubject ADD CONSTRAINT import_studysubject_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - -ALTER TABLE cds.import_nab ADD CONSTRAINT import_nab_assay_identifier_fkey - FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier); -ALTER TABLE cds.import_nab ADD CONSTRAINT import_nab_lab_code_fkey - FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code); -ALTER TABLE cds.import_nab ADD CONSTRAINT import_nab_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot); - - - --- These tables have container that is project container -TRUNCATE - cds.lab, - cds.nabantigen, - cds.icsantigen, - cds.elispotantigen, - cds.document, - cds.bamaantigen, - cds.publication, - cds.properties, - cds.product, - cds.assay -RESTART IDENTITY CASCADE; - --- These tables have container that is subfolder (study) container -TRUNCATE - cds.facts, - cds.feedback, - cds.gridbase, - cds.sites, - cds.study, - cds.studyassay, - cds.studydocument, - cds.studygroup, - cds.studygroupvisitmap, - cds.studypartgrouparmproduct, - cds.studyproductmap, - cds.studypublication, - cds.studyrelationship, - cds.subjectproductmap, - cds.treatmentarm, - cds.treatmentarmsubjectmap, - cds.visittagalignment, - cds.visittagmap -RESTART IDENTITY CASCADE; - --- Drop FKs -ALTER TABLE cds.nabantigen DROP CONSTRAINT nabantigen_assay_identifier_fkey; -ALTER TABLE cds.icsantigen DROP CONSTRAINT icsantigen_assay_identifier_fkey; -ALTER TABLE cds.elispotantigen DROP CONSTRAINT elispotantigen_assay_identifier_fkey; -ALTER TABLE cds.bamaantigen DROP CONSTRAINT bamaantigen_assay_identifier_fkey; - -ALTER TABLE cds.studypartgrouparmproduct DROP CONSTRAINT studypartgrouparmproduct_product_id_fkey; -ALTER TABLE cds.studypartgrouparmproduct DROP CONSTRAINT studypartgrouparmproduct_prot_fkey; -ALTER TABLE cds.studyrelationship DROP CONSTRAINT fk_study_relationship_prot; -ALTER TABLE cds.subjectproductmap DROP CONSTRAINT subjectproductmap_product_id_fkey; -ALTER TABLE cds.treatmentarmsubjectmap DROP CONSTRAINT treatmentarmsubjectmap_arm_id_fkey; -ALTER TABLE cds.visittagmap DROP CONSTRAINT visittagmap_arm_id_fkey; - --- Drop and Add PKs -ALTER TABLE cds.lab DROP CONSTRAINT pk_lab; -ALTER TABLE cds.lab ADD PRIMARY KEY (container, lab_code); - -ALTER TABLE cds.nabantigen DROP CONSTRAINT pk_nabantigen; -ALTER TABLE cds.nabantigen ADD PRIMARY KEY (container, antigen_name, target_cell, antigen_type); - -ALTER TABLE cds.icsantigen DROP CONSTRAINT pk_icsantigens; -ALTER TABLE cds.icsantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); - -ALTER TABLE cds.elispotantigen DROP CONSTRAINT pk_elispotantigen; -ALTER TABLE cds.elispotantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); - -ALTER TABLE cds.document DROP CONSTRAINT pk_document; -ALTER TABLE cds.document ADD PRIMARY KEY (container, document_id); - -ALTER TABLE cds.bamaantigen DROP CONSTRAINT pk_bamaantigen; -ALTER TABLE cds.bamaantigen ADD PRIMARY KEY (container, antigen_name, antigen_type); - -ALTER TABLE cds.publication DROP CONSTRAINT pk_publication; -ALTER TABLE cds.publication ADD PRIMARY KEY (container, id); - -ALTER TABLE cds.product DROP CONSTRAINT pk_product; -ALTER TABLE cds.product DROP CONSTRAINT uq_product; -ALTER TABLE cds.product DROP CONSTRAINT product_product_name_key; -ALTER TABLE cds.product ADD PRIMARY KEY (container, product_id); -ALTER TABLE cds.product ADD CONSTRAINT product_product_name_key UNIQUE (container, product_name); - -ALTER TABLE cds.assay DROP CONSTRAINT pk_assay; -ALTER TABLE cds.assay ADD PRIMARY KEY (container, assay_identifier); - -ALTER TABLE cds.study DROP CONSTRAINT pk_study; -ALTER TABLE cds.study ADD PRIMARY KEY (container, study_name); - -ALTER TABLE cds.studyassay DROP CONSTRAINT pk_studyassay; -ALTER TABLE cds.studyassay ADD PRIMARY KEY (container, prot, assay_identifier); - -ALTER TABLE cds.studydocument DROP CONSTRAINT pk_studydocument; -ALTER TABLE cds.studydocument ADD PRIMARY KEY (container, prot, document_id); - -ALTER TABLE cds.studypartgrouparmproduct DROP CONSTRAINT pk_studypartgrouparmproduct; -ALTER TABLE cds.studypartgrouparmproduct ADD PRIMARY KEY (container, prot, study_part, study_group, study_arm, product_id); - -ALTER TABLE cds.studypublication DROP CONSTRAINT pk_studypublication; -ALTER TABLE cds.studypublication ADD PRIMARY KEY (container, prot, publication_id); - -ALTER TABLE cds.studyrelationship DROP CONSTRAINT pk_studyrelationship; -ALTER TABLE cds.studyrelationship ADD PRIMARY KEY (container, prot, rel_prot); - -ALTER TABLE cds.treatmentarm DROP CONSTRAINT pk_treatmentarm; -ALTER TABLE cds.treatmentarm ADD PRIMARY KEY (container, arm_id); - --- New fields to reference product properly -ALTER TABLE cds.studyproductmap ADD COLUMN projectContainer ENTITYID NOT NULL; -ALTER TABLE cds.studypartgrouparmproduct ADD COLUMN projectContainer ENTITYID NOT NULL; -ALTER TABLE cds.subjectproductmap ADD COLUMN projectContainer ENTITYID NOT NULL; - --- Add FKs -ALTER TABLE cds.nabantigen ADD CONSTRAINT nabantigen_assay_identifier_fkey FOREIGN KEY (container, assay_identifier) REFERENCES - cds.assay (container, assay_identifier); - -ALTER TABLE cds.icsantigen ADD CONSTRAINT icsantigen_assay_identifier_fkey FOREIGN KEY (container, assay_identifier) REFERENCES - cds.assay (container, assay_identifier); - -ALTER TABLE cds.elispotantigen ADD CONSTRAINT elispotantigen_assay_identifier_fkey FOREIGN KEY (container, assay_identifier) REFERENCES - cds.assay (container, assay_identifier); - -ALTER TABLE cds.bamaantigen ADD CONSTRAINT bamaantigen_assay_identifier_fkey FOREIGN KEY (container, assay_identifier) REFERENCES - cds.assay (container, assay_identifier); - -ALTER TABLE cds.studypartgrouparmproduct ADD CONSTRAINT studypartgrouparmproduct_product_id_fkey FOREIGN KEY (projectContainer, product_id) REFERENCES - cds.product (container, product_id); -ALTER TABLE cds.studypartgrouparmproduct ADD CONSTRAINT studypartgrouparmproduct_prot_fkey FOREIGN KEY (container, prot) REFERENCES - cds.study (container, study_name); - -ALTER TABLE cds.studyproductmap ADD CONSTRAINT studyproductmap_product_id_fkey FOREIGN KEY (projectContainer, product_id) REFERENCES - cds.product (container, product_id); - -ALTER TABLE cds.studyrelationship ADD CONSTRAINT fk_study_relationship_prot FOREIGN KEY (container, prot) REFERENCES - cds.study (container, study_name); - -ALTER TABLE cds.subjectproductmap ADD CONSTRAINT subjectproductmap_product_id_fkey FOREIGN KEY (projectContainer, product_id) REFERENCES - cds.product (container, product_id); - -ALTER TABLE cds.treatmentarmsubjectmap ADD CONSTRAINT treatmentarmsubjectmap_arm_id_fkey FOREIGN KEY (container, arm_id) REFERENCES - cds.treatmentarm (container, arm_id); - -ALTER TABLE cds.visittagmap ADD CONSTRAINT visittagmap_arm_id_fkey FOREIGN KEY (container, arm_id) REFERENCES - cds.treatmentarm (container, arm_id); -; - -/* cds-18.11-18.12.sql */ - -ALTER TABLE cds.import_nabantigen DROP CONSTRAINT import_nabantigen_pkey; -ALTER TABLE cds.import_nabantigen ADD PRIMARY KEY (container, assay_identifier, antigen_name, target_cell, antigen_type); - -ALTER TABLE cds.nabantigen DROP CONSTRAINT nabantigen_pkey; -ALTER TABLE cds.nabantigen ADD PRIMARY KEY (container, assay_identifier, antigen_name, target_cell, antigen_type); - -CREATE TABLE cds.import_MAbMetadata ( - container ENTITYID NOT NULL, - mab_id VARCHAR(250) NOT NULL, - mab_name_std VARCHAR(250), - mab_lanlid VARCHAR(250), - mab_hxb2_location VARCHAR(250), - mab_ab_binding_type VARCHAR(250), - mab_isotype VARCHAR(250), - mab_donorid VARCHAR(250), - mab_donor_species VARCHAR(250), - mab_donor_clade VARCHAR(250), - - CONSTRAINT PK_import_MAbMetadata PRIMARY KEY (container, mab_id) -); - -CREATE TABLE cds.MAbMetadata ( - container ENTITYID NOT NULL, - mab_id VARCHAR(250) NOT NULL, - mab_name_std VARCHAR(250), - mab_lanlid VARCHAR(250), - mab_hxb2_location VARCHAR(250), - mab_ab_binding_type VARCHAR(250), - mab_isotype VARCHAR(250), - mab_donorid VARCHAR(250), - mab_donor_species VARCHAR(250), - mab_donor_clade VARCHAR(250), - - CONSTRAINT PK_MAbMetadata PRIMARY KEY (container, mab_id) -); - -CREATE TABLE cds.import_MAbMixMetadata ( - container ENTITYID NOT NULL, - mab_mix_id VARCHAR(250) NOT NULL, - mab_mix_name_std VARCHAR(250), - mab_mix_label VARCHAR(250), - - CONSTRAINT PK_import_MAbMixMetadata PRIMARY KEY (container, mab_mix_id) -); - -CREATE TABLE cds.MAbMixMetadata ( - container ENTITYID NOT NULL, - mab_mix_id VARCHAR(250) NOT NULL, - mab_mix_name_std VARCHAR(250), - mab_mix_label VARCHAR(250), - - CONSTRAINT PK_MAbMixMetadata PRIMARY KEY (container, mab_mix_id) -); - -CREATE TABLE cds.import_MAbMix ( - container ENTITYID NOT NULL, - mab_mix_id VARCHAR(250) NOT NULL, - mab_id VARCHAR(250) NOT NULL, - - CONSTRAINT PK_import_MAbMix PRIMARY KEY (container, mab_mix_id, mab_id), - - CONSTRAINT import_MAbMix_mab_mix_id_fkey - FOREIGN KEY (container, mab_mix_id) REFERENCES cds.import_MAbMixMetadata (container, mab_mix_id), - - CONSTRAINT import_MAbMix_mab_id_fkey - FOREIGN KEY (container, mab_id) REFERENCES cds.import_MAbMetadata (container, mab_id) -); - -CREATE TABLE cds.MAbMix ( - container ENTITYID NOT NULL, - mab_mix_id VARCHAR(250) NOT NULL, - mab_id VARCHAR(250) NOT NULL, - - CONSTRAINT PK_MAbMix PRIMARY KEY (container, mab_mix_id, mab_id), - - CONSTRAINT MAbMix_mab_mix_id_fkey - FOREIGN KEY (container, mab_mix_id) REFERENCES cds.MAbMixMetadata (container, mab_mix_id), - - CONSTRAINT MAbMix_mab_id_fkey - FOREIGN KEY (container, mab_id) REFERENCES cds.MAbMetadata (container, mab_id) -); - -CREATE TABLE cds.import_NABMAb ( - row_id SERIAL, - container ENTITYID NOT NULL, - - prot VARCHAR(250) NOT NULL, - mab_mix_id VARCHAR(250) NOT NULL, - mab_name_source VARCHAR(250), - target_cell VARCHAR(250), - assay_identifier VARCHAR(250), - summary_level VARCHAR(250), - clade VARCHAR(250), - neutralization_tier VARCHAR(250), - virus_dilution VARCHAR(250), - specimen_type VARCHAR(250), - lab_code VARCHAR(250), - virus VARCHAR(250), - virus_type VARCHAR(250), - - initial_concentration NUMERIC(15,4), - specimen_concentration_id INTEGER, - mab_concentration NUMERIC(15,4), - mab_concentration_units VARCHAR(250), - min_concentration NUMERIC(15,4), - max_concentration NUMERIC(15,4), - min_well_value NUMERIC(15,4), - max_well_value NUMERIC(15,4), - mean_well_value NUMERIC(15,4), - well_std_dev NUMERIC(15,4), - percent_neutralization NUMERIC(15,4), - neutralization_plus_minus NUMERIC(15,4), - titer_ic50 NUMERIC(15,4), - titer_ic80 NUMERIC(15,4), - nab_response_ic50 BOOLEAN, - nab_response_ic80 BOOLEAN, - slope NUMERIC(15,4), - - fit_min NUMERIC(15,4), - fit_max NUMERIC(15,4), - fit_asymmetry NUMERIC(15,4), - fit_slope NUMERIC(15,4), - fit_inflection NUMERIC(15,4), - fit_error NUMERIC(15,4), - - CONSTRAINT PK_import_NABMAb PRIMARY KEY (row_id), - - CONSTRAINT import_NABMAb_mab_mix_id_fkey - FOREIGN KEY (container, mab_mix_id) REFERENCES cds.import_MAbMixMetadata (container, mab_mix_id), - - CONSTRAINT import_NABMAb_prot_fkey - FOREIGN KEY (container, prot) REFERENCES cds.import_study (container, prot), - - CONSTRAINT import_NABMAb_assay_identifier_fkey - FOREIGN KEY (container, assay_identifier) REFERENCES cds.import_assay (container, assay_identifier), - - CONSTRAINT import_NABMAb_lab_code_fkey - FOREIGN KEY (container, lab_code) REFERENCES cds.import_lab (container, lab_code) -); - -/* cds-18.12-18.13.sql */ - -ALTER TABLE cds.import_NABMAb - RENAME COLUMN nab_response_ic50 to response_ic50; -ALTER TABLE cds.import_NABMAb - RENAME COLUMN nab_response_ic80 to response_ic80; - -ALTER TABLE cds.import_NABMAb - RENAME COLUMN titer_ic50 to titer_curve_ic50; -ALTER TABLE cds.import_NABMAb - RENAME COLUMN titer_ic80 to titer_curve_ic80; - -ALTER TABLE cds.import_NABMAb ALTER COLUMN titer_curve_ic50 TYPE double precision; -ALTER TABLE cds.import_NABMAb ALTER COLUMN titer_curve_ic80 TYPE double precision; - -ALTER TABLE cds.import_NABMAb ADD COLUMN curve_id INTEGER; -ALTER TABLE cds.import_NABMAb ADD COLUMN vaccine_matched BOOLEAN; -ALTER TABLE cds.import_NABMAb ADD COLUMN titer_point_ic50 double precision; -ALTER TABLE cds.import_NABMAb ADD COLUMN titer_point_ic80 double precision; - -/* Materialize the mabgridbase query */ -DROP TABLE IF EXISTS cds.mAbGridBase; - -CREATE TABLE cds.mAbGridBase ( - mab_mix_id VARCHAR(250), - mab_mix_name_std VARCHAR(250), - study VARCHAR(250), - virus VARCHAR(250), - clade VARCHAR(250), - neutralization_tier VARCHAR(250), - tier_clade_virus VARCHAR(250), - titer_curve_ic50 NUMERIC(15,4), - titer_curve_ic50_group VARCHAR(10), - - target_cell VARCHAR(250), - lab_code VARCHAR(250), - summary_level VARCHAR(250), - - curve_id INTEGER, - - container ENTITYID, - - CONSTRAINT PK_mAbGridBase PRIMARY KEY (container, mab_mix_id, tier_clade_virus, target_cell, lab_code, summary_level, curve_id) -); - -DROP TABLE IF EXISTS cds.mAbMetaGridBase; - -CREATE TABLE cds.mAbMetaGridBase ( - mab_mix_id VARCHAR(250), - mab_mix_name_std VARCHAR(250), - mab_id VARCHAR(250), - mab_hxb2_location VARCHAR(250), - mab_isotype VARCHAR(250), - mab_donor_species VARCHAR(250), - container ENTITYID, - - CONSTRAINT PK_mAbMetaGridBase PRIMARY KEY (container, mab_mix_id, mab_id) -); - -/* cds-18.13-18.14.sql */ - -ALTER TABLE cds.import_NABMAb - RENAME COLUMN response_ic50 to nab_response_ic50; -ALTER TABLE cds.import_NABMAb - RENAME COLUMN response_ic80 to nab_response_ic80; \ No newline at end of file