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Translated postgresql migration scripts to SQL Server up to v2.10 (#2238)
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‎src/main/resources/db/migration/sqlserver/V2.9.0.20210423125133__assets_tags.sql‎

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INSERT INTO ${ohdsiSchema}.sec_permission(id, value, description)
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VALUES
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'tag:get', 'List tags'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'tag:search:get', 'Search tags by name'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'tag:post', 'Create tag'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'tag:*:put', 'Update tag'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'tag:*:get', 'Get tag'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'tag:*:delete', 'Delete tag'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'cohortdefinition:*:tag:post', 'Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'cohortdefinition:*:tag:*:delete', 'Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'cohortdefinition:*:protectedtag:post','Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'cohortdefinition:*:protectedtag:*:delete','Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:tag:post','Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:tag:*:delete','Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:protectedtag:post','Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:protectedtag:*:delete','Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:check:post','Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'cohort-characterization:*:tag:post','Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'cohort-characterization:*:tag:*:delete','Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'cohort-characterization:*:protectedtag:post','Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'cohort-characterization:*:protectedtag:*:delete','Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'ir:*:tag:post','Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'ir:*:tag:*:delete','Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'ir:*:protectedtag:post','Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'ir:*:protectedtag:*:delete','Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'pathway-analysis:*:tag:post','Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'pathway-analysis:*:tag:*:delete','Unassign tag from cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'pathway-analysis:*:protectedtag:post','Assign tag to cohort definition'),
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(NEXT VALUE FOR ${ohdsiSchema}.sec_permission_id_seq, 'pathway-analysis:*:protectedtag:*:delete','Unassign tag from cohort definition')
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;
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INSERT INTO ${ohdsiSchema}.sec_role_permission(role_id, permission_id)
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SELECT sr.id, sp.id
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FROM ${ohdsiSchema}.sec_permission sp,
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${ohdsiSchema}.sec_role sr
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WHERE sp.value IN (
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'tag:get',
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'tag:search:get',
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'tag:post',
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'tag:*:put',
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'tag:*:get',
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'tag:*:delete',
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'cohortdefinition:*:tag:post',
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'cohortdefinition:*:tag:*:delete',
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'conceptset:*:tag:post',
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'conceptset:*:tag:*:delete',
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'conceptset:check:post',
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'cohort-characterization:*:tag:post',
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'cohort-characterization:*:tag:*:delete',
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'ir:*:tag:post',
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'ir:*:tag:*:delete',
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'pathway-analysis:*:tag:post',
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'pathway-analysis:*:tag:*:delete')
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AND sr.name IN ('Atlas users');
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INSERT INTO ${ohdsiSchema}.sec_role_permission(role_id, permission_id)
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SELECT sr.id, sp.id
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FROM ${ohdsiSchema}.sec_permission sp,
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${ohdsiSchema}.sec_role sr
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WHERE sp.value IN (
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'cohortdefinition:*:protectedtag:post',
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'cohortdefinition:*:protectedtag:*:delete',
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'conceptset:*:protectedtag:post',
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'conceptset:*:protectedtag:*:delete',
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'cohort-characterization:*:protectedtag:post',
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'cohort-characterization:*:protectedtag:*:delete',
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'ir:*:protectedtag:post',
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'ir:*:protectedtag:*:delete',
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'pathway-analysis:*:protectedtag:post',
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'pathway-analysis:*:protectedtag:*:delete')
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AND sr.name IN ('admin');
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CREATE SEQUENCE ${ohdsiSchema}.tags_seq;
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-- Possible types are:
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-- 0 - System (predefined) tags
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-- 1 - Custom tags
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-- 2 - Prizm tags
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CREATE TABLE ${ohdsiSchema}.tags
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(
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id INTEGER DEFAULT NEXT VALUE FOR ${ohdsiSchema}.tags_seq,
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name VARCHAR(50) NOT NULL,
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type INT NOT NULL DEFAULT 0,
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count INT NOT NULL DEFAULT 0,
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show_group BIT NOT NULL DEFAULT 0,
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icon VARCHAR(100) NULL,
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color VARCHAR(7) NULL,
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multi_selection BIT NOT NULL DEFAULT 0,
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permission_protected BIT NOT NULL DEFAULT 0,
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mandatory BIT NOT NULL DEFAULT 0,
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allow_custom BIT NOT NULL DEFAULT 0,
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description VARCHAR(MAX) NULL,
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created_by_id INTEGER,
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created_date DATETIME NOT NULL DEFAULT SYSDATETIMEOFFSET(),
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modified_by_id INTEGER,
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modified_date DATETIME,
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CONSTRAINT pk_tags_id PRIMARY KEY (id),
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CONSTRAINT fk_tags_sec_user_creator FOREIGN KEY (created_by_id) REFERENCES ${ohdsiSchema}.sec_user (id),
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CONSTRAINT fk_tags_sec_user_updater FOREIGN KEY (modified_by_id) REFERENCES ${ohdsiSchema}.sec_user (id)
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);
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CREATE UNIQUE INDEX tags_name_idx ON ${ohdsiSchema}.tags (name);
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CREATE TABLE ${ohdsiSchema}.tag_groups
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(
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tag_id INT NOT NULL,
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group_id INT NOT NULL,
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CONSTRAINT tag_groups_group_fk FOREIGN KEY (group_id) REFERENCES ${ohdsiSchema}.tags (id) ON DELETE CASCADE,
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CONSTRAINT tag_groups_tag_fk FOREIGN KEY (tag_id) REFERENCES ${ohdsiSchema}.tags (id) ON DELETE CASCADE
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);
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CREATE TABLE ${ohdsiSchema}.concept_set_tags
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(
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asset_id INT NOT NULL,
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tag_id INT NOT NULL,
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CONSTRAINT pk_concept_set_tags_id PRIMARY KEY (asset_id, tag_id),
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CONSTRAINT concept_set_tags_fk_sets FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.concept_set (concept_set_id) ON DELETE NO ACTION, --CHANGE ON DELETE ACTION BECAUSE OF ERROR
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CONSTRAINT concept_set_tags_fk_tags FOREIGN KEY (tag_id) REFERENCES ${ohdsiSchema}.tags (id) ON DELETE CASCADE
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);
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CREATE INDEX concept_set_tags_concept_id_idx ON ${ohdsiSchema}.concept_set_tags (asset_id);
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CREATE INDEX concept_set_tags_tag_id_idx ON ${ohdsiSchema}.concept_set_tags (tag_id);
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CREATE TABLE ${ohdsiSchema}.cohort_tags
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(
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asset_id INT NOT NULL,
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tag_id INT NOT NULL,
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CONSTRAINT pk_cohort_tags_id PRIMARY KEY (asset_id, tag_id),
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CONSTRAINT cohort_tags_fk_definitions FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.cohort_definition (id) ON DELETE CASCADE,
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CONSTRAINT cohort_tags_fk_tags FOREIGN KEY (tag_id) REFERENCES ${ohdsiSchema}.tags (id) ON DELETE CASCADE
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);
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CREATE INDEX cohort_tags_cohort_id_idx ON ${ohdsiSchema}.cohort_tags (asset_id);
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CREATE INDEX cohort_tags_tag_id_idx ON ${ohdsiSchema}.cohort_tags (tag_id);
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CREATE TABLE ${ohdsiSchema}.cohort_characterization_tags
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(
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asset_id bigint NOT NULL,
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tag_id INT NOT NULL,
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CONSTRAINT pk_cc_tags_id PRIMARY KEY (asset_id, tag_id),
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CONSTRAINT cc_tags_fk_ccs FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.cohort_characterization (id) ON DELETE CASCADE,
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CONSTRAINT cc_tags_fk_tags FOREIGN KEY (tag_id) REFERENCES ${ohdsiSchema}.tags (id) ON DELETE CASCADE
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);
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CREATE INDEX cc_tags_cc_id_idx ON ${ohdsiSchema}.cohort_characterization_tags (asset_id);
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CREATE INDEX cc_tags_tag_id_idx ON ${ohdsiSchema}.cohort_characterization_tags (tag_id);
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CREATE TABLE ${ohdsiSchema}.ir_tags
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(
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asset_id INT NOT NULL,
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tag_id INT NOT NULL,
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CONSTRAINT pk_ir_tags_id PRIMARY KEY (asset_id, tag_id),
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CONSTRAINT ir_tags_fk_irs FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.ir_analysis (id) ON DELETE CASCADE,
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CONSTRAINT ir_tags_fk_tags FOREIGN KEY (tag_id) REFERENCES ${ohdsiSchema}.tags (id) ON DELETE CASCADE
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);
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CREATE INDEX ir_tags_ir_id_idx ON ${ohdsiSchema}.ir_tags (asset_id);
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CREATE INDEX ir_tags_tag_id_idx ON ${ohdsiSchema}.ir_tags (tag_id);
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CREATE TABLE ${ohdsiSchema}.pathway_tags
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(
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asset_id INT NOT NULL,
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tag_id INT NOT NULL,
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CONSTRAINT pk_pathway_tags_id PRIMARY KEY (asset_id, tag_id),
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CONSTRAINT pathway_tags_fk_irs FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.pathway_analysis (id) ON DELETE CASCADE,
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CONSTRAINT pathway_tags_fk_tags FOREIGN KEY (tag_id) REFERENCES ${ohdsiSchema}.tags (id) ON DELETE CASCADE
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);
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CREATE INDEX pathway_tags_pathway_id_idx ON ${ohdsiSchema}.pathway_tags (asset_id);
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CREATE INDEX pathway_tags_tag_id_idx ON ${ohdsiSchema}.pathway_tags (tag_id);

‎src/main/resources/db/migration/sqlserver/V2.9.0.20210513111520__versioning.sql‎

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INSERT INTO ${ohdsiSchema}.sec_permission(id, value, description)
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VALUES
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohortdefinition:*:version:get','Get list of cohort versions'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohortdefinition:*:version:*:get','Get cohort version'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohortdefinition:*:version:*:put','Update cohort version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohortdefinition:*:version:*:delete','Delete cohort version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohortdefinition:*:version:*:createAsset:put','Copy cohort version as new cohort'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:version:get','Get list of concept set versions'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:version:*:get','Get concept set version'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:version:*:put','Update concept set version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:version:*:delete','Delete concept set version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:version:*:createAsset:put','Copy concept set version as new concept set'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:version:*:expression:get','Get expression for concept set items for default source'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'conceptset:*:version:*:expression:*:get','Get expression for concept set items for certain source'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohort-characterization:*:version:get','Get list of characterization versions'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohort-characterization:*:version:*:get','Get characterization version'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohort-characterization:*:version:*:put','Update characterization version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohort-characterization:*:version:*:delete','Delete characterization version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'cohort-characterization:*:version:*:createAsset:put','Copy characterization version as new cohort'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'ir:*:version:get','Get list of incidence rate analysis versions'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'ir:*:version:*:get','Get incidence rate analysis version'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'ir:*:version:*:put','Update incidence rate analysis version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'ir:*:version:*:delete','Delete incidence rate analysis version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'ir:*:version:*:createAsset:put','Copy incidence rate analysis version as new cohort'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'pathway-analysis:*:version:get','Get list of pathway analysis versions'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'pathway-analysis:*:version:*:get','Get pathway analysis version'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'pathway-analysis:*:version:*:put','Update pathway analysis version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'pathway-analysis:*:version:*:delete','Delete pathway analysis version info'),
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(NEXT VALUE for ${ohdsiSchema}.sec_permission_id_seq, 'pathway-analysis:*:version:*:createAsset:put','Copy pathway analysis version as new cohort');
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INSERT INTO ${ohdsiSchema}.sec_role_permission(role_id, permission_id)
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SELECT sr.id, sp.id
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FROM ${ohdsiSchema}.sec_permission SP,
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${ohdsiSchema}.sec_role sr
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WHERE sp.value IN (
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'cohortdefinition:*:version:get',
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'cohortdefinition:*:version:*:get',
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'cohortdefinition:*:version:*:put',
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'cohortdefinition:*:version:*:delete',
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'cohortdefinition:*:version:*:createAsset:put',
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'conceptset:*:version:get',
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'conceptset:*:version:*:get',
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'conceptset:*:version:*:put',
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'conceptset:*:version:*:delete',
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'conceptset:*:version:*:createAsset:put',
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'conceptset:*:version:*:expression:get',
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'conceptset:*:version:*:expression:*:get',
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'cohort-characterization:*:version:get',
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'cohort-characterization:*:version:*:get',
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'cohort-characterization:*:version:*:put',
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'cohort-characterization:*:version:*:delete',
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'cohort-characterization:*:version:*:createAsset:put',
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'ir:*:version:get',
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'ir:*:version:*:get',
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'ir:*:version:*:put',
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'ir:*:version:*:delete',
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'ir:*:version:*:createAsset:put',
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'pathway-analysis:*:version:get',
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'pathway-analysis:*:version:*:get',
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'pathway-analysis:*:version:*:put',
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'pathway-analysis:*:version:*:delete',
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'pathway-analysis:*:version:*:createAsset:put')
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AND sr.name IN ('Atlas users');
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-- Cohorts
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CREATE TABLE ${ohdsiSchema}.cohort_version
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(
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asset_id INT NOT NULL,
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comment VARCHAR(MAX) NULL,
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description VARCHAR(MAX) NULL,
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version INT NOT NULL DEFAULT 1,
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asset_json VARCHAR(MAX) NOT NULL,
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archived BIT NOT NULL DEFAULT 0,
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created_by_id INTEGER,
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created_date DATETIME NOT NULL DEFAULT (SYSDATETIMEOFFSET()),
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CONSTRAINT pk_cohort_version_id PRIMARY KEY (asset_id, version),
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CONSTRAINT fk_cohort_version_sec_user_creator FOREIGN KEY (created_by_id) REFERENCES ${ohdsiSchema}.sec_user (id),
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CONSTRAINT fk_cohort_version_asset_id FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.cohort_definition (id) ON DELETE CASCADE
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);
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CREATE INDEX cohort_version_asset_idx ON ${ohdsiSchema}.cohort_version (asset_id);
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-- Cohort characterizations
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CREATE TABLE ${ohdsiSchema}.cohort_characterization_version
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(
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asset_id bigint NOT NULL,
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comment VARCHAR(MAX) NULL,
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version INT NOT NULL DEFAULT 1,
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asset_json VARCHAR(MAX) NOT NULL,
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archived BIT NOT NULL DEFAULT 0,
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created_by_id INTEGER,
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created_date DATETIME NOT NULL DEFAULT (SYSDATETIMEOFFSET()),
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CONSTRAINT pk_cc_version_id PRIMARY KEY (asset_id, version),
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CONSTRAINT fk_cc_version_sec_user_creator FOREIGN KEY (created_by_id) REFERENCES ${ohdsiSchema}.sec_user (id),
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CONSTRAINT fk_cc_version_asset_id FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.cohort_characterization (id) ON DELETE CASCADE
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);
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CREATE INDEX cc_version_asset_idx ON ${ohdsiSchema}.cohort_characterization_version (asset_id);
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-- Concept sets
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CREATE TABLE ${ohdsiSchema}.concept_set_version
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(
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asset_id INT NOT NULL,
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comment VARCHAR(MAX) NULL,
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version INT NOT NULL DEFAULT 1,
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asset_json VARCHAR(MAX) NOT NULL,
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archived BIT NOT NULL DEFAULT 0,
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created_by_id INTEGER,
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created_date DATETIME NOT NULL DEFAULT (SYSDATETIMEOFFSET()),
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CONSTRAINT pk_concept_set_version_id PRIMARY KEY (asset_id, version),
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CONSTRAINT fk_concept_set_version_sec_user_creator FOREIGN KEY (created_by_id) REFERENCES ${ohdsiSchema}.sec_user (id),
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CONSTRAINT fk_concept_set_version_asset_id FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.concept_set (concept_set_id) ON DELETE CASCADE
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);
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CREATE INDEX concept_set_version_asset_idx ON ${ohdsiSchema}.concept_set_version (asset_id);
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-- Incidence rates
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CREATE TABLE ${ohdsiSchema}.ir_version
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(
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asset_id INT NOT NULL,
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comment VARCHAR(MAX) NULL,
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description VARCHAR(MAX) NULL,
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version INT NOT NULL DEFAULT 1,
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asset_json VARCHAR(MAX) NOT NULL,
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archived BIT NOT NULL DEFAULT 0,
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created_by_id INTEGER,
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created_date DATETIME NOT NULL DEFAULT (SYSDATETIMEOFFSET()),
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CONSTRAINT pk_ir_version_id PRIMARY KEY (asset_id, version),
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CONSTRAINT fk_ir_version_sec_user_creator FOREIGN KEY (created_by_id) REFERENCES ${ohdsiSchema}.sec_user (id),
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CONSTRAINT fk_ir_version_asset_id FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.ir_analysis (id) ON DELETE CASCADE
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);
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CREATE INDEX ir_version_asset_idx ON ${ohdsiSchema}.ir_version (asset_id);
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-- Pathways
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CREATE TABLE ${ohdsiSchema}.pathway_version
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(
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asset_id INT NOT NULL,
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comment VARCHAR(MAX) NULL,
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version INT NOT NULL DEFAULT 1,
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asset_json VARCHAR(MAX) NOT NULL,
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archived BIT NOT NULL DEFAULT 0,
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created_by_id INTEGER,
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created_date DATETIME NOT NULL DEFAULT (SYSDATETIMEOFFSET()),
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CONSTRAINT pk_pathway_version_id PRIMARY KEY (asset_id, version),
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CONSTRAINT fk_pathway_version_sec_user_creator FOREIGN KEY (created_by_id) REFERENCES ${ohdsiSchema}.sec_user (id),
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CONSTRAINT fk_pathway_version_asset_id FOREIGN KEY (asset_id) REFERENCES ${ohdsiSchema}.pathway_analysis (id) ON DELETE CASCADE
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);
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CREATE INDEX pathway_version_asset_idx ON ${ohdsiSchema}.pathway_version (asset_id);

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