Skip to content

Commit

Permalink
Add new table custom_protein_region_annotation to DB create, WB model
Browse files Browse the repository at this point in the history 
To match prev GIT commit.
Add custom_protein_region_annotation to DB create SQL, MySQL Workbench
Model File, and create new DB Upgrade SQL.
  • Loading branch information
@danjasuw
danjasuw committed May 2, 2018
1 parent 239eee4 commit 8f36e9d
Show file tree
Hide file tree
Showing 3 changed files with 135 additions and 66 deletions.
Binary file modified database_scripts/MySQL_Workbench_Model/Proxl_Database_MySQL_Workbench_Model.mwb
View file
Binary file not shown.
167 changes: 101 additions & 66 deletions database_scripts/install/create_empty_database.sql
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1181,6 +1181,103 @@ CREATE INDEX linkr_pr_srch_monolnk_mss_linker_fk_idx ON linker_per_search_crossl
CREATE INDEX linkr_pr_srch_monolnk_mss_search_fk_idx ON linker_per_search_crosslink_mass (search_id ASC);


-- -----------------------------------------------------
-- Table protein_sequence_v2
-- -----------------------------------------------------
DROP TABLE IF EXISTS protein_sequence_v2 ;

CREATE TABLE protein_sequence_v2 (
id INT UNSIGNED NOT NULL AUTO_INCREMENT,
sequence MEDIUMTEXT NOT NULL,
PRIMARY KEY (id))
ENGINE = InnoDB
DEFAULT CHARACTER SET = latin1
COLLATE = latin1_bin;

CREATE INDEX sequence ON protein_sequence_v2 (sequence(500) ASC);


-- -----------------------------------------------------
-- Table isotope_label
-- -----------------------------------------------------
DROP TABLE IF EXISTS isotope_label ;

CREATE TABLE isotope_label (
id INT UNSIGNED NOT NULL AUTO_INCREMENT,
name VARCHAR(50) NOT NULL,
PRIMARY KEY (id))
ENGINE = InnoDB;

CREATE INDEX name ON isotope_label (name ASC);


-- -----------------------------------------------------
-- Table protein_sequence_version
-- -----------------------------------------------------
DROP TABLE IF EXISTS protein_sequence_version ;

CREATE TABLE protein_sequence_version (
id INT UNSIGNED NOT NULL AUTO_INCREMENT,
protein_sequence_id INT UNSIGNED NOT NULL,
isotope_label_id INT UNSIGNED NOT NULL,
PRIMARY KEY (id),
CONSTRAINT fk_protein_sequence_version__prot_seq_id
FOREIGN KEY (protein_sequence_id)
REFERENCES protein_sequence_v2 (id)
ON DELETE RESTRICT
ON UPDATE RESTRICT,
CONSTRAINT fk_protein_sequence_version__isotope_label_id
FOREIGN KEY (isotope_label_id)
REFERENCES isotope_label (id)
ON DELETE NO ACTION
ON UPDATE NO ACTION)
ENGINE = InnoDB
DEFAULT CHARACTER SET = latin1
COLLATE = latin1_bin
COMMENT = 'This table is the FK on many other tables';

CREATE UNIQUE INDEX search_id_prot_seq_id_ann_id ON protein_sequence_version (protein_sequence_id ASC, isotope_label_id ASC);

CREATE INDEX srch_prt_sqnc_annttn_prot_seq_id_idx ON protein_sequence_version (protein_sequence_id ASC);

CREATE INDEX fk_protein__isotope_label_id_idx ON protein_sequence_version (isotope_label_id ASC);


-- -----------------------------------------------------
-- Table custom_protein_region_annotation
-- -----------------------------------------------------
DROP TABLE IF EXISTS custom_protein_region_annotation ;

CREATE TABLE custom_protein_region_annotation (
protein_sequence_version_id INT(10) UNSIGNED NOT NULL,
project_id INT(10) UNSIGNED NOT NULL,
start_position MEDIUMINT(8) UNSIGNED NOT NULL,
end_position MEDIUMINT(8) UNSIGNED NOT NULL,
annotation_color VARCHAR(255) NOT NULL,
annotation_text VARCHAR(20000) NOT NULL,
created_by INT(10) UNSIGNED NOT NULL,
created_date TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
PRIMARY KEY (protein_sequence_version_id, project_id, start_position, end_position),
CONSTRAINT cust_prtn_rgn_anno_auth_user_fk
FOREIGN KEY (created_by)
REFERENCES auth_user (id)
ON DELETE RESTRICT
ON UPDATE RESTRICT,
CONSTRAINT cust_prtn_rgn_anno_project_fk
FOREIGN KEY (project_id)
REFERENCES project (id)
ON DELETE CASCADE,
CONSTRAINT cust_prtn_rgn_anno_protn_s_v_id_fk
FOREIGN KEY (protein_sequence_version_id)
REFERENCES protein_sequence_version (id)
ON DELETE CASCADE)
ENGINE = InnoDB;

CREATE INDEX cust_prtn_rgn_anno_auth_user_fk ON custom_protein_region_annotation (created_by ASC);

CREATE INDEX cust_prtn_rgn_anno_project_fk ON custom_protein_region_annotation (project_id ASC);


-- -----------------------------------------------------
-- Table cutoffs_applied_on_import
-- -----------------------------------------------------
Expand Down Expand Up @@ -1477,22 +1574,6 @@ CREATE INDEX search_rep_pept_idx ON srch_rep_pept__prot_seq_id_pos_looplink (sea
CREATE INDEX srch_rppp_prt_sq_d_ps_lplnk_srch_rppptpptd ON srch_rep_pept__prot_seq_id_pos_looplink (search_reported_peptide_peptide_id ASC);


-- -----------------------------------------------------
-- Table protein_sequence_v2
-- -----------------------------------------------------
DROP TABLE IF EXISTS protein_sequence_v2 ;

CREATE TABLE protein_sequence_v2 (
id INT UNSIGNED NOT NULL AUTO_INCREMENT,
sequence MEDIUMTEXT NOT NULL,
PRIMARY KEY (id))
ENGINE = InnoDB
DEFAULT CHARACTER SET = latin1
COLLATE = latin1_bin;

CREATE INDEX sequence ON protein_sequence_v2 (sequence(500) ASC);


-- -----------------------------------------------------
-- Table annotation
-- -----------------------------------------------------
Expand All @@ -1513,52 +1594,6 @@ CREATE INDEX name ON annotation (name(100) ASC);
CREATE INDEX tax_name_desc ON annotation (taxonomy ASC, name(100) ASC, description(100) ASC);


-- -----------------------------------------------------
-- Table isotope_label
-- -----------------------------------------------------
DROP TABLE IF EXISTS isotope_label ;

CREATE TABLE isotope_label (
id INT UNSIGNED NOT NULL AUTO_INCREMENT,
name VARCHAR(50) NOT NULL,
PRIMARY KEY (id))
ENGINE = InnoDB;

CREATE INDEX name ON isotope_label (name ASC);


-- -----------------------------------------------------
-- Table protein_sequence_version
-- -----------------------------------------------------
DROP TABLE IF EXISTS protein_sequence_version ;

CREATE TABLE protein_sequence_version (
id INT UNSIGNED NOT NULL AUTO_INCREMENT,
protein_sequence_id INT UNSIGNED NOT NULL,
isotope_label_id INT UNSIGNED NOT NULL,
PRIMARY KEY (id),
CONSTRAINT fk_protein_sequence_version__prot_seq_id
FOREIGN KEY (protein_sequence_id)
REFERENCES protein_sequence_v2 (id)
ON DELETE RESTRICT
ON UPDATE RESTRICT,
CONSTRAINT fk_protein_sequence_version__isotope_label_id
FOREIGN KEY (isotope_label_id)
REFERENCES isotope_label (id)
ON DELETE NO ACTION
ON UPDATE NO ACTION)
ENGINE = InnoDB
DEFAULT CHARACTER SET = latin1
COLLATE = latin1_bin
COMMENT = 'This table is the FK on many other tables';

CREATE UNIQUE INDEX search_id_prot_seq_id_ann_id ON protein_sequence_version (protein_sequence_id ASC, isotope_label_id ASC);

CREATE INDEX srch_prt_sqnc_annttn_prot_seq_id_idx ON protein_sequence_version (protein_sequence_id ASC);

CREATE INDEX fk_protein__isotope_label_id_idx ON protein_sequence_version (isotope_label_id ASC);


-- -----------------------------------------------------
-- Table search__protein_sequence_version__annotation
-- -----------------------------------------------------
Expand Down Expand Up @@ -2323,10 +2358,6 @@ CREATE INDEX unified_rp_dynamic_mod__rp_matched_peptide_id_fk_idx ON unified_rep
CREATE INDEX unified_rep_pep_isotope_label_lookup_isotope_label_id_fk_idx ON unified_rep_pep_isotope_label_lookup (isotope_label_id ASC);


SET SQL_MODE=@OLD_SQL_MODE;
SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS;
SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS;


DELIMITER $$

Expand All @@ -2347,3 +2378,7 @@ END$$

DELIMITER ;

SET SQL_MODE=@OLD_SQL_MODE;
SET FOREIGN_KEY_CHECKS=@OLD_FOREIGN_KEY_CHECKS;
SET UNIQUE_CHECKS=@OLD_UNIQUE_CHECKS;

34 changes: 34 additions & 0 deletions database_scripts/upgrades/2018_05_add__custom_protein_region_annotation.sql
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,34 @@


-- New table custom_protein_region_annotation


CREATE TABLE custom_protein_region_annotation (
protein_sequence_version_id INT(10) UNSIGNED NOT NULL,
project_id INT(10) UNSIGNED NOT NULL,
start_position MEDIUMINT(8) UNSIGNED NOT NULL,
end_position MEDIUMINT(8) UNSIGNED NOT NULL,
annotation_color VARCHAR(255) NOT NULL,
annotation_text VARCHAR(20000) NOT NULL,
created_by INT(10) UNSIGNED NOT NULL,
created_date TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
PRIMARY KEY (protein_sequence_version_id, project_id, start_position, end_position),
CONSTRAINT cust_prtn_rgn_anno_auth_user_fk
FOREIGN KEY (created_by)
REFERENCES auth_user (id)
ON DELETE RESTRICT
ON UPDATE RESTRICT,
CONSTRAINT cust_prtn_rgn_anno_project_fk
FOREIGN KEY (project_id)
REFERENCES project (id)
ON DELETE CASCADE,
CONSTRAINT cust_prtn_rgn_anno_protn_s_v_id_fk
FOREIGN KEY (protein_sequence_version_id)
REFERENCES protein_sequence_version (id)
ON DELETE CASCADE)
ENGINE = InnoDB;

CREATE INDEX cust_prtn_rgn_anno_auth_user_fk ON custom_protein_region_annotation (created_by ASC);

CREATE INDEX cust_prtn_rgn_anno_project_fk ON custom_protein_region_annotation (project_id ASC);

0 comments on commit 8f36e9d

Please sign in to comment.