diff --git a/resources/schemas/dbscripts/postgresql/cds-0.000-23.000.sql b/resources/schemas/dbscripts/postgresql/cds-0.000-24.000.sql similarity index 87% rename from resources/schemas/dbscripts/postgresql/cds-0.000-23.000.sql rename to resources/schemas/dbscripts/postgresql/cds-0.000-24.000.sql index 41f80c534..4b0a25da5 100644 --- a/resources/schemas/dbscripts/postgresql/cds-0.000-23.000.sql +++ b/resources/schemas/dbscripts/postgresql/cds-0.000-24.000.sql @@ -2371,4 +2371,406 @@ ALTER TABLE cds.studyReport ALTER COLUMN cds_report_id DROP NOT NULL; ALTER TABLE cds.studyReport ADD COLUMN rowId SERIAL; ALTER TABLE cds.studyReport ADD CONSTRAINT PK_CDS_STUDY_REPORT PRIMARY KEY (rowId); -ALTER TABLE cds.studyReport ADD CONSTRAINT UQ_CDS_STUDY_REPORT UNIQUE (prot, cds_report_id, container, cds_report_link, cds_report_label); \ No newline at end of file +ALTER TABLE cds.studyReport ADD CONSTRAINT UQ_CDS_STUDY_REPORT UNIQUE (prot, cds_report_id, container, cds_report_link, cds_report_label); + +CREATE TABLE cds.import_assay_combined_antigen_metadata +( + antigen_cds_id VARCHAR(250) NOT NULL, + antigen_full_name VARCHAR(250), + antigen_short_name VARCHAR(250), + antigen_plot_label VARCHAR(250), + antigen_name_other VARCHAR(250), + antigen_dna_construct INTEGER, + antigen_category VARCHAR(250), + antigen_type_component VARCHAR(250), + antigen_type_region VARCHAR(250), + antigen_type_scaffold VARCHAR(250), + antigen_type_modifiers VARCHAR(250), + antigen_type_tags VARCHAR(250), + antigen_type_virus_type VARCHAR(250), + antigen_type_backbone VARCHAR(250), + antigen_type_reporter_molecule VARCHAR(250), + antigen_type_differentiate VARCHAR(250), + antigen_type_control VARCHAR(250), + isolate_name_component VARCHAR(250), + isolate_species VARCHAR(250), + isolate_donor_id VARCHAR(250), + isolate_differentiate VARCHAR(250), + isolate_clade VARCHAR(250), + isolate_clone VARCHAR(250), + isolate_mutations VARCHAR(250), + isolate_neut_tier VARCHAR(250), + isolate_clone_pi VARCHAR(250), + isolate_country_origin VARCHAR(250), + isolate_year_isolated INTEGER, + isolate_fiebig_stage VARCHAR(250), + antigen_accession_num INTEGER, + antigen_amino_acid_sequence VARCHAR(250), + production_component VARCHAR(250), + isolate_host_cell VARCHAR(250), + antigen_purification VARCHAR(250), + antigen_reagents VARCHAR(250), + antigen_manufacturer VARCHAR(250), + antigen_codon_optimize VARCHAR(250), + antigen_source VARCHAR(250), + isolate_transfection_method VARCHAR(250), + isolate_TF_status VARCHAR(250), + isolate_PV_backbone_system VARCHAR(250), + container ENTITYID NOT NULL, + + CONSTRAINT PK_import_assay_combined_antigen_metadata PRIMARY KEY (antigen_cds_id, container) +); + +CREATE TABLE cds.assay_combined_antigen_metadata +( + antigen_cds_id VARCHAR(250) NOT NULL, + antigen_full_name VARCHAR(250), + antigen_short_name VARCHAR(250), + antigen_plot_label VARCHAR(250), + antigen_name_other VARCHAR(250), + antigen_dna_construct INTEGER, + antigen_category VARCHAR(250), + antigen_type_component VARCHAR(250), + antigen_type_region VARCHAR(250), + antigen_type_scaffold VARCHAR(250), + antigen_type_modifiers VARCHAR(250), + antigen_type_tags VARCHAR(250), + antigen_type_virus_type VARCHAR(250), + antigen_type_backbone VARCHAR(250), + antigen_type_reporter_molecule VARCHAR(250), + antigen_type_differentiate VARCHAR(250), + antigen_type_control VARCHAR(250), + isolate_name_component VARCHAR(250), + isolate_species VARCHAR(250), + isolate_donor_id VARCHAR(250), + isolate_differentiate VARCHAR(250), + isolate_clade VARCHAR(250), + isolate_clone VARCHAR(250), + isolate_mutations VARCHAR(250), + isolate_neut_tier VARCHAR(250), + isolate_clone_pi VARCHAR(250), + isolate_country_origin VARCHAR(250), + isolate_year_isolated INTEGER, + isolate_fiebig_stage VARCHAR(250), + antigen_accession_num INTEGER, + antigen_amino_acid_sequence VARCHAR(250), + production_component VARCHAR(250), + isolate_host_cell VARCHAR(250), + antigen_purification VARCHAR(250), + antigen_reagents VARCHAR(250), + antigen_manufacturer VARCHAR(250), + antigen_codon_optimize VARCHAR(250), + antigen_source VARCHAR(250), + isolate_transfection_method VARCHAR(250), + isolate_TF_status VARCHAR(250), + isolate_PV_backbone_system VARCHAR(250), + container ENTITYID NOT NULL, + + CONSTRAINT PK_assay_combined_antigen_metadata PRIMARY KEY (antigen_cds_id, container) +); + +CREATE TABLE cds.sequence +( + sequence_id VARCHAR(100) NOT NULL, + sequence_nt VARCHAR(10000), + source VARCHAR(100), + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_sequence PRIMARY KEY (sequence_id) +); + +CREATE TABLE cds.run_log +( + run_number VARCHAR(100) NOT NULL, + run_application VARCHAR(10), + run_information VARCHAR(10000), + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_run_log PRIMARY KEY (run_number) +); + +CREATE TABLE cds.allele_sequence +( + allele VARCHAR(100) NOT NULL, + allele_sequence_nt VARCHAR(1000), + release_date TIMESTAMP, + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_allele_sequence PRIMARY KEY (allele) +); + +CREATE TABLE cds.sequence_headers +( + sequence_header_id SERIAL, + header VARCHAR(1000), + sequence_id VARCHAR(100), + source VARCHAR(100), + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_sequence_headers PRIMARY KEY (sequence_header_id), + CONSTRAINT FK_cds_sequence_headers_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id) +); + +CREATE INDEX IX_cds_sequence_headers_sequence_id ON cds.sequence_headers(sequence_id); + +CREATE TABLE cds.sequence_germline +( + sequence_germline_id SERIAL, + allele VARCHAR(100), + sequence_id VARCHAR(100), + percent_identity NUMERIC(15,4), + matches INT, + alignment_length INT, + score NUMERIC(15,4), + run_number VARCHAR(100), + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_sequence_germline PRIMARY KEY (sequence_germline_id), + CONSTRAINT FK_cds_sequence_germline_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id) +); + +CREATE INDEX IX_cds_sequence_germline_sequence_id ON cds.sequence_germline(sequence_id); + +CREATE TABLE cds.antibody_sequence +( + mab_id VARCHAR(100) NOT NULL, + chain VARCHAR(10) NOT NULL, + sequence_id VARCHAR(100), + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_antibody_sequence PRIMARY KEY (mab_id, chain), + CONSTRAINT FK_cds_antibody_sequence_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id) +); + +CREATE INDEX IX_cds_antibody_sequence_sequence_id ON cds.antibody_sequence(sequence_id); + +CREATE TABLE cds.alignment +( + alignment_id SERIAL, + sequence_id VARCHAR(100), + locus VARCHAR(10), + stop_codon VARCHAR(1), + vj_in_frame VARCHAR(1), + productive VARCHAR(1), + rev_comp VARCHAR(1), + complete_vdj VARCHAR(1), + v_call VARCHAR(25), + d_call VARCHAR(25), + j_call VARCHAR(25), + sequence_alignment VARCHAR(1000), + germline_alignment VARCHAR(1000), + sequence_alignment_aa VARCHAR(1000), + germline_alignment_aa VARCHAR(1000), + v_alignment_start INT, + v_alignment_end INT, + d_alignment_start INT, + d_alignment_end INT, + j_alignment_start INT, + j_alignment_end INT, + v_sequence_alignment VARCHAR(1000), + v_sequence_alignment_aa VARCHAR(1000), + v_germline_alignment VARCHAR(1000), + v_germline_alignment_aa VARCHAR(1000), + d_sequence_alignment VARCHAR(100), + d_sequence_alignment_aa VARCHAR(100), + d_germline_alignment VARCHAR(100), + d_germline_alignment_aa VARCHAR(100), + j_sequence_alignment VARCHAR(100), + j_sequence_alignment_aa VARCHAR(100), + j_germline_alignment VARCHAR(100), + j_germline_alignment_aa VARCHAR(100), + fwr1 VARCHAR(100), + fwr1_aa VARCHAR(100), + cdr1 VARCHAR(100), + cdr1_aa VARCHAR(100), + fwr2 VARCHAR(100), + fwr2_aa VARCHAR(100), + cdr2 VARCHAR(100), + cdr2_aa VARCHAR(100), + fwr3 VARCHAR(1000), + fwr3_aa VARCHAR(100), + fwr4 VARCHAR(100), + fwr4_aa VARCHAR(100), + cdr3 VARCHAR(100), + cdr3_aa VARCHAR(100), + junction VARCHAR(100), + junction_length INT, + junction_aa VARCHAR(100), + junction_aa_length INT, + v_score NUMERIC(15,4), + d_score NUMERIC(15,4), + j_score NUMERIC(15,4), + v_cigar VARCHAR(1000), + d_cigar VARCHAR(1000), + j_cigar VARCHAR(1000), + v_support NUMERIC(15,4), + d_support NUMERIC(15,4), + j_support NUMERIC(15,4), + v_identity NUMERIC(15,4), + d_identity NUMERIC(15,4), + j_identity NUMERIC(15,4), + v_sequence_start INT, + v_sequence_end INT, + v_germline_start INT, + v_germline_end INT, + d_sequence_start INT, + d_sequence_end INT, + d_germline_start INT, + d_germline_end INT, + j_sequence_start INT, + j_sequence_end INT, + j_germline_start INT, + j_germline_end INT, + fwr1_start INT, + fwr1_end INT, + cdr1_start INT, + cdr1_end INT, + fwr2_start INT, + fwr2_end INT, + cdr2_start INT, + cdr2_end INT, + fwr3_start INT, + fwr3_end INT, + fwr4_start INT, + fwr4_end INT, + cdr3_start INT, + cdr3_end INT, + np1 VARCHAR(100), + np1_length INT, + np2 VARCHAR(100), + np2_length INT, + run_number VARCHAR(100), + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_alignment_alignment_id PRIMARY KEY (alignment_id), + CONSTRAINT FK_cds_alignment_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id) +); + +CREATE INDEX IX_cds_alignment_sequence_id ON cds.alignment(sequence_id); + +ALTER TABLE cds.sequence_headers RENAME TO sequence_header; + +DROP TABLE cds.run_log; + +CREATE TABLE cds.run_log +( + run_application VARCHAR(10) NOT NULL, + run_information VARCHAR(10000), + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_run_log PRIMARY KEY (run_application) +); + +ALTER TABLE cds.sequence DROP COLUMN source; + +ALTER TABLE cds.sequence_germline DROP COLUMN run_number; +ALTER TABLE cds.alignment DROP COLUMN run_number; + +ALTER TABLE cds.sequence_germline ADD COLUMN run_application VARCHAR(10); +ALTER TABLE cds.alignment ADD COLUMN run_application VARCHAR(10); + +CREATE TABLE cds.antibody_class +( + mab_class_id VARCHAR(30) NOT NULL, + mab_class_name VARCHAR(50), + description TEXT, + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_antibody_class PRIMARY KEY (mab_class_id) +); + +ALTER TABLE cds.import_MAbMetadata ADD COLUMN mab_class_id VARCHAR(30); +ALTER TABLE cds.MAbMetadata ADD COLUMN mab_class_id VARCHAR(30); + +ALTER TABLE cds.alignment + ALTER COLUMN cdr3 TYPE VARCHAR(200), + ALTER junction TYPE VARCHAR(200), + ALTER COLUMN np1 TYPE VARCHAR(200), + ALTER COLUMN np2 TYPE VARCHAR(200); + +CREATE TABLE cds.preferred_allele +( + rowid SERIAL, + sequence_id VARCHAR(100), + allele VARCHAR(100), + status BOOLEAN, + note TEXT, + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_preferred_allele PRIMARY KEY (rowid), + CONSTRAINT FK_cds_preferred_allele_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id), + CONSTRAINT FK_cds_preferred_allele FOREIGN KEY (allele) REFERENCES cds.allele_sequence(allele) +); + +CREATE INDEX IX_cds_preferred_allele_sequence_id ON cds.preferred_allele(sequence_id); +CREATE INDEX IX_cds_preferred_allele ON cds.preferred_allele(allele); + +ALTER TABLE cds.sequence_header RENAME COLUMN source TO source_id; +ALTER TABLE cds.antibody_sequence ADD COLUMN lineage BOOLEAN; +ALTER TABLE cds.antibody_sequence DROP CONSTRAINT PK_cds_antibody_sequence; +ALTER TABLE cds.antibody_sequence ADD CONSTRAINT PK_cds_antibody_sequence PRIMARY KEY (mab_id, sequence_id); + +DROP TABLE cds.run_log; +CREATE TABLE cds.alignment_run +( + run_application VARCHAR(10) NOT NULL, + run_information VARCHAR(10000), + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_alignment_run PRIMARY KEY (run_application) +); + +CREATE TABLE cds.header_source +( + source_id VARCHAR(30), + source VARCHAR(1000), + notes TEXT, + container ENTITYID NOT NULL, + + CONSTRAINT PK_cds_header_source_id PRIMARY KEY (source_id) +); + +ALTER TABLE cds.antibody_sequence DROP COLUMN chain; +ALTER TABLE cds.header_source RENAME COLUMN notes TO note; + +TRUNCATE TABLE cds.MAbMix CASCADE; +TRUNCATE TABLE cds.mabmetadata CASCADE; +TRUNCATE TABLE cds.sequence_germline CASCADE; +TRUNCATE TABLE cds.allele_sequence CASCADE; +TRUNCATE TABLE cds.alignment CASCADE; +TRUNCATE TABLE cds.alignment_run CASCADE; +TRUNCATE TABLE cds.sequence_header CASCADE; +TRUNCATE TABLE cds.header_source CASCADE; +TRUNCATE TABLE cds.antibody_sequence CASCADE; +TRUNCATE TABLE cds.antibody_class CASCADE; +TRUNCATE TABLE cds.sequence CASCADE; + +ALTER TABLE cds.sequence_germline ADD CONSTRAINT FK_cds_sequence_germline_allele FOREIGN KEY (allele) REFERENCES cds.allele_sequence (allele); +CREATE INDEX IX_cds_sequence_germline_allele ON cds.sequence_germline (allele); + +ALTER TABLE cds.alignment ADD CONSTRAINT FK_cds_alignment_v_call FOREIGN KEY (v_call) REFERENCES cds.allele_sequence (allele); +CREATE INDEX IX_cds_alignment_v_call ON cds.alignment (v_call); + +ALTER TABLE cds.alignment ADD CONSTRAINT FK_cds_alignment_d_call FOREIGN KEY (d_call) REFERENCES cds.allele_sequence (allele); +CREATE INDEX IX_cds_alignment_d_call ON cds.alignment (d_call); + +ALTER TABLE cds.alignment ADD CONSTRAINT FK_cds_alignment_j_call FOREIGN KEY (j_call) REFERENCES cds.allele_sequence (allele); +CREATE INDEX IX_cds_alignment_j_call ON cds.alignment (j_call); + +ALTER TABLE cds.sequence_germline ADD CONSTRAINT FK_cds_sequence_germline_run_application FOREIGN KEY (run_application) REFERENCES cds.alignment_run (run_application); +CREATE INDEX IX_cds_sequence_germline_run_application ON cds.sequence_germline (run_application); + +ALTER TABLE cds.alignment ADD CONSTRAINT FK_cds_alignment_run_application FOREIGN KEY (run_application) REFERENCES cds.alignment_run (run_application); +CREATE INDEX IX_cds_alignment_run_application ON cds.alignment (run_application); + +ALTER TABLE cds.sequence_header ADD CONSTRAINT FK_cds_sequence_header_source_id FOREIGN KEY (source_id) REFERENCES cds.header_source (source_id); +CREATE INDEX IX_cds_sequence_header_source_id ON cds.sequence_header(source_id); + +ALTER TABLE cds.antibody_sequence ADD CONSTRAINT FK_cds_antibody_sequence_mab_id FOREIGN KEY (container, mab_id) REFERENCES cds.mabmetadata (container, mab_id); +CREATE INDEX IX_cds_antibody_sequence_mab_id ON cds.antibody_sequence (container, mab_id); + +ALTER TABLE cds.mabmetadata ADD CONSTRAINT FK_cds_mabmetadata_mab_class_id FOREIGN KEY (mab_class_id) REFERENCES cds.antibody_class (mab_class_id); +CREATE INDEX IX_cds_mabmetadata_mab_class_id ON cds.mabmetadata (mab_class_id); + +ALTER TABLE cds.import_MAbMix DROP CONSTRAINT import_MAbMix_mab_id_fkey; +DROP TABLE cds.import_mabmetadata; \ No newline at end of file diff --git a/resources/schemas/dbscripts/postgresql/cds-23.000-23.001.sql b/resources/schemas/dbscripts/postgresql/cds-23.000-23.001.sql deleted file mode 100644 index b2e537550..000000000 --- a/resources/schemas/dbscripts/postgresql/cds-23.000-23.001.sql +++ /dev/null @@ -1,95 +0,0 @@ -CREATE TABLE cds.import_assay_combined_antigen_metadata -( - antigen_cds_id VARCHAR(250) NOT NULL, - antigen_full_name VARCHAR(250), - antigen_short_name VARCHAR(250), - antigen_plot_label VARCHAR(250), - antigen_name_other VARCHAR(250), - antigen_dna_construct INTEGER, - antigen_category VARCHAR(250), - antigen_type_component VARCHAR(250), - antigen_type_region VARCHAR(250), - antigen_type_scaffold VARCHAR(250), - antigen_type_modifiers VARCHAR(250), - antigen_type_tags VARCHAR(250), - antigen_type_virus_type VARCHAR(250), - antigen_type_backbone VARCHAR(250), - antigen_type_reporter_molecule VARCHAR(250), - antigen_type_differentiate VARCHAR(250), - antigen_type_control VARCHAR(250), - isolate_name_component VARCHAR(250), - isolate_species VARCHAR(250), - isolate_donor_id VARCHAR(250), - isolate_differentiate VARCHAR(250), - isolate_clade VARCHAR(250), - isolate_clone VARCHAR(250), - isolate_mutations VARCHAR(250), - isolate_neut_tier VARCHAR(250), - isolate_clone_pi VARCHAR(250), - isolate_country_origin VARCHAR(250), - isolate_year_isolated INTEGER, - isolate_fiebig_stage VARCHAR(250), - antigen_accession_num INTEGER, - antigen_amino_acid_sequence VARCHAR(250), - production_component VARCHAR(250), - isolate_host_cell VARCHAR(250), - antigen_purification VARCHAR(250), - antigen_reagents VARCHAR(250), - antigen_manufacturer VARCHAR(250), - antigen_codon_optimize VARCHAR(250), - antigen_source VARCHAR(250), - isolate_transfection_method VARCHAR(250), - isolate_TF_status VARCHAR(250), - isolate_PV_backbone_system VARCHAR(250), - container ENTITYID NOT NULL, - - CONSTRAINT PK_import_assay_combined_antigen_metadata PRIMARY KEY (antigen_cds_id, container) -); - -CREATE TABLE cds.assay_combined_antigen_metadata -( - antigen_cds_id VARCHAR(250) NOT NULL, - antigen_full_name VARCHAR(250), - antigen_short_name VARCHAR(250), - antigen_plot_label VARCHAR(250), - antigen_name_other VARCHAR(250), - antigen_dna_construct INTEGER, - antigen_category VARCHAR(250), - antigen_type_component VARCHAR(250), - antigen_type_region VARCHAR(250), - antigen_type_scaffold VARCHAR(250), - antigen_type_modifiers VARCHAR(250), - antigen_type_tags VARCHAR(250), - antigen_type_virus_type VARCHAR(250), - antigen_type_backbone VARCHAR(250), - antigen_type_reporter_molecule VARCHAR(250), - antigen_type_differentiate VARCHAR(250), - antigen_type_control VARCHAR(250), - isolate_name_component VARCHAR(250), - isolate_species VARCHAR(250), - isolate_donor_id VARCHAR(250), - isolate_differentiate VARCHAR(250), - isolate_clade VARCHAR(250), - isolate_clone VARCHAR(250), - isolate_mutations VARCHAR(250), - isolate_neut_tier VARCHAR(250), - isolate_clone_pi VARCHAR(250), - isolate_country_origin VARCHAR(250), - isolate_year_isolated INTEGER, - isolate_fiebig_stage VARCHAR(250), - antigen_accession_num INTEGER, - antigen_amino_acid_sequence VARCHAR(250), - production_component VARCHAR(250), - isolate_host_cell VARCHAR(250), - antigen_purification VARCHAR(250), - antigen_reagents VARCHAR(250), - antigen_manufacturer VARCHAR(250), - antigen_codon_optimize VARCHAR(250), - antigen_source VARCHAR(250), - isolate_transfection_method VARCHAR(250), - isolate_TF_status VARCHAR(250), - isolate_PV_backbone_system VARCHAR(250), - container ENTITYID NOT NULL, - - CONSTRAINT PK_assay_combined_antigen_metadata PRIMARY KEY (antigen_cds_id, container) -); \ No newline at end of file diff --git a/resources/schemas/dbscripts/postgresql/cds-23.001-23.002.sql b/resources/schemas/dbscripts/postgresql/cds-23.001-23.002.sql deleted file mode 100644 index 2df91e7f4..000000000 --- a/resources/schemas/dbscripts/postgresql/cds-23.001-23.002.sql +++ /dev/null @@ -1,178 +0,0 @@ -CREATE TABLE cds.sequence -( - sequence_id VARCHAR(100) NOT NULL, - sequence_nt VARCHAR(10000), - source VARCHAR(100), - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_sequence PRIMARY KEY (sequence_id) -); - -CREATE TABLE cds.run_log -( - run_number VARCHAR(100) NOT NULL, - run_application VARCHAR(10), - run_information VARCHAR(10000), - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_run_log PRIMARY KEY (run_number) -); - -CREATE TABLE cds.allele_sequence -( - allele VARCHAR(100) NOT NULL, - allele_sequence_nt VARCHAR(1000), - release_date TIMESTAMP, - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_allele_sequence PRIMARY KEY (allele) -); - -CREATE TABLE cds.sequence_headers -( - sequence_header_id SERIAL, - header VARCHAR(1000), - sequence_id VARCHAR(100), - source VARCHAR(100), - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_sequence_headers PRIMARY KEY (sequence_header_id), - CONSTRAINT FK_cds_sequence_headers_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id) -); - -CREATE INDEX IX_cds_sequence_headers_sequence_id ON cds.sequence_headers(sequence_id); - -CREATE TABLE cds.sequence_germline -( - sequence_germline_id SERIAL, - allele VARCHAR(100), - sequence_id VARCHAR(100), - percent_identity NUMERIC(15,4), - matches INT, - alignment_length INT, - score NUMERIC(15,4), - run_number VARCHAR(100), - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_sequence_germline PRIMARY KEY (sequence_germline_id), - CONSTRAINT FK_cds_sequence_germline_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id) -); - -CREATE INDEX IX_cds_sequence_germline_sequence_id ON cds.sequence_germline(sequence_id); - -CREATE TABLE cds.antibody_sequence -( - mab_id VARCHAR(100) NOT NULL, - chain VARCHAR(10) NOT NULL, - sequence_id VARCHAR(100), - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_antibody_sequence PRIMARY KEY (mab_id, chain), - CONSTRAINT FK_cds_antibody_sequence_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id) -); - -CREATE INDEX IX_cds_antibody_sequence_sequence_id ON cds.antibody_sequence(sequence_id); - -CREATE TABLE cds.alignment -( - alignment_id SERIAL, - sequence_id VARCHAR(100), - locus VARCHAR(10), - stop_codon VARCHAR(1), - vj_in_frame VARCHAR(1), - productive VARCHAR(1), - rev_comp VARCHAR(1), - complete_vdj VARCHAR(1), - v_call VARCHAR(25), - d_call VARCHAR(25), - j_call VARCHAR(25), - sequence_alignment VARCHAR(1000), - germline_alignment VARCHAR(1000), - sequence_alignment_aa VARCHAR(1000), - germline_alignment_aa VARCHAR(1000), - v_alignment_start INT, - v_alignment_end INT, - d_alignment_start INT, - d_alignment_end INT, - j_alignment_start INT, - j_alignment_end INT, - v_sequence_alignment VARCHAR(1000), - v_sequence_alignment_aa VARCHAR(1000), - v_germline_alignment VARCHAR(1000), - v_germline_alignment_aa VARCHAR(1000), - d_sequence_alignment VARCHAR(100), - d_sequence_alignment_aa VARCHAR(100), - d_germline_alignment VARCHAR(100), - d_germline_alignment_aa VARCHAR(100), - j_sequence_alignment VARCHAR(100), - j_sequence_alignment_aa VARCHAR(100), - j_germline_alignment VARCHAR(100), - j_germline_alignment_aa VARCHAR(100), - fwr1 VARCHAR(100), - fwr1_aa VARCHAR(100), - cdr1 VARCHAR(100), - cdr1_aa VARCHAR(100), - fwr2 VARCHAR(100), - fwr2_aa VARCHAR(100), - cdr2 VARCHAR(100), - cdr2_aa VARCHAR(100), - fwr3 VARCHAR(1000), - fwr3_aa VARCHAR(100), - fwr4 VARCHAR(100), - fwr4_aa VARCHAR(100), - cdr3 VARCHAR(100), - cdr3_aa VARCHAR(100), - junction VARCHAR(100), - junction_length INT, - junction_aa VARCHAR(100), - junction_aa_length INT, - v_score NUMERIC(15,4), - d_score NUMERIC(15,4), - j_score NUMERIC(15,4), - v_cigar VARCHAR(1000), - d_cigar VARCHAR(1000), - j_cigar VARCHAR(1000), - v_support NUMERIC(15,4), - d_support NUMERIC(15,4), - j_support NUMERIC(15,4), - v_identity NUMERIC(15,4), - d_identity NUMERIC(15,4), - j_identity NUMERIC(15,4), - v_sequence_start INT, - v_sequence_end INT, - v_germline_start INT, - v_germline_end INT, - d_sequence_start INT, - d_sequence_end INT, - d_germline_start INT, - d_germline_end INT, - j_sequence_start INT, - j_sequence_end INT, - j_germline_start INT, - j_germline_end INT, - fwr1_start INT, - fwr1_end INT, - cdr1_start INT, - cdr1_end INT, - fwr2_start INT, - fwr2_end INT, - cdr2_start INT, - cdr2_end INT, - fwr3_start INT, - fwr3_end INT, - fwr4_start INT, - fwr4_end INT, - cdr3_start INT, - cdr3_end INT, - np1 VARCHAR(100), - np1_length INT, - np2 VARCHAR(100), - np2_length INT, - run_number VARCHAR(100), - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_alignment_alignment_id PRIMARY KEY (alignment_id), - CONSTRAINT FK_cds_alignment_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id) -); - -CREATE INDEX IX_cds_alignment_sequence_id ON cds.alignment(sequence_id); \ No newline at end of file diff --git a/resources/schemas/dbscripts/postgresql/cds-23.002-23.003.sql b/resources/schemas/dbscripts/postgresql/cds-23.002-23.003.sql deleted file mode 100644 index 3b0e348b3..000000000 --- a/resources/schemas/dbscripts/postgresql/cds-23.002-23.003.sql +++ /dev/null @@ -1,33 +0,0 @@ -ALTER TABLE cds.sequence_headers RENAME TO sequence_header; - -DROP TABLE cds.run_log; - -CREATE TABLE cds.run_log -( - run_application VARCHAR(10) NOT NULL, - run_information VARCHAR(10000), - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_run_log PRIMARY KEY (run_application) -); - -ALTER TABLE cds.sequence DROP COLUMN source; - -ALTER TABLE cds.sequence_germline DROP COLUMN run_number; -ALTER TABLE cds.alignment DROP COLUMN run_number; - -ALTER TABLE cds.sequence_germline ADD COLUMN run_application VARCHAR(10); -ALTER TABLE cds.alignment ADD COLUMN run_application VARCHAR(10); - -CREATE TABLE cds.antibody_class -( - mab_class_id VARCHAR(30) NOT NULL, - mab_class_name VARCHAR(50), - description TEXT, - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_antibody_class PRIMARY KEY (mab_class_id) -); - -ALTER TABLE cds.import_MAbMetadata ADD COLUMN mab_class_id VARCHAR(30); -ALTER TABLE cds.MAbMetadata ADD COLUMN mab_class_id VARCHAR(30); \ No newline at end of file diff --git a/resources/schemas/dbscripts/postgresql/cds-23.003-23.004.sql b/resources/schemas/dbscripts/postgresql/cds-23.003-23.004.sql deleted file mode 100644 index 6cfcceb44..000000000 --- a/resources/schemas/dbscripts/postgresql/cds-23.003-23.004.sql +++ /dev/null @@ -1,22 +0,0 @@ -ALTER TABLE cds.alignment - ALTER COLUMN cdr3 TYPE VARCHAR(200), - ALTER junction TYPE VARCHAR(200), - ALTER COLUMN np1 TYPE VARCHAR(200), - ALTER COLUMN np2 TYPE VARCHAR(200); - -CREATE TABLE cds.preferred_allele -( - rowid SERIAL, - sequence_id VARCHAR(100), - allele VARCHAR(100), - status BOOLEAN, - note TEXT, - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_preferred_allele PRIMARY KEY (rowid), - CONSTRAINT FK_cds_preferred_allele_sequence_id FOREIGN KEY (sequence_id) REFERENCES cds.sequence(sequence_id), - CONSTRAINT FK_cds_preferred_allele FOREIGN KEY (allele) REFERENCES cds.allele_sequence(allele) -); - -CREATE INDEX IX_cds_preferred_allele_sequence_id ON cds.preferred_allele(sequence_id); -CREATE INDEX IX_cds_preferred_allele ON cds.preferred_allele(allele); diff --git a/resources/schemas/dbscripts/postgresql/cds-23.004-23.005.sql b/resources/schemas/dbscripts/postgresql/cds-23.004-23.005.sql deleted file mode 100644 index 0b43f3a1d..000000000 --- a/resources/schemas/dbscripts/postgresql/cds-23.004-23.005.sql +++ /dev/null @@ -1,24 +0,0 @@ -ALTER TABLE cds.sequence_header RENAME COLUMN source TO source_id; -ALTER TABLE cds.antibody_sequence ADD COLUMN lineage BOOLEAN; -ALTER TABLE cds.antibody_sequence DROP CONSTRAINT PK_cds_antibody_sequence; -ALTER TABLE cds.antibody_sequence ADD CONSTRAINT PK_cds_antibody_sequence PRIMARY KEY (mab_id, sequence_id); - -DROP TABLE cds.run_log; -CREATE TABLE cds.alignment_run -( - run_application VARCHAR(10) NOT NULL, - run_information VARCHAR(10000), - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_alignment_run PRIMARY KEY (run_application) -); - -CREATE TABLE cds.header_source -( - source_id VARCHAR(30), - source VARCHAR(1000), - notes TEXT, - container ENTITYID NOT NULL, - - CONSTRAINT PK_cds_header_source_id PRIMARY KEY (source_id) -); \ No newline at end of file diff --git a/resources/schemas/dbscripts/postgresql/cds-23.005-23.006.sql b/resources/schemas/dbscripts/postgresql/cds-23.005-23.006.sql deleted file mode 100644 index 7715f60cb..000000000 --- a/resources/schemas/dbscripts/postgresql/cds-23.005-23.006.sql +++ /dev/null @@ -1,2 +0,0 @@ -ALTER TABLE cds.antibody_sequence DROP COLUMN chain; -ALTER TABLE cds.header_source RENAME COLUMN notes TO note; \ No newline at end of file diff --git a/resources/schemas/dbscripts/postgresql/cds-23.006-23.007.sql b/resources/schemas/dbscripts/postgresql/cds-23.006-23.007.sql deleted file mode 100644 index d34309dad..000000000 --- a/resources/schemas/dbscripts/postgresql/cds-23.006-23.007.sql +++ /dev/null @@ -1,41 +0,0 @@ -TRUNCATE TABLE cds.MAbMix CASCADE; -TRUNCATE TABLE cds.mabmetadata CASCADE; -TRUNCATE TABLE cds.sequence_germline CASCADE; -TRUNCATE TABLE cds.allele_sequence CASCADE; -TRUNCATE TABLE cds.alignment CASCADE; -TRUNCATE TABLE cds.alignment_run CASCADE; -TRUNCATE TABLE cds.sequence_header CASCADE; -TRUNCATE TABLE cds.header_source CASCADE; -TRUNCATE TABLE cds.antibody_sequence CASCADE; -TRUNCATE TABLE cds.antibody_class CASCADE; -TRUNCATE TABLE cds.sequence CASCADE; - -ALTER TABLE cds.sequence_germline ADD CONSTRAINT FK_cds_sequence_germline_allele FOREIGN KEY (allele) REFERENCES cds.allele_sequence (allele); -CREATE INDEX IX_cds_sequence_germline_allele ON cds.sequence_germline (allele); - -ALTER TABLE cds.alignment ADD CONSTRAINT FK_cds_alignment_v_call FOREIGN KEY (v_call) REFERENCES cds.allele_sequence (allele); -CREATE INDEX IX_cds_alignment_v_call ON cds.alignment (v_call); - -ALTER TABLE cds.alignment ADD CONSTRAINT FK_cds_alignment_d_call FOREIGN KEY (d_call) REFERENCES cds.allele_sequence (allele); -CREATE INDEX IX_cds_alignment_d_call ON cds.alignment (d_call); - -ALTER TABLE cds.alignment ADD CONSTRAINT FK_cds_alignment_j_call FOREIGN KEY (j_call) REFERENCES cds.allele_sequence (allele); -CREATE INDEX IX_cds_alignment_j_call ON cds.alignment (j_call); - -ALTER TABLE cds.sequence_germline ADD CONSTRAINT FK_cds_sequence_germline_run_application FOREIGN KEY (run_application) REFERENCES cds.alignment_run (run_application); -CREATE INDEX IX_cds_sequence_germline_run_application ON cds.sequence_germline (run_application); - -ALTER TABLE cds.alignment ADD CONSTRAINT FK_cds_alignment_run_application FOREIGN KEY (run_application) REFERENCES cds.alignment_run (run_application); -CREATE INDEX IX_cds_alignment_run_application ON cds.alignment (run_application); - -ALTER TABLE cds.sequence_header ADD CONSTRAINT FK_cds_sequence_header_source_id FOREIGN KEY (source_id) REFERENCES cds.header_source (source_id); -CREATE INDEX IX_cds_sequence_header_source_id ON cds.sequence_header(source_id); - -ALTER TABLE cds.antibody_sequence ADD CONSTRAINT FK_cds_antibody_sequence_mab_id FOREIGN KEY (container, mab_id) REFERENCES cds.mabmetadata (container, mab_id); -CREATE INDEX IX_cds_antibody_sequence_mab_id ON cds.antibody_sequence (container, mab_id); - -ALTER TABLE cds.mabmetadata ADD CONSTRAINT FK_cds_mabmetadata_mab_class_id FOREIGN KEY (mab_class_id) REFERENCES cds.antibody_class (mab_class_id); -CREATE INDEX IX_cds_mabmetadata_mab_class_id ON cds.mabmetadata (mab_class_id); - -ALTER TABLE cds.import_MAbMix DROP CONSTRAINT import_MAbMix_mab_id_fkey; -DROP TABLE cds.import_mabmetadata; \ No newline at end of file