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Commit 7739bae

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author
Scott Christley
committed
update SQL DDL
1 parent 6d457e2 commit 7739bae

3 files changed

Lines changed: 23 additions & 13 deletions

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‎project/sqlddl/ak_postgres_schema.sql‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1479,19 +1479,19 @@ CREATE TABLE "AIRRSequencingAssay" (
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sequencing_facility TEXT,
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sequencing_run_date TIMESTAMP WITHOUT TIME ZONE,
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sequencing_kit TEXT,
1482+
sequencing_files TEXT,
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specimen TEXT,
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type TEXT,
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assay_type "AssayTypeOntology",
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has_specified_output TEXT,
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name TEXT,
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description TEXT,
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akc_id TEXT NOT NULL,
1489-
sequencing_files_id INTEGER,
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PRIMARY KEY (akc_id),
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FOREIGN KEY(sequencing_files) REFERENCES "AIRRSequencingData" (akc_id),
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FOREIGN KEY(specimen) REFERENCES "Specimen" (akc_id),
1492-
FOREIGN KEY(has_specified_output) REFERENCES "AKDataItem" (akc_id),
1493-
FOREIGN KEY(sequencing_files_id) REFERENCES "SequencingData" (id)
1494-
);COMMENT ON TABLE "AIRRSequencingAssay" IS 'None';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_run_id IS 'ID of sequencing run assigned by the sequencing facility';COMMENT ON COLUMN "AIRRSequencingAssay".total_reads_passing_qc_filter IS 'Number of usable reads for analysis';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_platform IS 'Designation of sequencing instrument used';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_facility IS 'Name and address of sequencing facility';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_run_date IS 'Date of sequencing run';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_kit IS 'Name, manufacturer, order and lot numbers of sequencing kit';COMMENT ON COLUMN "AIRRSequencingAssay".specimen IS 'The specimen that was input for an assay';COMMENT ON COLUMN "AIRRSequencingAssay".assay_type IS 'The specific type of an assay';COMMENT ON COLUMN "AIRRSequencingAssay".has_specified_output IS 'output data item';COMMENT ON COLUMN "AIRRSequencingAssay".name IS 'A human-readable name for a thing';COMMENT ON COLUMN "AIRRSequencingAssay".description IS 'A human-readable description for a thing';COMMENT ON COLUMN "AIRRSequencingAssay".akc_id IS 'A unique identifier for a thing in the AKC.';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_files_id IS 'Set of sequencing files produced by the sequencing run';
1493+
FOREIGN KEY(has_specified_output) REFERENCES "AKDataItem" (akc_id)
1494+
);COMMENT ON TABLE "AIRRSequencingAssay" IS 'None';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_run_id IS 'ID of sequencing run assigned by the sequencing facility';COMMENT ON COLUMN "AIRRSequencingAssay".total_reads_passing_qc_filter IS 'Number of usable reads for analysis';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_platform IS 'Designation of sequencing instrument used';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_facility IS 'Name and address of sequencing facility';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_run_date IS 'Date of sequencing run';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_kit IS 'Name, manufacturer, order and lot numbers of sequencing kit';COMMENT ON COLUMN "AIRRSequencingAssay".sequencing_files IS 'Set of sequencing files produced by the sequencing run';COMMENT ON COLUMN "AIRRSequencingAssay".specimen IS 'The specimen that was input for an assay';COMMENT ON COLUMN "AIRRSequencingAssay".assay_type IS 'The specific type of an assay';COMMENT ON COLUMN "AIRRSequencingAssay".has_specified_output IS 'output data item';COMMENT ON COLUMN "AIRRSequencingAssay".name IS 'A human-readable name for a thing';COMMENT ON COLUMN "AIRRSequencingAssay".description IS 'A human-readable description for a thing';COMMENT ON COLUMN "AIRRSequencingAssay".akc_id IS 'A unique identifier for a thing in the AKC.';
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CREATE TABLE "TCellReceptorEpitopeBindingAssay" (
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epitope TEXT,
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specimen TEXT,

‎project/sqlddl/ak_schema.sql‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -170,14 +170,14 @@
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-- * Slot: sequencing_facility Description: Name and address of sequencing facility
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-- * Slot: sequencing_run_date Description: Date of sequencing run
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-- * Slot: sequencing_kit Description: Name, manufacturer, order and lot numbers of sequencing kit
173+
-- * Slot: sequencing_files Description: Set of sequencing files produced by the sequencing run
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-- * Slot: specimen Description: The specimen that was input for an assay
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-- * Slot: type Description:
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-- * Slot: assay_type Description: The specific type of an assay
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-- * Slot: has_specified_output Description: output data item
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-- * Slot: name Description: A human-readable name for a thing
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-- * Slot: description Description: A human-readable description for a thing
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-- * Slot: akc_id Description: A unique identifier for a thing in the AKC.
180-
-- * Slot: sequencing_files_id Description: Set of sequencing files produced by the sequencing run
181181
-- # Class: "TCellReceptorEpitopeBindingAssay" Description: ""
182182
-- * Slot: epitope Description: The epitope being measured
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-- * Slot: specimen Description: The specimen that was input for an assay
@@ -2599,18 +2599,18 @@ CREATE TABLE "AIRRSequencingAssay" (
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sequencing_facility TEXT,
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sequencing_run_date TIMESTAMP WITHOUT TIME ZONE,
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sequencing_kit TEXT,
2602+
sequencing_files TEXT,
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specimen TEXT,
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type TEXT,
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assay_type VARCHAR,
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has_specified_output TEXT,
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name TEXT,
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description TEXT,
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akc_id TEXT NOT NULL,
2609-
sequencing_files_id INTEGER,
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PRIMARY KEY (akc_id),
2611+
FOREIGN KEY(sequencing_files) REFERENCES "AIRRSequencingData" (akc_id),
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FOREIGN KEY(specimen) REFERENCES "Specimen" (akc_id),
2612-
FOREIGN KEY(has_specified_output) REFERENCES "AKDataItem" (akc_id),
2613-
FOREIGN KEY(sequencing_files_id) REFERENCES "SequencingData" (id)
2613+
FOREIGN KEY(has_specified_output) REFERENCES "AKDataItem" (akc_id)
26142614
);
26152615
CREATE TABLE "TCellReceptorEpitopeBindingAssay" (
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epitope TEXT,

‎project/sqlddl/ak_schema_modify.sql‎

Lines changed: 15 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1211,6 +1211,16 @@ CREATE TABLE "AKDataSet" (
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PRIMARY KEY (akc_id)
12121212
);
12131213
CREATE TABLE "SequenceData" (
1214+
sequencing_data_id TEXT,
1215+
file_type VARCHAR(5),
1216+
filename TEXT,
1217+
read_direction VARCHAR(7),
1218+
read_length INTEGER,
1219+
paired_filename TEXT,
1220+
paired_read_direction VARCHAR(7),
1221+
paired_read_length INTEGER,
1222+
index_filename TEXT,
1223+
index_length INTEGER,
12141224
type TEXT,
12151225
akc_id TEXT NOT NULL,
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PRIMARY KEY (akc_id)
@@ -2582,7 +2592,7 @@ CREATE TABLE "Assay" (
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sequencing_facility TEXT,
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sequencing_run_date TIMESTAMP WITHOUT TIME ZONE,
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sequencing_kit TEXT,
2585-
sequencing_files_id INTEGER,
2595+
sequencing_files TEXT,
25862596

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epitope TEXT,
25882598
measurement_category VARCHAR(21),
@@ -2597,7 +2607,7 @@ CREATE TABLE "Assay" (
25972607
PRIMARY KEY (akc_id),
25982608
FOREIGN KEY(specimen) REFERENCES "Specimen" (akc_id),
25992609
FOREIGN KEY(has_specified_output) REFERENCES "AKDataItem" (akc_id),
2600-
FOREIGN KEY(sequencing_files_id) REFERENCES "SequencingData" (id),
2610+
FOREIGN KEY(sequencing_files) REFERENCES "SequenceData" (akc_id),
26012611
FOREIGN KEY(epitope) REFERENCES "Epitope" (akc_id)
26022612
);
26032613
CREATE TABLE "AIRRSequencingAssay" (
@@ -2608,18 +2618,18 @@ CREATE TABLE "AIRRSequencingAssay" (
26082618
sequencing_facility TEXT,
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sequencing_run_date TIMESTAMP WITHOUT TIME ZONE,
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sequencing_kit TEXT,
2621+
sequencing_files TEXT,
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specimen TEXT,
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type TEXT,
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assay_type VARCHAR,
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has_specified_output TEXT,
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name TEXT,
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description TEXT,
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akc_id TEXT NOT NULL,
2618-
sequencing_files_id INTEGER,
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PRIMARY KEY (akc_id),
2630+
FOREIGN KEY(sequencing_files) REFERENCES "AIRRSequencingData" (akc_id),
26202631
FOREIGN KEY(specimen) REFERENCES "Specimen" (akc_id),
2621-
FOREIGN KEY(has_specified_output) REFERENCES "AKDataItem" (akc_id),
2622-
FOREIGN KEY(sequencing_files_id) REFERENCES "SequencingData" (id)
2632+
FOREIGN KEY(has_specified_output) REFERENCES "AKDataItem" (akc_id)
26232633
);
26242634
CREATE TABLE "TCellReceptorEpitopeBindingAssay" (
26252635
epitope TEXT,

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