Repository consolidation, part 3

pepdb/.gitattributes

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+# Convert text files to OS line-endings on checkout, and LF on check-in
+*               text=auto !eol
+
+# Text files to convert
+*.css           text diff=css
+*.htm           text diff=html
+*.html          text diff=html
+*.java          text diff=java
+*.js            text
+*.json          text
+*.jsp           text
+*.jspf          text
+*.jspx          text
+*.properties    text
+*.py            text diff=python
+*.sql           text
+*.tld           text
+*.ts            text
+*.txt           text
+*.xml           text
+*.yml           text
+
+# Keep unix endings
+*.bash          text eol=lf
+*.sh            text eol=lf
+
+# Keep Windows endings
+*.bat           text eol=crlf
+*.cmd           text eol=crlf
+
+# Known binary files -- Don't change (binary is a macro for -text -diff)
+*.bin           binary
+*.class         binary
+*.dll           binary
+*.ear           binary
+*.exe           binary
+*.gif           binary
+*.gz            binary
+*.ico           binary
+*.jar           binary
+*.jpg           binary
+*.jpeg          binary
+*.png           binary
+*.so            binary
+*.tar           binary
+*.war           binary
+*.zip           binary

pepdb/build.gradle

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+plugins {
+    id 'org.labkey.build.module'
+}

pepdb/module.properties

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+ModuleClass: org.scharp.atlas.pepdb.PepDBModule
+ManageVersion: false

pepdb/resources/schemas/dbscripts/postgresql/pepdb-0.00-0.02.sql

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+/*
+ * Copyright (c) 2003-2005 Fred Hutchinson Cancer Research Center
+ *
+ * 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.
+ */
+
+BEGIN;
+
+CREATE SCHEMA pepdb;
+
+CREATE TABLE pepdb.clade (
+    clade_id serial NOT NULL,
+    clade_desc text,
+
+    CONSTRAINT PK_clade PRIMARY KEY (clade_id)
+);
+
+CREATE TABLE pepdb.pathogen (
+    pathogen_id serial NOT NULL,
+    pathogen_desc text,
+
+    CONSTRAINT PK_pathogen PRIMARY KEY (pathogen_id)
+);
+
+CREATE TABLE pepdb.group_type (
+    group_type_id serial NOT NULL,
+    group_type_desc text,
+
+    CONSTRAINT PK_group_type PRIMARY KEY (group_type_id)
+);
+
+CREATE TABLE pepdb.pep_align_ref (
+    pep_align_ref_id serial NOT NULL,
+    pep_align_ref_desc text,
+
+    CONSTRAINT PK_pep_align_ref PRIMARY KEY (pep_align_ref_id)
+);
+
+CREATE TABLE pepdb.peptide_group (
+    _ts TIMESTAMP DEFAULT now(),
+    CreatedBy USERID,
+    Created TIMESTAMP,
+    ModifiedBy USERID,
+    Modified TIMESTAMP,
+
+    peptide_group_id serial NOT NULL,
+    peptide_group_name text NOT NULL UNIQUE,
+    pathogen_id integer,
+    seq_ref text,
+    clade_id integer,
+    pep_align_ref_id integer,
+    group_type_id integer,
+
+    CONSTRAINT PK_peptide_group PRIMARY KEY (peptide_group_id),
+    CONSTRAINT FK_peptide_group1 FOREIGN KEY(pathogen_id) REFERENCES pepdb.pathogen(pathogen_id),
+    CONSTRAINT FK_peptide_group2 FOREIGN KEY(clade_id) REFERENCES pepdb.clade(clade_id),
+    CONSTRAINT FK_peptide_group3 FOREIGN KEY(group_type_id) REFERENCES pepdb.group_type(group_type_id),
+    CONSTRAINT FK_peptide_group4 FOREIGN KEY(pep_align_ref_id) REFERENCES pepdb.pep_align_ref(pep_align_ref_id)
+);
+
+CREATE TABLE pepdb.protein_category (
+    protein_cat_id serial NOT NULL,
+    protein_cat_desc text,
+
+    CONSTRAINT PK_protein_category PRIMARY KEY (protein_cat_id)
+);
+
+CREATE TABLE pepdb.optimal_epitope_list(
+    optimal_epitope_list_id serial NOT NULL,
+    optimal_epitope_list_desc text,
+
+    CONSTRAINT PK_optimal_epitope_list PRIMARY KEY (optimal_epitope_list_id)
+);
+
+
+CREATE TABLE pepdb.peptides (
+    _ts TIMESTAMP DEFAULT now(),
+    CreatedBy USERID,
+    Created TIMESTAMP,
+    ModifiedBy USERID,
+    Modified TIMESTAMP,
+
+    peptide_id serial NOT NULL,    
+    peptide_sequence text NOT NULL UNIQUE,    
+    protein_cat_id integer,
+    amino_acid_start_pos integer,
+    amino_acid_end_pos integer,
+    sequence_length integer,
+    child boolean,
+    parent boolean DEFAULT false NOT NULL,
+    src_file_name text,
+    storage_location text,
+    optimal_epitope_list_id integer,
+    hla_restriction text,
+
+    CONSTRAINT PK_peptides PRIMARY KEY (peptide_id),
+    CONSTRAINT FK_peptides1 FOREIGN KEY(protein_cat_id) REFERENCES pepdb.protein_category(protein_cat_id),
+    CONSTRAINT FK_peptides2 FOREIGN KEY(optimal_epitope_list_id) REFERENCES pepdb.optimal_epitope_list(optimal_epitope_list_id)
+);
+
+
+CREATE TABLE pepdb.peptide_group_assignment (
+    _ts TIMESTAMP DEFAULT now(),
+    CreatedBy USERID,
+    Created TIMESTAMP,
+    ModifiedBy USERID,
+    Modified TIMESTAMP,
+
+    peptide_group_assignment_id serial NOT NULL UNIQUE,
+    peptide_id integer NOT NULL,
+    peptide_group_id integer NOT NULL,
+    peptide_id_in_group integer,
+    frequency_number float,
+    frequency_number_date date,
+    in_current_file boolean DEFAULT false,
+
+    CONSTRAINT PK_peptide_group_assignment PRIMARY KEY (peptide_id,peptide_group_id),
+    CONSTRAINT FK_peptide_group_assignment1 FOREIGN KEY(peptide_id) REFERENCES pepdb.peptides(peptide_id),
+    CONSTRAINT FK_peptide_group_assignment2 FOREIGN KEY(peptide_group_id) REFERENCES pepdb.peptide_group(peptide_group_id)
+);
+
+CREATE TABLE pepdb.parent (
+    _ts TIMESTAMP DEFAULT now(),
+    CreatedBy USERID,
+    Created TIMESTAMP,
+    ModifiedBy USERID,
+    Modified TIMESTAMP,
+
+    peptide_id integer NOT NULL,
+    linked_parent integer NOT NULL,
+
+    CONSTRAINT PK_parent PRIMARY KEY (peptide_id,linked_parent),
+    CONSTRAINT FK_parent1 FOREIGN KEY(peptide_id) REFERENCES pepdb.peptides(peptide_id),
+    CONSTRAINT FK_parent2 FOREIGN KEY(linked_parent) REFERENCES pepdb.peptides(peptide_id)    
+);
+
+CREATE TABLE pepdb.pool_type (
+    pool_type_id serial NOT NULL,
+    pool_type_desc text,
+
+    CONSTRAINT PK_pool_type PRIMARY KEY (pool_type_id)
+);
+
+CREATE TABLE pepdb.peptide_pool (
+    _ts TIMESTAMP DEFAULT now(),
+    CreatedBy USERID,
+    Created TIMESTAMP,
+    ModifiedBy USERID,
+    Modified TIMESTAMP,
+
+    peptide_pool_id serial NOT NULL,
+    peptide_pool_name text,
+    pool_type_id integer,
+    comment text,
+
+    CONSTRAINT PK_peptide_pool PRIMARY KEY (peptide_pool_id),
+    CONSTRAINT FK_peptide_pool1 FOREIGN KEY(pool_type_id) REFERENCES pepdb.pool_type(pool_type_id)
+);
+
+
+CREATE TABLE pepdb.peptide_pool_assignment (
+    _ts TIMESTAMP DEFAULT now(),
+    CreatedBy USERID,
+    Created TIMESTAMP,
+    ModifiedBy USERID,
+    Modified TIMESTAMP,
+
+    peptide_pool_assignment_id serial NOT NULL UNIQUE,
+    peptide_pool_id integer NOT NULL,
+    peptide_id integer NOT NULL,
+
+    CONSTRAINT PK_peptide_pool_assignment PRIMARY KEY (peptide_pool_id,peptide_id),
+    CONSTRAINT FK_peptide_pool_assignment1 FOREIGN KEY(peptide_pool_id) REFERENCES pepdb.peptide_pool(peptide_pool_id),
+    CONSTRAINT FK_peptide_pool_assignment2 FOREIGN KEY(peptide_id) REFERENCES pepdb.peptides(peptide_id)
+);
+
+CREATE VIEW pepdb.parent_child_details AS
+select par.peptide_id AS child_id,pchild.peptide_sequence AS child_sequence,
+pchild.protein_cat_id AS child_protein,pchild.sequence_length AS child_seq_length,
+pchild.amino_acid_start_pos AS child_AAStart,pchild.amino_acid_end_pos AS child_AAEnd,
+pchild.optimal_epitope_list_id AS child_optimal_epitope_list_id,pchild.hla_restriction AS child_hla_restriction,
+par.linked_parent AS parent_id,pparent.peptide_sequence AS parent_sequence,
+pparent.protein_cat_id AS parent_protein,pparent.sequence_length AS parent_seq_length,
+pparent.amino_acid_start_pos AS parent_AAStart,pparent.amino_acid_end_pos AS parent_AAEnd 
+from pepdb.parent par LEFT JOIN pepdb.peptides pchild ON (par.peptide_id = pchild.peptide_id)
+LEFT JOIN pepdb.peptides pparent ON(par.linked_parent = pparent.peptide_id);
+
+CREATE VIEW pepdb.group_peptides AS
+SELECT src.peptide_id, src.peptide_group_id, src.peptide_id_in_group,
+    pgroup.peptide_group_name,pgroup.pathogen_id,
+    p.peptide_sequence,p.protein_cat_id,
+    p.sequence_length,p.amino_acid_start_pos,p.amino_acid_end_pos,
+     p.child, p.parent,p.optimal_epitope_list_id,p.hla_restriction,
+     src.frequency_number,src.frequency_number_date,src.in_current_file
+FROM ((pepdb.peptide_group_assignment src LEFT JOIN pepdb.peptide_group pgroup ON ((src.peptide_group_id
+    = pgroup.peptide_group_id))) LEFT JOIN pepdb.peptides p ON ((src.peptide_id =
+    p.peptide_id)));
+
+CREATE VIEW pepdb.pool_peptides AS
+SELECT src.peptide_id, p.peptide_sequence, src.peptide_pool_id, pp.pool_type_id, pp.peptide_pool_name, pt.pool_type_desc
+FROM
+pepdb.peptides p,
+pepdb.peptide_pool_assignment src
+LEFT JOIN pepdb.peptide_pool pp
+LEFT JOIN pepdb.pool_type pt ON(pp.pool_type_id = pt.pool_type_id) ON (src.peptide_pool_id = pp.peptide_pool_id)
+WHERE (src.peptide_id = p.peptide_id);
+
+SELECT pg_catalog.setval(pg_catalog.pg_get_serial_sequence('pepdb.peptides', 'peptide_id'), 500000, true);
+SELECT pg_catalog.setval(pg_catalog.pg_get_serial_sequence('pepdb.peptide_pool', 'peptide_pool_id'), 500000, true);
+
+COMMIT;
+
+
+
+
+
+
+