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authorFrederick Muriuki Muriithi2023-04-04 12:13:11 +0300
committerFrederick Muriuki Muriithi2023-04-04 12:13:11 +0300
commit02e5c81e5d1281b66aa14ce47563997e845cea95 (patch)
tree4cb640d62c020979b90f0a3caf12ece73d94df25 /migrations/auth
parent98e9726405df3cce81356534335259a446b0c458 (diff)
downloadgenenetwork3-02e5c81e5d1281b66aa14ce47563997e845cea95.tar.gz
Add tables to link genotype data
Diffstat (limited to 'migrations/auth')
-rw-r--r--migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py2
-rw-r--r--migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py29
-rw-r--r--migrations/auth/20230404_02_la33P-create-genotype-resources-table.py22
3 files changed, 52 insertions, 1 deletions
diff --git a/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py b/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
index 6bd8782..d0ff541 100644
--- a/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
+++ b/migrations/auth/20230322_02_Ll854-create-phenotype-resources-table.py
@@ -16,7 +16,7 @@ steps = [
data_link_id TEXT NOT NULL,
PRIMARY KEY(resource_id, data_link_id),
UNIQUE (data_link_id) -- ensure data is linked to only one resource
- )
+ ) WITHOUT ROWID
""",
"DROP TABLE IF EXISTS phenotype_resources")
]
diff --git a/migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py b/migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py
new file mode 100644
index 0000000..02e8718
--- /dev/null
+++ b/migrations/auth/20230404_01_VKxXg-create-linked-genotype-data-table.py
@@ -0,0 +1,29 @@
+"""
+Create linked genotype data table
+"""
+
+from yoyo import step
+
+__depends__ = {'20230322_02_Ll854-create-phenotype-resources-table'}
+
+steps = [
+ step(
+ """
+ CREATE TABLE IF NOT EXISTS linked_genotype_data
+ -- Link genotype data in MariaDB to user groups in auth system
+ (
+ data_link_id TEXT NOT NULL PRIMARY KEY, -- A new ID for the auth system
+ group_id TEXT NOT NULL, -- The user group the data is linked to
+ SpeciesId TEXT NOT NULL, -- The species in MariaDB
+ InbredSetId TEXT NOT NULL, -- The traits group in MariaDB
+ GenoFreezeId TEXT NOT NULL, -- The dataset Id in MariaDB
+ dataset_name TEXT, -- dataset Name in MariaDB
+ dataset_fullname, -- dataset FullName in MariaDB
+ dataset_shortname, -- dataset ShortName in MariaDB
+ FOREIGN KEY (group_id)
+ REFERENCES groups(group_id) ON UPDATE CASCADE ON DELETE RESTRICT
+ UNIQUE (SpeciesId, InbredSetId, GenoFreezeId)
+ ) WITHOUT ROWID
+ """,
+ "DROP TABLE IF EXISTS linked_genotype_data")
+]
diff --git a/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py b/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py
new file mode 100644
index 0000000..2d3a3bc
--- /dev/null
+++ b/migrations/auth/20230404_02_la33P-create-genotype-resources-table.py
@@ -0,0 +1,22 @@
+"""
+Create genotype resources table
+"""
+
+from yoyo import step
+
+__depends__ = {'20230404_01_VKxXg-create-linked-genotype-data-table'}
+
+steps = [
+ step(
+ """
+ CREATE TABLE IF NOT EXISTS genotype_resources
+ -- Link genotype data to specific resource
+ (
+ resource_id TEXT NOT NULL, -- A resource can have multiple items
+ data_link_id TEXT NOT NULL,
+ PRIMARY KEY (resource_id, data_link_id),
+ UNIQUE (data_link_id) -- ensure data is linked to single resource
+ ) WITHOUT ROWID
+ """,
+ "DROP TABLE IF EXISTS genotype_resources")
+]