====== SEQ-DB ======

SEQ model schema : {{:seqdb.pdf|}}

 ===== List of tables =====

  *[[#bio_sequence|bio_sequence]]
  *[[#parsing_rule|parsing_rule]]
  *[[#repository|repository]]
  *[[#repository_identifier|repository_identifier]]
  *[[#se_db|se_db]]
  *[[#se_db_identifier|se_db_identifier]]
  *[[#se_db_instance|se_db_instance]]
  
  
=====bio_sequence=====
=== (Physical Name: bio_sequence) ===
Proteine sequence.
^Logical Column Name ^Physical Column Name  ^Type  ^PK  ^Nullable ^Remarks ^
| id (PK)  | id | BIGINT | PK | NOT NULL | Auto incremented Id. |
| sequence   | sequence | CLOB |  |  | Protein sequence (AA or DNA alphabet) normalized to Upper Case. |
| hash   | hash | VARCHAR(64) |  |  | SHA-256 hash of normalized (Upper Case) sequence (as ASCII / ISO 8859-1 byte array). |

**id (PK)  (id)**
Auto incremented Id 

**sequence   (sequence)**
Protein sequence (AA or DNA alphabet) normalized to Upper Case.
Unicity constraint enforced by unicity on "hash" (SHA-256) column. 

**hash   (hash)**
SHA-256 hash of normalized (Upper Case) sequence (as ASCII / ISO 8859-1 byte array).
Hash must be UNIQUE . 


===Referenced By===
  *  [[#se_db_identifier|se_db_identifier]] referencing (bio_sequence_id)


  
=====parsing_rule=====
=== (Physical Name: parsing_rule) ===

^Logical Column Name ^Physical Column Name  ^Type  ^PK  ^Nullable ^Remarks ^
| id (PK)  | id | BIGINT | PK | NOT NULL | |
| name   | name | VARCHAR(255) |  |  | UNIQUE . |
| release   | release | VARCHAR(255) |  |  | Rule to parse SEDbInstance version string from source fileName. |
| se_db_identifier   | se_db_identifier | VARCHAR(255) |  |  | |
| repository_identifier   | repository_identifier | VARCHAR(255) |  |  | |
| repo_id_from_se_id   | repo_id_from_se_id | VARCHAR(255) |  |  | |

**id (PK)  (id)**
 

**name   (name)**
UNIQUE . 

**release   (release)**
Rule to parse SEDbInstance version string from source fileName. 

**se_db_identifier   (se_db_identifier)**
 

**repository_identifier   (repository_identifier)**
 

**repo_id_from_se_id   (repo_id_from_se_id)**
 


===Referenced By===
  *  [[#se_db|se_db]] referencing (parsing_rule_id)


  
=====repository=====
=== (Physical Name: repository) ===
Standard Repository.
^Logical Column Name ^Physical Column Name  ^Type  ^PK  ^Nullable ^Remarks ^
| id (PK)  | id | BIGINT | PK | NOT NULL | |
| name   | name | VARCHAR(255) |  |  | UNIQUE . |
| url   | url | CLOB |  |  | |

**id (PK)  (id)**
 

**name   (name)**
UNIQUE . 

**url   (url)**
 


===Referenced By===
  *  [[#se_db|se_db]] referencing (repository_id)
  *  [[#repository_identifier|repository_identifier]] referencing (repository_id)


  
=====repository_identifier=====
=== (Physical Name: repository_identifier) ===

^Logical Column Name ^Physical Column Name  ^Type  ^PK  ^Nullable ^Remarks ^
| id (PK)  | id | BIGINT | PK | NOT NULL | |
| value   | value | VARCHAR(255) |  |  | UNIQUE for given repository. |
| repository_id   [[#repository|(FK)]]  | repository_id | BIGINT |  |  | |

**id (PK)  (id)**
 

**value   (value)**
UNIQUE for given repository. 

**repository_id   [[#repository|(FK)]]  (repository_id)**
 


===References===
  *  [[#repository|repository]] through (id)
===Referenced By===
  *  [[#se_db_identifier|se_db_identifier]] referencing (repository_identifier_id)


  
=====se_db=====
=== (Physical Name: se_db) ===
Search Engine Db.
^Logical Column Name ^Physical Column Name  ^Type  ^PK  ^Nullable ^Remarks ^
| id (PK)  | id | BIGINT | PK | NOT NULL | |
| name   | name | VARCHAR(255) |  |  | UNIQUE . |
| alphabet   | alphabet | VARCHAR(3) |  |  | Alphabet used for sequences (AA, DNA. |
| parsing_rule_id   [[#parsing_rule|(FK)]]  | parsing_rule_id | BIGINT |  |  | |
| repository_id   [[#repository|(FK)]]  | repository_id | BIGINT |  |  | |

**id (PK)  (id)**
 

**name   (name)**
UNIQUE . 

**alphabet   (alphabet)**
Alphabet used for sequences (AA, DNA...) 

**parsing_rule_id   [[#parsing_rule|(FK)]]  (parsing_rule_id)**
 

**repository_id   [[#repository|(FK)]]  (repository_id)**
 


===References===
  *  [[#repository|repository]] through (id)
  *  [[#parsing_rule|parsing_rule]] through (id)
===Referenced By===
  *  [[#se_db_instance|se_db_instance]] referencing (se_db_id)


  
=====se_db_identifier=====
=== (Physical Name: se_db_identifier) ===

^Logical Column Name ^Physical Column Name  ^Type  ^PK  ^Nullable ^Remarks ^
| id (PK)  | id | BIGINT | PK | NOT NULL | |
| value   | value | VARCHAR(255) |  |  | UNIQUE for given se_db_instance. |
| inferred   | inferred | BOOLEAN |  |  | True if this se_db_identifier is inferred by sequence repository service (SE Db source cannot be loaded or protein description does not match). |
| se_db_instance_id   [[#se_db_instance|(FK)]]  | se_db_instance_id | BIGINT |  |  | |
| bio_sequence_id   [[#bio_sequence|(FK)]]  | bio_sequence_id | BIGINT |  |  | |
| repository_identifier_id   [[#repository_identifier|(FK)]]  | repository_identifier_id | BIGINT |  |  | |

**id (PK)  (id)**
 

**value   (value)**
UNIQUE for given se_db_instance. 

**inferred   (inferred)**
True if this se_db_identifier is inferred by sequence repository service (SE Db source cannot be loaded or protein description does not match). 

**se_db_instance_id   [[#se_db_instance|(FK)]]  (se_db_instance_id)**
 

**bio_sequence_id   [[#bio_sequence|(FK)]]  (bio_sequence_id)**
 

**repository_identifier_id   [[#repository_identifier|(FK)]]  (repository_identifier_id)**
 


===References===
  *  [[#bio_sequence|bio_sequence]] through (id)
  *  [[#repository_identifier|repository_identifier]] through (id)
  *  [[#se_db_instance|se_db_instance]] through (id)


  
=====se_db_instance=====
=== (Physical Name: se_db_instance) ===
Unique version of a SE Db.
^Logical Column Name ^Physical Column Name  ^Type  ^PK  ^Nullable ^Remarks ^
| id (PK)  | id | BIGINT | PK | NOT NULL | |
| release   | release | VARCHAR(50) |  |  | Version string, if date must be yyyyMMdd . |
| source_path   | source_path | CLOB |  |  | Can be the pathname of a FASTA file relative to Search Engine file system. |
| source_last_modified_time   | source_last_modified_time | TIMESTAMP |  |  | FASTA file last modified date or SEDbInstance creation timestamp. |
| se_db_id   [[#se_db|(FK)]]  | se_db_id | BIGINT |  |  | |

**id (PK)  (id)**
 

**release   (release)**
Version string, if date must be yyyyMMdd .
UNIQUE for given seq_db_id . 

**source_path   (source_path)**
Can be the pathname of a FASTA file relative to Search Engine file system. 

**source_last_modified_time   (source_last_modified_time)**
FASTA file last modified date or SEDbInstance creation timestamp. 

**se_db_id   [[#se_db|(FK)]]  (se_db_id)**
 


===References===
  *  [[#se_db|se_db]] through (id)
===Referenced By===
  *  [[#se_db_identifier|se_db_identifier]] referencing (se_db_instance_id)