Db status check (#124)

* Add `pyard-status` command to check the status of all tables in the databases. This will help to see if there are missing tables and also to compare number of data between versions.

```
-------------------------------------------
IMGT DB Version: 3450
-------------------------------------------
|Table Name          |Rows                |
|-----------------------------------------|
|dup_g               |                  50|
|dup_lg              |                   2|
|dup_lgx             |                   2|
|g_group             |               10841|
|lg_group            |               10841|
|lgx_group           |               10841|
|exon_group          |                9724|
|p_group             |                9724|
|alleles             |               33525|
|xx_codes            |                1690|
|who_alleles         |               31552|
|who_group           |               31930|
-------------------------------------------
```

The missing tables are noted and the database can be rebuilt with `pyard-import --re-install`

-------------------------------------------
IMGT DB Version: 3290
-------------------------------------------
|Table Name          |Rows                |
|-----------------------------------------|
|dup_g               |                  17|
|dup_lg              |                   0|
|dup_lgx             |                   0|
|g_group             |                2786|
|lg_group            |                2786|
|lgx_group           |                2786|
MISSING: exon_group table
MISSING: p_group table
|alleles             |               18451|
|xx_codes            |                 946|
MISSING: who_alleles table
MISSING: who_group table
-------------------------------------------
```

* Bump version: 0.6.8 → 0.6.9

Author: pbashyal-nmdp

README.rst

@@ -135,3 +135,7 @@ Command Line Tools
 
     $ pyard -v 3290 --gl 'A1' -r lgx
     A*01:01/A*01:02/A*01:03/A*01:06/A*01:07/A*01:08/A*01:09/A*01:10/A*01:12/ ...
+
+    # Show the status of all py-ard databases
+    $ pyard-status
+

pyard/__init__.py

@@ -24,4 +24,4 @@
 from .pyard import ARD
 
 __author__ = """NMDP Bioinformatics"""
-__version__ = '0.6.8'
+__version__ = '0.6.9'

pyard/db.py

@@ -90,6 +90,21 @@ def tables_exist(connection: sqlite3.Connection, table_names: List[str]):
     return all([table_exists(connection, table_name) for table_name in table_names])
 
 
+def count_rows(connection: sqlite3.Connection, table_name: str) -> int:
+    """
+    Count number of rows in the table.
+
+    :param connection: db connection of type sqlite.Connection
+    :param table_name: table in the sqlite db
+    :return: bool indicating whether table_name exists as a table
+    """
+    query = f"SELECT count(*) from '{table_name}'"
+    cursor = connection.execute(query)
+    result = cursor.fetchone()
+    cursor.close()
+    return result[0]
+
+
 def mac_code_to_alleles(connection: sqlite3.Connection, code: str) -> List[str]:
     """
     Look up the MAC code in the database and return corresponding list

scripts/pyard-status

@@ -0,0 +1,81 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#    py-ard
+#    Copyright (c) 2020 Be The Match operated by National Marrow Donor Program. All Rights Reserved.
+#
+#    This library is free software; you can redistribute it and/or modify it
+#    under the terms of the GNU Lesser General Public License as published
+#    by the Free Software Foundation; either version 3 of the License, or (at
+#    your option) any later version.
+#
+#    This library is distributed in the hope that it will be useful, but WITHOUT
+#    ANY WARRANTY; with out even the implied warranty of MERCHANTABILITY or
+#    FITNESS FOR A PARTICULAR PURPOSE.  See the GNU Lesser General Public
+#    License for more details.
+#
+#    You should have received a copy of the GNU Lesser General Public License
+#    along with this library;  if not, write to the Free Software Foundation,
+#    Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
+#
+#    > http://www.fsf.org/licensing/licenses/lgpl.html
+#    > http://www.opensource.org/licenses/lgpl-license.php
+#
+import argparse
+import os
+import pathlib
+import re
+
+from pyard import db, data_repository
+
+
+def get_data_dir(data_dir):
+    if data_dir:
+        path = pathlib.Path(data_dir)
+        if not path.exists() or not path.is_dir():
+            raise RuntimeError(f"{data_dir} is not a valid directory")
+        data_dir = path
+    else:
+        data_dir = db.get_pyard_db_install_directory()
+    return data_dir
+
+
+if __name__ == '__main__':
+    parser = argparse.ArgumentParser(
+        usage="""
+        [--data-dir <directory for db file>]\n
+        """,
+        description="""
+        py-ard tool to provide a status report for reference SQLite databases.
+        """
+    )
+    parser.add_argument(
+        "--data-dir",
+        dest="data_dir"
+    )
+    args = parser.parse_args()
+    data_dir = get_data_dir(args.data_dir)
+    # print(data_dir)
+
+    imgt_regex = re.compile(r'pyard-(.+)\.sqlite3')
+    for _, _, filenames in os.walk(data_dir):
+        for filename in filenames:
+            # Get imgt version from the filename
+            # eg: get 3440 from 'pyard-3440.sqlite3'
+            match = imgt_regex.match(filename)
+            imgt_version = match.group(1)  # Get first group
+            db_connection = db.create_db_connection(data_dir, imgt_version)
+            print('-' * 43)
+            print(f"IMGT DB Version: {imgt_version}")
+            print('-' * 43)
+            print(f"|{'Table Name':20}|{'Rows':20}|")
+            print(f"|{'-' * 41}|")
+            for table in data_repository.ars_mapping_tables + \
+                         data_repository.code_mapping_tables:
+                if db.table_exists(db_connection, table):
+                    total_rows = db.count_rows(db_connection, table)
+                    print(f"|{table:20}|{total_rows:20}|")
+                else:
+                    print(f"MISSING: {table} table")
+            print('-' * 43)
+            db_connection.close()

setup.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.6.8
+current_version = 0.6.9
 commit = True
 tag = True
 

setup.py

@@ -42,7 +42,7 @@
 
 setup(
     name='py-ard',
-    version='0.6.8',
+    version='0.6.9',
     description="ARD reduction for HLA with Python",
     long_description=readme + '\n\n' + history,
     author="CIBMTR",
@@ -55,6 +55,7 @@
     scripts=[
         'scripts/pyard',
         'scripts/pyard-import',
+        'scripts/pyard-status',
         'scripts/pyard-reduce-csv'
     ],
     install_requires=requirements,