Merge pull request #300 from COSIMA/update_db_script

Add a script to update a database

cosima_cookbook/database_update.py

@@ -0,0 +1,31 @@
+import argparse
+import pathlib
+
+import cosima_cookbook as cc
+
+
+def main(argv=None):
+    parser = argparse.ArgumentParser(description="Update COSIMA cookbook database.")
+    parser.add_argument(
+        "dirs", type=pathlib.Path, nargs="+", help="Directories to index."
+    )
+    parser.add_argument(
+        "-db",
+        "--database",
+        dest="db",
+        action="store",
+        default="cosima_master.db",
+        help="Database to update.",
+    )
+    args = parser.parse_args(argv)
+
+    print(cc)
+
+    print("Establishing a DB connection to: {}".format(args.db))
+    session = cc.database.create_session(args.db, timeout=30)
+
+    for dir in args.dirs:
+        print("Indexing: {}".format(dir))
+        cc.database.build_index(
+            dir, session, prune="delete", force=False, followsymlinks=True, nfiles=1000
+        )

setup.py

@@ -25,7 +25,11 @@
         'ipywidgets',
         'lxml',
     ],
-
+    entry_points={
+        'console_scripts': [
+            'cosima_cookbook-update_db = cosima_cookbook.database_update:main',
+        ]
+    },
     extras_require = {
         'build': ['distributed', 'pytest']
     }

test/test_indexing.py

@@ -38,7 +38,7 @@ def test_find_files():
 
     # Test works with alternative suffix
     files = database.find_files("test/", "*.py")
-    assert len(files) == 8
+    assert len(files) == 9
 
     for f in files:
         assert Path(f).suffix == ".py"

test/test_update.py

@@ -0,0 +1,13 @@
+import shlex
+from cosima_cookbook import database_update
+
+
+def test_database_update(tmpdir):
+
+    args = shlex.split(
+        "-db {db} test/data/update/experiment_a test/data/update/experiment_b".format(
+            db=tmpdir.join("test.db")
+        )
+    )
+
+    database_update.main(args)