api: add transitive search

* Adds an extra Model that keeps track of all the equivalent IDs.
  (closes #49)

* Enables transitive queries to fetch all the related claims (through
  `/claims?type=xxx&value=yyy&recurse=1`.

* Adds a new API resource `/eqids` to list all the equivalent IDs
  (one can also filter by a specific id using the argument `eqid=`).

* Adds command `claimstore index` in order to do operations with
  indeces. For instance: `claimstore index clear_eqids` and
  `claimstore index rebuild_eqids`.

Signed-off-by: Jose Benito Gonzalez Lopez <jose.benito.gonzalez@cern.ch>

claimstore/ext/sqlalchemy.py

@@ -37,16 +37,12 @@
 def setup_app(app):
     """Setup sqlalchemy."""
     # Add extension CLI to application.
-    app.cli.add_command(dropalldb)
+    app.cli.add_command(database)
     db.init_app(app)
 
 
-@click.command()
+@click.group()
 @with_appcontext
-def dropalldb():
-    """Drop database."""
-    if click.confirm('Are you sure you want to drop the whole database?'):
-        db.drop_all()
-        click.echo('Database dropped')
-    else:
-        click.echo('Command aborted')
+def database():
+    """Database related commands."""
+    pass

claimstore/modules/claims/cli.py

@@ -25,17 +25,18 @@
 import click
 from flask_cli import with_appcontext
 
-from claimstore.ext.sqlalchemy import db
+from claimstore.ext.sqlalchemy import database, db
 from claimstore.modules.claims.fixtures.claim import load_all_claims
 from claimstore.modules.claims.fixtures.claimant import load_all_claimants
 from claimstore.modules.claims.fixtures.pid import load_all_pids
 from claimstore.modules.claims.fixtures.predicate import load_all_predicates
+from claimstore.modules.claims.models import EquivalentIdentifier
 
 
-@click.command()
+@database.command()
 @click.option('--config', help='Path to a folder with the db configuration')
 @with_appcontext
-def initdb(config):
+def create(config):
     """Create database and populate it with basic data.
 
     The database will be populated with the predicates, persistent identifiers
@@ -66,10 +67,10 @@ def initdb(config):
     click.echo('Database initialisation completed.')
 
 
-@click.command()
+@database.command()
 @click.option('--data', help='Path to a folder with data (claims)')
 @with_appcontext
-def populatedb(data):
+def populate(data):
     """Populate database with claims.
 
     The database will be populated with the claims that are defined in
@@ -98,8 +99,46 @@ def populatedb(data):
         click.echo('Database populate completed.')
     except Exception:
         click.echo(
-            'Claims could not be loaded. Try `claimstore initdb` first.'
+            'Claims could not be loaded. Try `claimstore database create` '
+            'first.'
         )
 
 
-commands = [initdb, populatedb]
+@database.command()
+@with_appcontext
+def drop():
+    """Drop the whole database."""
+    if click.confirm('Are you sure you want to drop the whole database?'):
+        db.drop_all()
+        click.echo('Database dropped')
+    else:
+        click.echo('Command aborted')
+
+
+@click.group()
+@with_appcontext
+def eqid():
+    """Command providing actions to alter the Equivalent Identifier index."""
+    pass
+
+
+@eqid.command('drop')
+@with_appcontext
+def drop_eqid():
+    """Delete all the entries in the eqid index."""
+    if click.confirm('Are you sure to drop the whole index?'):
+        EquivalentIdentifier.clear()
+        click.echo('Index cleared.')
+    else:
+        click.echo('Command aborted')
+
+
+@eqid.command()
+@with_appcontext
+def reindex():
+    """Process all claims to rebuild the eqid index."""
+    EquivalentIdentifier.rebuild()
+    click.echo('Index rebuilt.')
+
+
+commands = [eqid]

claimstore/modules/claims/config.py

@@ -0,0 +1,23 @@
+# -*- coding: utf-8 -*-
+#
+# This file is part of ClaimStore.
+# Copyright (C) 2015 CERN.
+#
+# ClaimStore is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# ClaimStore is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with ClaimStore; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307,
+# USA.
+
+"""Module configuration."""
+
+CFG_EQUIVALENT_PREDICATES = ['is_same_as', 'is_variant_of']

claimstore/modules/claims/fixtures/claim.py

@@ -68,20 +68,32 @@ def load_all_claims(test_app=None, config_path=None):
 
 
 @pytest.fixture
-def dummy_claim():
+def dummy_subject():
+    """Fixture of a dummy subject."""
+    return {
+        "type": "CDS_RECORD_ID",
+        "value": "test-2001192"
+    }
+
+
+@pytest.fixture
+def dummy_object():
+    """Fixture of a dummy object."""
+    return {
+        "type": "CDS_REPORT_NUMBER",
+        "value": "CMS-PAS-HIG-14-008"
+    }
+
+
+@pytest.fixture
+def dummy_claim(dummy_subject, dummy_object):
     """Fixture that creates a dummy claim."""
     return {
         "claimant": "dummy_claimant",
-        "subject": {
-            "type": "CDS_RECORD_ID",
-            "value": "2001192"
-        },
+        "subject": dummy_subject,
         "predicate": "is_same_as",
         "certainty": 1.0,
-        "object": {
-            "type": "CDS_REPORT_NUMBER",
-            "value": "CMS-PAS-HIG-14-008"
-        },
+        "object": dummy_object,
         "arguments": {
             "human": 0,
             "actor": "CDS_submission"

claimstore/modules/claims/fixtures/claimant.py

@@ -95,6 +95,15 @@ def dummy_claimant():
     }
 
 
+@pytest.fixture
+def create_dummy_claimant(webtest_app, dummy_claimant):
+    """Add dummy claimant to the database."""
+    webtest_app.post_json(
+        '/subscribe',
+        dummy_claimant
+    )
+
+
 @pytest.fixture
 def all_claimants(db):
     """Fixture that loads all claimants."""