More work on the drugbank importer, got xpath figured out finally

mercy/importers/drugbank.py

@@ -0,0 +1,31 @@
+import mercy.MercyApplication
+import xml.dom.pulldom
+from mercy.models.drugbank import *
+import sqlalchemy.exc
+import xpath
+
+class DrugBankImporter:
+    def __init__(self, *args, **kwargs):
+        self.__db = mercy.MercyApplication.get_db()
+
+    def _saveobj(self, obj):
+        self.__db.session.add(obj)
+        self.__db.session.commit()
+
+    def read(self, fname):
+        events = xml.dom.pulldom.parse(fname)
+        for event, node in events:
+            if event == xml.dom.pulldom.START_ELEMENT and node.tagName == 'drug':
+                events.expandNode(node)
+                self.__convert_drug(node)
+
+    def __convert_drug(self, node):
+        drug = Drug()
+        drug.name = xpath.findvalue('name', node)
+        drug.indication = xpath.findvalue('indication', node)
+        drug.fda_product_id = xpath.findvalue('external-identifiers/external-identifier[starts-with(resource, "National Drug Code Directory")]/identifier', node)
+        drug.wikipedia = xpath.findvalue('external-links/external-link[starts-with(resource, "Wikipedia")]/url', node)
+        if not drug.fda_product_id:
+            return
+        print str(drug)
+        #self._saveobj(drug)

mercy/models/drugbank.py

@@ -18,7 +18,8 @@ class Drug(SimpleModel, db.Model):
 
     __repr_keys__ = { 'id': basestring,
                       'name': basestring,
-                      'ndc_id': basestring
+                      'fda_product_id': basestring,
+                      'wikipedia': basestring
                       }
 
 class Price(SimpleModel, db.Model):

mercy/models/simplemodel.py

@@ -20,7 +20,7 @@ class SimpleModel():
         values = []
         for (name, otype) in self.__class__.__repr_keys__.iteritems():
             if otype == basestring:
-                values += "'{}'".format(str(getattr(self.__class__, name)))
+                values.append("'{}'".format(str(getattr(self, name))))
             else:
-                values += str(getattr(self.__class__, name))
+                values.append(str(getattr(self, name)))
         return "<{}({})>".format(self.__class__.__name__, ', '.join(values))

scripts/mercy-import-drugbank

@@ -0,0 +1,6 @@
+#!/usr/bin/env python
+
+import sys
+import mercy.importers.drugbank
+
+sys.exit(mercy.importers.drugbank.DrugBankImporter().read(sys.argv[1]))

setup.py

@@ -17,7 +17,8 @@ if __name__ == "__main__":
                           "sqlalchemy",
                           "alembic",
                           "psycopg2",
-                          "flask-sqlalchemy"],
+                          "flask-sqlalchemy",
+                          "py-dom-xpath"],
         scripts=["scripts/mercy.wsgi"],
         packages=["mercy",
                   "mercy/models",