Merge branch 'master' of github.com:akesterson/mercy

.gitignore

@@ -1 +1,2 @@
 virtualenv
+version.sh

Makefile

@@ -1,13 +1,8 @@
 MAJOR:=$(shell bash -c 'source version.sh ; echo $$MAJOR')
 BUILD:=$(shell bash -c 'source version.sh ; echo $$BUILD')
 OS_NAME:=$(shell bash -c 'source version.sh ; echo $$OS_NAME')
-ifeq "$(OS_NAME)" "win"
+PIP=$(shell pwd)/virtualenv/bin/pip
-	PIP=$(shell pwd)/virtualenv/Scripts/pip
+VIRTUALENV_PKGS_DIR=$(shell pwd)/virtualenv/lib/python2.7/site-packages
-	VIRTUALENV_PKGS_DIR=$(shell pwd)/virtualenv/Lib/site-packages
-else
-	PIP=$(shell pwd)/virtualenv/bin/pip
-	VIRTUALENV_PKGS_DIR=$(shell pwd)/virtualenv/lib/site-packages
-endif
 VIRTUALENV=$(shell which virtualenv)
 PYTHON=$(shell which python)
 

README.md

@@ -1,28 +1,31 @@
 mercy
 =====
 
-Mercy is a web application designed to facilitate payments between people who need prescriptions but can't afford them, and charitable people who can afford them
+This project comprises the entirety of The Mercy Project; everything needed to deploy and serve The Mercy Project currently lives in this repository.
 
-The Idea
+If you came here looking for more information about what (in general) The Mercy Project is, please see http://www.mercyproject.us for more information
-========
 
-* Patient: "Here's my prescription, Mr Pharmacist"
+Python Application
-* Pharmacist: "Sure thing. That'll be $150 USD."
+===================
-* Patient: "I can't afford that! Can you submit it to Mercy for me?"
-* Pharmacist: "Sure thing. We'll call you when it gets filled."
 
-... Meanwhile, back at stately Charitable Person Manor ...
+The mercy/ directory contains all of the python code used to serve the Mercy website and perform all necessary functions.
 
-* Charitable Person's Phone: *DING*
+Alembic ORM database upgrade scripts
-* Charitable Person: "Huh? Oh! Mercy is telling me there's a new prescription I can pay for. I love helping people!"
+====================================
-* Charitable person clicks some buttons
-* Charitable Person: "*CLICK* Paid! Enjoy some good health, stranger. Now to post it on my facebook wall and collect the new achievement for buying my first Leukemia drug..."
 
-... Back at the pharmacy ...
+The alembic/ directory contains scripts used by the alembic flask extension to automatically upgrade and downgrade the postgres database used by Mercy.
 
-* Pharmacist : "Hello, Patient? I just wanted to let you know that your prescription is filled and has been paid in full."
+Puppet Modules for Deployment
-* Patient: "That's so great! I'll come pick it up right away. Now I won't die because my medication is too *!#&$# expensive!"
+==============================
 
-Then everyone rides dinosaurs into the sunset, happy and healthy. It's pretty awesome.
+The puppet code necessary to deploy Mercy onto Linux servers lives in the puppet/ directory.
 
-(That's the idea anyway. WE'll see if reality follows.)
+Nagios Checks for Monitoring the Mercy Platform
+===============================================
+
+These live in the nagios/ directory.
+
+Automated Test Suites
+=====================
+
+tests/ currently holds any and all automated testing (Python Nosetests, currently) for all of the code listed above.

alembic/env.py

@@ -2,7 +2,11 @@ from __future__ import with_statement
 from alembic import context
 from sqlalchemy import engine_from_config, pool
 from logging.config import fileConfig
+import mercy.MercyApplication
+import mercy.models
+import mercy.config
 
+db = mercy.MercyApplication.get_db()
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
 config = context.config
@@ -15,7 +19,7 @@ fileConfig(config.config_file_name)
 # for 'autogenerate' support
 # from myapp import mymodel
 # target_metadata = mymodel.Base.metadata
-target_metadata = None
+target_metadata = db.Model.metadata
 
 # other values from the config, defined by the needs of env.py,
 # can be acquired:
@@ -47,6 +51,10 @@ def run_migrations_online():
     and associate a connection with the context.
 
     """
+
+    alembic_config = config.get_section(config.config_ini_section)
+    alembic_config['sqlalchemy.url'] = mercy.config.SQLALCHEMY_URI
+
     engine = engine_from_config(
                 config.get_section(config.config_ini_section),
                 prefix='sqlalchemy.',

alembic/versions/2b64ad923738_initial_schema.py

@@ -0,0 +1,158 @@
+"""Initial schema
+
+Revision ID: 2b64ad923738
+Revises: None
+Create Date: 2013-10-27 11:46:11.475707
+
+"""
+
+# revision identifiers, used by Alembic.
+revision = '2b64ad923738'
+down_revision = None
+
+from alembic import op
+import sqlalchemy as sa
+
+
+def upgrade():
+    ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('fda_products',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('productid', sa.String(), index=True, unique=True, nullable=False),
+    sa.Column('ndc', sa.String(), index=True, nullable=False),
+    sa.Column('type', sa.String(), nullable=False),
+    sa.Column('proprietaryName', sa.String(), nullable=False),
+    sa.Column('proprietaryNameSuffix', sa.String(), nullable=True),
+    sa.Column('genericName', sa.String(), nullable=False),
+    sa.Column('marketingCategoryName', sa.String(), nullable=False),
+    sa.Column('labelerName', sa.String(), nullable=False),
+    sa.Column('deaSchedule', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('drugbank_packagers',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.Column('url', sa.String(), nullable=True),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('name')
+    )
+    op.create_table('drugbank_manufacturers',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('name')
+    )
+    op.create_table('fda_pharma_classes',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('name')
+    )
+    op.create_table('fda_product_substances',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('drugbank_categories',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('name')
+    )
+    op.create_table('fda_pharma_class_maps',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('product_id', sa.Integer(), nullable=False),
+    sa.Column('pharma_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['pharma_id'], ['fda_pharma_classes.id'], ),
+    sa.ForeignKeyConstraint(['product_id'], ['fda_products.id'], ),
+    sa.PrimaryKeyConstraint('id', 'pharma_id')
+    )
+    op.create_table('drugbank_drugs',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('dbid', sa.String(), unique=True, nullable=True),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.Column('indication', sa.String(), nullable=False),
+    sa.Column('fda_product_id', sa.String(), nullable=True),
+    sa.Column('wikipedia', sa.String(), nullable=True),
+    sa.ForeignKeyConstraint(['fda_product_id'], ['fda_products.productid'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('fda_product_substance_map',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('product_id', sa.Integer(), nullable=False),
+    sa.Column('substance_id', sa.Integer(), nullable=False),
+    sa.Column('quantity', sa.Float(), nullable=False),
+    sa.Column('units', sa.String(), nullable=False),
+    sa.ForeignKeyConstraint(['product_id'], ['fda_products.id'], ),
+    sa.ForeignKeyConstraint(['substance_id'], ['fda_product_substances.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('drugbank_synonyms',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('drug_id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_packager_maps',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('drug_id', sa.Integer(), nullable=False),
+    sa.Column('packager_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.ForeignKeyConstraint(['packager_id'], ['drugbank_packagers.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_genericnames',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('drug_id', sa.Integer(), nullable=False),
+    sa.Column('name', sa.String(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_prices',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('drug_id', sa.Integer(), nullable=False),
+    sa.Column('description', sa.String(), nullable=False),
+    sa.Column('currency', sa.String(), nullable=False),
+    sa.Column('cost', sa.Float(), nullable=False),
+    sa.Column('unit', sa.String(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_manufacturer_maps',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('drug_id', sa.Integer(), nullable=False),
+    sa.Column('manufacturer_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.ForeignKeyConstraint(['manufacturer_id'], ['drugbank_manufacturers.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    op.create_table('drugbank_category_maps',
+    sa.Column('id', sa.Integer(), primary_key=True, autoincrement=True, nullable=False),
+    sa.Column('drug_id', sa.Integer(), nullable=False),
+    sa.Column('category_id', sa.Integer(), nullable=False),
+    sa.ForeignKeyConstraint(['category_id'], ['drugbank_categories.id'], ),
+    sa.ForeignKeyConstraint(['drug_id'], ['drugbank_drugs.id'], ),
+    sa.PrimaryKeyConstraint('drug_id')
+    )
+    ### end Alembic commands ###
+
+
+def downgrade():
+    ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('drugbank_category_maps')
+    op.drop_table('drugbank_manufacturer_maps')
+    op.drop_table('drugbank_prices')
+    op.drop_table('drugbank_genericnames')
+    op.drop_table('drugbank_packager_maps')
+    op.drop_table('drugbank_synonyms')
+    op.drop_table('fda_product_substance_map')
+    op.drop_table('drugbank_drugs')
+    op.drop_table('fda_pharma_class_maps')
+    op.drop_table('drugbank_categories')
+    op.drop_table('fda_product_substances')
+    op.drop_table('fda_pharma_classes')
+    op.drop_table('fda_products')
+    op.drop_table('drugbank_manufacturers')
+    op.drop_table('drugbank_packagers')
+    ### end Alembic commands ###

alembic/versions/58f6a99bd6ec_create_fda_product_t.py

@@ -1,100 +0,0 @@
-"""create fda_product table
-
-Revision ID: 58f6a99bd6ec
-Revises: None
-Create Date: 2013-10-19 21:21:03.977000
-
-"""
-
-# revision identifiers, used by Alembic.
-revision = '58f6a99bd6ec'
-down_revision = None
-
-from alembic import op
-import sqlalchemy as sa
-
-
-def upgrade():
-    op.create_table(
-        'fda_products',
-        sa.Column('id', sa.String, primary_key=True),
-        sa.Column('ndc', sa.String, nullable=False),
-        sa.Column('type', sa.String, nullable=False),
-        sa.Column('proprietaryName', sa.String, nullable=False, index=True),
-        sa.Column('proprietaryNameSuffix', sa.String),
-        sa.Column('genericName', sa.String, nullable=False),
-        sa.Column('marketingCategoryName', sa.String, nullable=False),
-        sa.Column('labelerName', sa.String, nullable=False),
-        sa.Column('deaSchedule', sa.String, nullable=False)
-        )
-    op.create_table(
-        'fda_product_substances',
-        sa.Column('fda_product_id',
-                  sa.String,
-                  sa.ForeignKey('fda_products.id'),
-                  nullable=False),
-        sa.Column('substanceName', sa.String, nullable=False),
-        sa.Column('strengthNumber', sa.String, nullable=False),
-        sa.Column('strengthUnit', sa.String, nullable=False),
-        sa.Column('pharmaClasses', sa.String, nullable=False)
-        )
-    op.create_table(
-        'drugbank_drugs',
-        sa.Column('id', sa.String, primary_key=True, unique=True),
-        sa.Column('name', sa.String, nullable=False, index=True),
-        sa.Column('indication', sa.String, nullable=False),
-        sa.Column('ndc_id', sa.String, sa.ForeignKey('fda_products.id'), nullable=True),
-        sa.Column('wikipedia', sa.String, nullable=True)
-        )
-    op.create_table(
-        'drugbank_prices',
-        sa.Column('id', sa.String, sa.ForeignKey('drugbank_drugs.id'), nullable=False),
-        sa.Column('description', sa.String, nullable=False),
-        sa.Column('currency', sa.String, nullable=False),
-        sa.Column('cost', sa.Float, nullable=False, index=True),
-        sa.Column('unit', sa.String, nullable=False)
-        )
-    op.create_table(
-        'drugbank_categories',
-        sa.Column('id', sa.Integer, primary_key=True, autoincrement=True),
-        sa.Column('name', sa.String, nullable=False)
-        )
-    op.create_table(
-        'drugbank_drug_categories',
-        sa.Column('id', sa.String, sa.ForeignKey('drugbank_drugs.id'), nullable=False),
-        sa.Column('category_id', sa.Integer, sa.ForeignKey('drugbank_categories.id'), nullable=False)
-        )
-    op.create_table(
-        'drugbank_packagers',
-        sa.Column('id', sa.String, sa.ForeignKey('drugbank_drugs.id'), nullable=False),
-        sa.Column('name', sa.String, nullable=False),
-        sa.Column('url', sa.String, nullable=False)
-        )
-    op.create_table(
-        'drugbank_manufacturers',
-        sa.Column('id', sa.String, sa.ForeignKey('drugbank_drugs.id'), nullable=False),
-        sa.Column('name', sa.String, nullable=False),
-        sa.Column('generic', sa.Boolean, nullable=False)
-        )
-    op.create_table(
-        'drugbank_genericnames',
-        sa.Column('id', sa.String, sa.ForeignKey('drugbank_drugs.id'), nullable=False),
-        sa.Column('name', sa.String, index=True, nullable=False)
-        )
-    op.create_table(
-        'drugbank_synonyms',
-        sa.Column('id', sa.String, sa.ForeignKey('drugbank_drugs.id'), nullable=False),
-        sa.Column('name', sa.String, index=True, nullable=False)
-        )
-
-def downgrade():
-    op.drop_table("drugbank_synonyms")
-    op.drop_table("drugbank_genericnames")
-    op.drop_table("drugbank_manufacturers")
-    op.drop_table("drugbank_packagers")
-    op.drop_table("drugbank_drug_categories")
-    op.drop_table("drugbank_categories")
-    op.drop_table("drugbank_prices")
-    op.drop_table("drugbank_drugs")
-    op.drop_table("fda_product_substances")
-    op.drop_table("fda_products")

mercy/MercyApplication.py

@@ -1,4 +1,22 @@
 import flask
+import mercy.config
+from flask.ext.sqlalchemy import SQLAlchemy
 
 class MercyApplication(flask.Flask):
     pass
+
+app = None
+db = None
+
+def get_db():
+    global db
+    if not db:
+        db = SQLAlchemy(get_app())
+    return db
+
+def get_app():
+    global app
+    if not app:
+        app = MercyApplication("mercy")
+        app.config['SQLALCHEMY_DATABASE_URI'] = mercy.config.SQLALCHEMY_URI
+    return app

mercy/config.py

@@ -0,0 +1 @@
+SQLALCHEMY_URI = 'postgresql://mercy:mercy@postgresql.aklabs.net/mercy'

mercy/exceptions.py

@@ -0,0 +1,3 @@
+class CorruptTarError(Exception):
+    pass
+

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/importers/fda.py

@@ -0,0 +1,107 @@
+import mercy.MercyApplication
+import xml.etree.cElementTree as ET
+from mercy.models.fda import Product
+from mercy.models.fda import ProductSubstance
+from mercy.models.fda import ProductSubstanceMap
+from mercy.models.fda import PharmaceuticalClass
+from mercy.models.fda import PharmaceuticalClassMap
+import sqlalchemy.exc
+import csv
+
+class FDAImporter:
+    def __init__(self, *args, **kwargs):
+        self.__db = mercy.MercyApplication.get_db()
+
+    def read(self, fname, startIdx=0):
+        with open(fname, "r") as ifile:
+            reader = csv.DictReader(ifile, delimiter="\t")
+            idx = 0
+            for row in reader:
+                if idx < startIdx:
+                    print "Skipping from {} to {}".format(idx, startIdx)
+                    idx += 1
+                    continue
+                retries = 0
+                print "{} : {}".format(idx, row)
+                while retries < 3 :
+                    try:
+                        self._convert_row(row)
+                        retries = 3
+                    except sqlalchemy.exc.DatabaseError, e:
+                        retries += 1
+                        if retries == 3:
+                            raise e
+                        else:
+                            continue
+                idx += 1
+
+
+    def _saveobj(self, obj):
+        self.__db.session.add(obj)
+        self.__db.session.commit()
+
+    def _convert_row(self, row):
+        # The FDA CSV is HIGHLY irregular. This function is needlessly large because of that/
+        product = Product.query.filter_by(productid=row['PRODUCTID']).first()
+        if not product:
+            product = Product()
+        product.productid = row['PRODUCTID']
+        product.ndc = row['PRODUCTNDC']
+        product.type = row['PRODUCTTYPENAME']
+        product.proprietaryName = row['PROPRIETARYNAME']
+        product.proprietaryNameSuffix = row['PROPRIETARYNAMESUFFIX']
+        product.genericName = row['NONPROPRIETARYNAME']
+        product.marketingCategoryName = row['MARKETINGCATEGORYNAME']
+        product.labelerName = row['LABELERNAME']
+        product.deaSchedule = (row['DEASCHEDULE'] if row['DEASCHEDULE'] else '')
+        self._saveobj(product)
+
+        # Strip the substances off of the product and make objects for them
+        substanceNames = [x.strip().lstrip() for x in row['SUBSTANCENAME'].split(';')]
+        tmpQtys = [x.strip().lstrip() for x in row['ACTIVE_NUMERATOR_STRENGTH'].split(';')]
+        # The list addition here is to make sure we have an equal number of values in
+        # quantities as we do in substance names, because the FDA CSV does not ensure
+        # that all substance names have a quantity or unit listed. So unknown quantities
+        # get entered as '0', unknown units of measure become '?'.
+        substanceQtys = [(float(x) if x else 0.0) for x in tmpQtys] + ([0] * (len(substanceNames) - len(tmpQtys)))
+        substanceUnits = [x.strip().lstrip() for x in row['ACTIVE_INGRED_UNIT'].split(';')]
+        substanceUnits += (['?'] * (len(substanceNames) - len(substanceUnits)))
+
+        for idx in range(0, len(substanceNames)):
+            substance = None
+            substanceName = substanceNames[idx]
+
+            substance = ProductSubstance.query.filter_by(name=substanceName).first()
+            if not substance:
+                substance = ProductSubstance()
+                substance.name = substanceName
+                self._saveobj(substance)
+            substanceMap = ProductSubstanceMap.query.filter_by(product_id=product.id,
+                                                               substance_id=substance.id,
+                                                               quantity=substanceQtys[idx],
+                                                               units=substanceUnits[idx]).first()
+            if not substanceMap:
+                substanceMap = ProductSubstanceMap()
+                substanceMap.product_id = product.id
+                substanceMap.substance_id = substance.id
+                substanceMap.quantity = substanceQtys[idx]
+                substanceMap.units = substanceUnits[idx]
+                self._saveobj(substanceMap)
+
+        pharmaClassList = row.get('PHARM_CLASSES')
+        pharmaClasses = [x.strip().lstrip() for x in (pharmaClassList if pharmaClassList else '').split(',')]
+        for pharmaClass in pharmaClasses:
+            pharmaObj = PharmaceuticalClass.query.filter_by(name=pharmaClass).first()
+            if not pharmaObj:
+                pharmaObj = PharmaceuticalClass()
+                pharmaObj.name = pharmaClass
+                self._saveobj(pharmaObj)
+            mapObj = PharmaceuticalClassMap.query.filter_by(
+                product_id=product.id,
+                pharma_id=pharmaObj.id).first()
+            if not mapObj:
+                mapObj = PharmaceuticalClassMap()
+                mapObj.product_id = product.id
+                mapObj.pharma_id = pharmaObj.id
+                self._saveobj(mapObj)
+        return

mercy/models/__init__.py

@@ -0,0 +1,3 @@
+import simplemodel
+import fda
+import drugbank

mercy/models/drugbank.py

@@ -0,0 +1,78 @@
+import sqlalchemy as sa
+from mercy.models.simplemodel import SimpleModel
+import mercy.MercyApplication
+from mercy.models.fda import Product
+import sqlalchemy.dialects.postgresql as pgdialect
+
+db = mercy.MercyApplication.get_db()
+
+class Drug(SimpleModel, db.Model):
+    __tablename__ = "drugbank_drugs"
+
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    dbid = sa.Column(sa.String, index=True, unique=True)
+    name = sa.Column(sa.String, nullable=False, index=True)
+    indication = sa.Column(sa.String, nullable=False)
+    fda_product_id = sa.Column(sa.String, sa.ForeignKey(Product.productid), nullable=True)
+    wikipedia = sa.Column(sa.String, nullable=True)
+
+    __repr_keys__ = { 'id': basestring,
+                      'name': basestring,
+                      'fda_product_id': basestring,
+                      'wikipedia': basestring
+                      }
+
+class Price(SimpleModel, db.Model):
+    __tablename__ = "drugbank_prices"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    drug_id = sa.Column(sa.Integer, sa.ForeignKey(Drug.id), nullable=False)
+    description = sa.Column(sa.String, nullable=False)
+    currency = sa.Column(sa.String, nullable=False)
+    cost = sa.Column(sa.Float, nullable=False, index=True)
+    unit = sa.Column(sa.String, nullable=False)
+
+class CategoryName(SimpleModel, db.Model):
+    __tablename__ = "drugbank_categories"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    name = sa.Column(sa.String, nullable=False, unique=True)
+
+class CategoryMap(SimpleModel, db.Model):
+    __tablename__ = "drugbank_category_maps"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    drug_id = sa.Column(sa.Integer, sa.ForeignKey(Drug.id), nullable=False)
+    category_id = sa.Column(sa.Integer, sa.ForeignKey(CategoryName.id), nullable=False)
+
+class Packager(SimpleModel, db.Model):
+    __tablename__ = "drugbank_packagers"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    name = sa.Column(sa.String, nullable=False, unique=True)
+    url = sa.Column(sa.String, nullable=True)
+
+class PackagerMap(SimpleModel, db.Model):
+    __tablename__ = "drugbank_packager_maps"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    drug_id = sa.Column(sa.String, sa.ForeignKey(Drug.id), nullable=False)
+    packager_id = sa.Column(sa.Integer, sa.ForeignKey(Packager.id), nullable=False)
+
+class Manufacturer(SimpleModel, db.Model):
+    __tablename__ = "drugbank_manufacturers"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    name = sa.Column(sa.String, nullable=False, unique=True)
+
+class ManufacturerMap(SimpleModel, db.Model):
+    __tablename__ = "drugbank_manufacturer_maps"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    drug_id = sa.Column(sa.Integer, sa.ForeignKey(Drug.id), nullable=False)
+    manufacturer_id = sa.Column(sa.Integer, sa.ForeignKey(Manufacturer.id), nullable=False)
+
+class GenericName(SimpleModel, db.Model):
+    __tablename__ = "drugbank_genericnames"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    drug_id = sa.Column(sa.Integer, sa.ForeignKey(Drug.id), nullable=False)
+    name = sa.Column(sa.String, nullable=False)
+
+class Synonym(SimpleModel, db.Model):
+    __tablename__ = "drugbank_synonyms"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    drug_id = sa.Column(sa.Integer, sa.ForeignKey(Drug.id), nullable=False)
+    name = sa.Column(sa.String, nullable=False)

mercy/models/fda.py

@@ -0,0 +1,63 @@
+import sqlalchemy as sa
+from mercy.models.simplemodel import SimpleModel
+import mercy.MercyApplication
+import sqlalchemy.dialects.postgresql as pgdialect
+
+db = mercy.MercyApplication.get_db()
+
+class Product(SimpleModel, db.Model):
+    __tablename__ = 'fda_products'
+
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    productid = sa.Column(sa.String, index=True, unique=True, nullable=False)
+    ndc = sa.Column(sa.String, index=True, nullable=False)
+    type = sa.Column(sa.String, nullable=False)
+    proprietaryName = sa.Column(sa.String, nullable=False, index=True)
+    proprietaryNameSuffix = sa.Column(sa.String)
+    genericName = sa.Column(sa.String, nullable=False, index=True)
+    marketingCategoryName = sa.Column(sa.String, nullable=False)
+    labelerName = sa.Column(sa.String, nullable=False)
+    deaSchedule = sa.Column(sa.String, nullable=False)
+
+    __repr_keys__ = { 'id': basestring,
+                      'ndc': basestring,
+                      'genericName': basestring,
+                      'proprietaryName': basestring,
+                      'proprietaryNameSuffix': basestring}
+
+class ProductSubstance(SimpleModel, db.Model):
+    __tablename__ = 'fda_product_substances'
+
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    name = sa.Column(sa.String, nullable=False)
+
+class ProductSubstanceMap(SimpleModel, db.Model):
+    __tablename__ = 'fda_product_substance_map'
+
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    product_id = sa.Column(sa.Integer,
+                           sa.ForeignKey(Product.id),
+                           nullable=False)
+    substance_id = sa.Column(sa.Integer,
+                             sa.ForeignKey(ProductSubstance.id),
+                             nullable=False,
+                             index=True)
+    quantity = sa.Column(sa.Float, nullable=False)
+    units = sa.Column(sa.String, nullable=False)
+
+
+class PharmaceuticalClass(SimpleModel, db.Model):
+    __tablename__ = "fda_pharma_classes"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    name = sa.Column(sa.String, nullable=False, unique=True)
+
+class PharmaceuticalClassMap(SimpleModel, db.Model):
+    __tablename__ = "fda_pharma_class_maps"
+    id = sa.Column(sa.Integer, primary_key=True, autoincrement=True, nullable=False)
+    product_id = sa.Column(sa.Integer,
+                           sa.ForeignKey(Product.id),
+                           nullable=False)
+    pharma_id = sa.Column(sa.Integer,
+                          sa.ForeignKey(PharmaceuticalClass.id),
+                          primary_key=True,
+                          nullable=False)

mercy/models/simplemodel.py

@@ -0,0 +1,26 @@
+import mercy.MercyApplication
+
+db = mercy.MercyApplication.get_db()
+
+class SimpleModel():
+    def __init__(self, *args, **kwargs):
+        db.Model.__init__(self, *args, **kwargs)
+        for (k, v) in kwargs.iteritems():
+            if hasattr(self, k):
+                setattr(self, k, v)
+            else:
+                raise AttributeError("Invalid attribute {} => {}".format(k, v))
+
+    def __repr__(self, *args, **kwargs):
+        try:
+            getattr(self.__class__, "__repr_keys__")
+        except AttributeError, e:
+            return db.Model.__repr__(self, *args, **kwargs)
+
+        values = []
+        for (name, otype) in self.__class__.__repr_keys__.iteritems():
+            if otype == basestring:
+                values.append("'{}'".format(str(getattr(self, name))))
+            else:
+                values.append(str(getattr(self, name)))
+        return "<{}({})>".format(self.__class__.__name__, ', '.join(values))

mercy/version.py

@@ -1 +1 @@
-VERSION="0.0-0"
+VERSION="0.0-1"

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]))

scripts/mercy-import-fda

@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+
+import sys
+import mercy.importers.fda
+
+startIdx = 0
+if ( len(sys.argv) >= 3 ):
+    startIdx = int(sys.argv[2])
+
+sys.exit(mercy.importers.fda.FDAImporter().read(sys.argv[1], startIdx=startIdx))

scripts/mercy.wsgi

@@ -1,14 +1,6 @@
-from mercy.MercyApplication import MercyApplication
+import mercy.MercyApplication
 
-class ScriptNameStripper(object):
+app = get_application()
-    def __init__(self, app):
-        self.app = app
-
-    def __call_(self, environ, start_response):
-        environ['SCRIPT_NAME'] = ''
-        return self.app(environ, start_response)
-
-app = ScriptNameStripper(MercyApplication())
 
 if __name__ == "__main__":
     app.run()

scripts/mercy_app.py

@@ -1,7 +1,6 @@
 #!/usr/bin/env python
 
-from mercy.MercyApplication import MercyApplication
+from mercy.MercyApplication import app
 
 if __name__ == "__main__":
-    app = MercyApplication("mercy")
     app.run()

setup.py

@@ -8,7 +8,7 @@ if __name__ == "__main__":
         name="mercy",
         url="https://www.github.com/akesterson/mercy",
         version=mercy.version.VERSION,
-        description="A flask application that facilitates paying for prescriptions",
+        description="A web application that facilitates charitable prescription payments",
         long_description="",
         author=("Andrew Kesterson"),
         author_email="andrew@aklabs.net",
@@ -16,9 +16,13 @@ if __name__ == "__main__":
         install_requires=["flask",
                           "sqlalchemy",
                           "alembic",
-                          "psycopg2"],
+                          "psycopg2",
-        scripts=[],
+                          "flask-sqlalchemy",
-        packages=["mercy"],
+                          "py-dom-xpath"],
+        scripts=["scripts/mercy.wsgi"],
+        packages=["mercy",
+                  "mercy/models",
+                  "mercy/importers"],
         data_files=[],
         classifiers=[
             'Development Status :: 1 - Planning',

tests/importers/test_fda_importer.py

@@ -0,0 +1,120 @@
+import os
+import nose
+from nose.tools import raises
+import mercy.models
+import mercy.importers.fda
+import mercy.exceptions
+
+COMPARISON_KEYS={
+    'productid': 'PRODUCTID',
+    'ndc': 'PRODUCTNDC',
+    'type': 'PRODUCTTYPENAME',
+    'proprietaryName': 'PROPRIETARYNAME',
+    'proprietaryNameSuffix': 'PROPRIETARYNAMESUFFIX',
+    'genericName': 'NONPROPRIETARYNAME',
+    'marketingCategoryName': 'MARKETINGCATEGORYNAME',
+    'labelerName': 'LABELERNAME',
+    'deaSchedule': 'DEASCHEDULE'
+    }
+
+CSV_KEYS=[
+    'PRODUCTID',
+    'PRODUCTNDC',
+    'PRODUCTTYPENAME',
+    'PROPRIETARYNAME',
+    'PROPRIETARYNAMESUFFIX',
+    'NONPROPRIETARYNAME',
+    'DOSAGEFORMNAME',
+    'ROUTENAME',
+    'STARTMARKETINGDATE',
+    'ENDMARKETINGDATE',
+    'MARKETINGCATEGORYNAME',
+    'APPLICATIONNUMBER',
+    'LABELERNAME',
+    'SUBSTANCENAME',
+    'ACTIVE_NUMERATOR_STRENGTH',
+    'ACTIVE_INGRED_UNIT',
+    'PHARM_CLASSES',
+    'DEASCHEDULE'
+    ]
+
+CANNED_ROWS=[
+    {'PRODUCTID': '0002-3230_b1642902-4a44-495a-8790-39598b168276',
+     'PRODUCTNDC': '0002-3230',
+     'PRODUCTTYPENAME': 'HUMAN PRESCRIPTION DRUG',
+     'PROPRIETARYNAME': 'Symbyax',
+     'PROPRIETARYNAMESUFFIX': '',
+     'NONPROPRIETARYNAME': 'Olanzapine and Fluoxetine hydrochloride',
+     'DOSAGEFORMNAME': 'CAPSULE',
+     'ROUTENAME': 'ORAL',
+     'STARTMARKETINGDATE': '20070409',
+     'ENDMARKETINGDATE': '',
+     'MARKETINGCATEGORYNAME': 'NDA',
+     'APPLICATIONNUMBER': 'NDA021520',
+     'LABELERNAME': 'Eli Lilly and Company',
+     'SUBSTANCENAME': 'FLUOXETINE HYDROCHLORIDE; OLANZAPINE',
+     'ACTIVE_NUMERATOR_STRENGTH': '25; 3',
+     'ACTIVE_INGRED_UNIT': 'mg/1; mg/1',
+     'PHARM_CLASSES': 'Atypical Antipsychotic [EPC],Serotonin Reuptake Inhibitor [EPC],Serotonin Uptake Inhibitors [MoA]',
+     'DEASCHEDULE': ''
+     },
+    {'PRODUCTID': '0002-3231_b1642902-4a44-495a-8790-39598b168276',
+     'PRODUCTNDC': '0002-3231',
+     'PRODUCTTYPENAME': 'HUMAN PRESCRIPTION DRUG',
+     'PROPRIETARYNAME': 'Symbyax',
+     'PROPRIETARYNAMESUFFIX': '',
+     'NONPROPRIETARYNAME': 'Olanzapine and Fluoxetine hydrochloride',
+     'DOSAGEFORMNAME': 'CAPSULE',
+     'ROUTENAME': 'ORAL',
+     'STARTMARKETINGDATE': '20070409',
+     'ENDMARKETINGDATE': '',
+     'MARKETINGCATEGORYNAME': 'NDA',
+     'APPLICATIONNUMBER': 'NDA021521',
+     'LABELERNAME': 'Eli Lilly and Company',
+     'SUBSTANCENAME': 'FLUOXETINE HYDROCHLORIDE; OLANZAPINE',
+     'ACTIVE_NUMERATOR_STRENGTH': '25; 6',
+     'ACTIVE_INGRED_UNIT': 'mg/1; mg/1',
+     'PHARM_CLASSES': 'Atypical Antipsychotic [EPC],Serotonin Reuptake Inhibitor [EPC],Serotonin Uptake Inhibitors [MoA]',
+     'DEASCHEDULE': ''
+     }
+    ]
+
+FIXTUREFILE=os.path.abspath(
+    os.path.join(
+        os.path.dirname(__file__),
+        "..",
+        "fixtures",
+        "fda_database.txt"
+        )
+    )
+
+FIXTUREFILE_BAD=os.path.abspath(
+    os.path.join(
+        os.path.dirname(__file__),
+        "..",
+        "fixtures",
+        "fda_database_bad.txt"
+        )
+    )
+
+def test_fda_import_populates_table():
+    with open(FIXTUREFILE, 'w') as ofile:
+        ofile.write("{}\n".format('\t'.join(CSV_KEYS)))
+        for row in CANNED_ROWS:
+            values = []
+            for key in CSV_KEYS:
+                values.append(row[key])
+            ofile.write("{}\n".format('\t'.join(values)))
+    importer = mercy.importers.fda.FDAImporter()
+    importer.read(FIXTUREFILE)
+    for row in CANNED_ROWS:
+        product = mercy.models.fda.Product.query.filter_by(productid = row['PRODUCTID']).first()
+        assert(product)
+        for (k, v) in COMPARISON_KEYS.iteritems():
+            assert(getattr(product, k) == row[v])
+        mapquery = mercy.models.fda.ProductSubstanceMap.query
+        substanceMaps = [x for x in mapquery.filter_by(product_id=product.id)]
+        assert(len(substanceMaps) == len(row['ACTIVE_NUMERATOR_STRENGTH'].split(';')))
+        # TO DO : This test doesn't look at the contents of the
+        # substances or substance maps, only that the right
+        # number of substance maps come out

version.sh

@@ -1,15 +0,0 @@
-TAG="build,0.0,0"
-BRANCH="master"
-MAJOR="0.0"
-BUILD="0"
-SHA1="9b83e26ec3d0e3d1526a4226a8ac0c8580a77bcf"
-OS_NAME="${OS_NAME:-win}"
-OS_VERSION="${OS_VERSION:-}"
-ARCH="${ARCH:-i686}"
-VERSION="0.0-0"
-BUILDHOST="akesterson-pc"
-BUILDUSER="akesterson-pc\akesterson"
-BUILDDIR="/c/Users/akesterson/source/upstream/git/akesterson/mercy"
-SOURCE="git@github.com:akesterson/mercy.git"
-REBUILDING=0
-CHANGELOG=""