Use gridfs

.gitignore

@@ -2,5 +2,5 @@ secret/secret.key
 secret/orcid_details.json
 *.pyc
 .ipynb_checkpoints
-config.json
+config/config.json
 static/js/config.js

CheckDatabase.ipynb

@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 31,
+   "execution_count": 16,
    "metadata": {},
    "outputs": [
     {
@@ -20,39 +20,61 @@
     "\n",
     "import json\n",
     "import re\n",
-    "from bson import json_util\n",
     "from datetime import datetime\n",
     "from gridfs import GridFS, NoFile\n",
-    "from flask import Flask\n",
-    "from flask_cors import CORS, cross_origin\n",
     "from pymongo import MongoClient\n",
     "from bson.objectid import ObjectId\n",
-    "from db_interface import addMagresFile, databaseSearch, removeMagresFiles"
+    "from db_interface import addMagresFile, databaseSearch, removeMagresFiles, editMagresFile\n",
+    "from db_schema import magresVersionSchema"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 2,
+   "execution_count": 17,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['notes', 'doi', 'csd-ref']"
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "opt_re = re.compile('Optional\\(\\'([a-zA-Z\\-]+)\\'\\)')\n",
+    "[opt_re.match(str(k)).groups()[0] for k in magresVersionSchema._schema.keys() if opt_re.match(str(k)) != None]"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 38,
    "metadata": {},
    "outputs": [],
    "source": [
     "# MAGRES database\n",
-    "client = MongoClient(host='wigner.esc.rl.ac.uk')\n",
+    "host = 'wigner.esc.rl.ac.uk'\n",
+    "#host = 'www.ccpnc.ac.uk'\n",
+    "\n",
+    "client = MongoClient(host=host, port=27017)\n",
     "ccpnc = client.ccpnc"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
+   "execution_count": 39,
    "metadata": {},
    "outputs": [
     {
      "data": {
       "text/plain": [
-       "'\"2018-01-31 15:02:43.662361\"'"
+       "'\"2018-04-24 11:35:16.527528\"'"
       ]
      },
-     "execution_count": 22,
+     "execution_count": 39,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -63,57 +85,101 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": 40,
    "metadata": {},
    "outputs": [],
+   "source": [
+    "for f in ccpnc.test.find({'x': 5}):\n",
+    "    print f"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 41,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
    "source": [
     "magresMdata = ccpnc.magresMetadata"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 32,
-   "metadata": {},
+   "execution_count": 42,
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
-   "source": []
+   "source": [
+    "magresIndex = ccpnc.magresIndex"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 43,
+   "metadata": {},
+   "outputs": [
+    {
+     "ename": "TypeError",
+     "evalue": "'NoneType' object has no attribute '__getitem__'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m                                 Traceback (most recent call last)",
+      "\u001b[0;32m<ipython-input-43-e6d2291f596f>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mmagresIndex\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfind_one\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0;34m'chemname'\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0;34m'TestDOI'\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m'_id'\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
+      "\u001b[0;31mTypeError\u001b[0m: 'NoneType' object has no attribute '__getitem__'"
+     ]
+    }
+   ],
+   "source": [
+    "magresIndex.find_one({'chemname': 'TestDOI'})['_id']"
+   ]
   },
   {
    "cell_type": "code",
-   "execution_count": 45,
+   "execution_count": 44,
    "metadata": {},
    "outputs": [
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "{u'chemname': u'TestOne', u'metadataID': u'5a71e1290c81be3fcf3ac176', u'latest_version': {u'date': datetime.datetime(2018, 1, 31, 15, 30, 49, 989000), u'doi': u'10.0001', u'magresFilesID': u'5a71e12a0c81be3fcf3ac177'}, u'values': [{u'iso': [29.559937639131203, 30.22618664854139, 30.072254456072027, 26.953990818833876, 27.373946759128433, 31.888119371185127], u'species': u'H'}, {u'iso': [156.1229153499832, 109.35753044488325], u'species': u'C'}, {u'iso': [267.0122765992025], u'species': u'O'}], u'orcid': {u'path': u'0000-0003-4851-1144', u'host': u'orcid.org', u'uri': u'http://orcid.org/0000-0003-4851-1144'}, u'formula': [{u'species': u'C', u'n': 2}, {u'species': u'H', u'n': 6}, {u'species': u'O', u'n': 1}], u'_id': ObjectId('5a71e12a0c81be3fcf3ac179')}\n"
+      "5a71e12a0c81be3fcf3ac179\n",
+      "TestOne\n",
+      "5a71e1530c81be3fcf3ac17f\n",
+      "TestTwo\n",
+      "5a746e080c81be236bff2994\n",
+      "TestThree\n",
+      "5aa13de33207861d13ab2ac4\n",
+      "TestFour\n"
      ]
     }
    ],
    "source": [
-    "reg = re.compile('estOne')\n",
-    "for f in ccpnc.magresIndex.find({'chemname': {'$regex': reg}}):\n",
-    "    print f"
+    "for f in magresIndex.find({}):\n",
+    "    print f['_id']\n",
+    "    print magresMdata.find({'_id': ObjectId(f['metadataID'])}).next()['chemname']"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 30,
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "<pymongo.results.InsertOneResult at 0x7f3e7d3920a0>"
-      ]
-     },
-     "execution_count": 11,
-     "metadata": {},
-     "output_type": "execute_result"
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "TestOne\n",
+      "TestDOI\n"
+     ]
     }
    ],
    "source": [
-    "magresMdata.insert_one({'thing': 'date', 'date': datetime.now()})"
+    "reg = re.compile('Test')\n",
+    "for f in ccpnc.magresIndex.find({'$and': [{'chemname': {'$regex': reg}}]}):\n",
+    "    print f['chemname']"
    ]
   },
   {
@@ -138,7 +204,9 @@
   {
    "cell_type": "code",
    "execution_count": 25,
-   "metadata": {},
+   "metadata": {
+    "collapsed": true
+   },
    "outputs": [],
    "source": [
     "magresFilesFS = GridFS(ccpnc, 'magresFilesFS')"

config/config.ultron.json

@@ -0,0 +1 @@
+{"pythonpath": [], "db_url": "localhost", "db_port": 27017}