Notebooks

.gitignore

@@ -78,3 +78,5 @@ output.report
 uuids_list.txt
 
 .python-version
+
+*/.ipynb_checkpoints/

jupyter_notebooks/profiling/timing-tests-sno-33.py

@@ -0,0 +1,68 @@
+
+# coding: utf-8
+
+# In[1]:
+
+
+
+# In[2]:
+
+import sys
+sys.path.append('..')
+import qancode
+import numpy as np
+import pandas as pd
+
+
+# In[3]:
+
+#compare any two encoded instances here
+qa = qancode.QANCODE(rc_url="https://test.encodedcc.org", prod_url='https://sno68-on-dev.demo.encodedcc.org/')
+
+
+# In[4]:
+
+res = qa.check_response_time(item_types=["/","/search/?type=Experiment"], n=50)
+
+
+# In[5]:
+
+res
+
+
+# In[6]:
+
+qa.check_response_time(item_types=["/search/?searchTerm=K562", "/search/?searchTerm=DNA+binding", "/search/?searchTerm=human", "/search/?searchTerm=H3K36me3", "/search/?searchTerm=CTCF"], n=50)
+
+
+# In[7]:
+
+qa.check_response_time(item_types=['/ENCSR255XZG/', '/ENCSR749ILN/', '/ENCSR688GVV/', '/ENCSR301HAG/','/ENCSR315NAC/', '/ENCSR856JJB/'], n=50)
+
+
+# In[8]:
+
+qa.check_response_time(item_types=['/experiments/ENCSR255XZG/', '/experiments/ENCSR749ILN/', '/experiments/ENCSR688GVV/', '/experiments/ENCSR301HAG/','/experiments/ENCSR315NAC/', '/experiments/ENCSR856JJB/'], n=50)
+
+
+# In[10]:
+
+qa.check_response_time(json=True, item_types=['/ENCSR255XZG/', '/ENCSR749ILN/', '/ENCSR688GVV/', '/ENCSR301HAG/','/ENCSR315NAC/', '/ENCSR856JJB/'], n=50)
+
+
+# In[ ]:
+
+qa.check_response_time(item_types=['/ENCSR480OHP/','/ENCSR000EMB/','/ENCSR323QIP/','/ENCSR718AXQ/','/ENCSR165BGV/','/ENCSR384KAN/','/ENCSR330FXL/','/ENCSR825UNV/'], n=50)
+
+
+# In[ ]:
+
+qa.check_response_time(item_types=['/ENCAB830JLB/','/ENCAB000BKR/','/ENCAB284TTY/','/ENCAB294YUD/','/ENCAB000AOC/','/ENCAB301QZF/','/ENCAB000ANM/','/ENCAB000ANU/','/ENCAB445KMF/','/ENCAB000BAY/'], n=50)
+
+
+# In[ ]:
+
+qa.check_response_time(item_types=['/ENCBS787TFV/','/ENCBS676QAV/','/ENCBS996IWU/','/ENCBS913XJP/','/ENCBS565NTN/','/ENCBS896YZO/','/ENCBS280NYD/'], n=50)
+
+
+# ## 

jupyter_notebooks/profiling/v79rc1 vs v77-test.ipynb

@@ -0,0 +1,279 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "import sys\n",
+    "sys.path.append('../..')\n",
+    "import qancode"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "#comparing to v65rc2 site\n",
+    "qa = qancode.QANCODE(rc_url=\"https://v79rc1-master.demo.encodedcc.org/\", prod_url=\"https://test.encodedcc.org/\")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Checking response time\n",
+      "\n",
+      "*** item_type: /\n",
+      "------------------------- https://test.encodedcc.org// -------------------------\n",
+      "\u001b[36mAverage es_time: 2.443 ± 1.396 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.509 ± 0.021 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 5.237 ± 1.01 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage wsgi_time: 11.828 ± 1.797 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage total time: 20.017 ± 3.473 ms (n=100)\u001b[0m\n",
+      "------------------ https://v79rc1-master.demo.encodedcc.org// ------------------\n",
+      "\u001b[36mAverage es_time: 2.038 ± 0.241 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.361 ± 0.032 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 3.991 ± 0.732 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage wsgi_time: 9.506 ± 0.798 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage total time: 15.895 ± 1.532 ms (n=100)\u001b[0m\n",
+      "\n",
+      "\n",
+      "*** item_type: /search/?type=Experiment\n",
+      "------------- https://test.encodedcc.org//search/?type=Experiment --------------\n",
+      "\u001b[31mAverage es_time: 24.699 ± 10.871 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.507 ± 0.023 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 140.946 ± 11.738 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 182.266 ± 17.143 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage total time: 348.418 ± 34.2 ms (n=100)\u001b[0m\n",
+      "------ https://v79rc1-master.demo.encodedcc.org//search/?type=Experiment -------\n",
+      "\u001b[31mAverage es_time: 22.949 ± 10.685 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.475 ± 0.019 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 123.067 ± 14.795 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 162.2 ± 20.174 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage total time: 308.692 ± 40.393 ms (n=100)\u001b[0m\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "qa.check_response_time(item_types=[\"/\",\"/search/?type=Experiment\"], n=100)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Checking response time\n",
+      "\n",
+      "*** item_type: /search/?searchTerm=K562\n",
+      "------------- https://test.encodedcc.org//search/?searchTerm=K562 --------------\n",
+      "\u001b[31mAverage es_time: 250.489 ± 48.89 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.531 ± 0.02 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 33.264 ± 10.438 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 296.063 ± 52.472 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 580.347 ± 102.992 ms (n=100)\u001b[0m\n",
+      "------ https://v79rc1-master.demo.encodedcc.org//search/?searchTerm=K562 -------\n",
+      "\u001b[31mAverage es_time: 208.883 ± 35.957 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.437 ± 0.018 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 23.045 ± 6.471 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 239.354 ± 37.294 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 471.72 ± 74.319 ms (n=100)\u001b[0m\n",
+      "\n",
+      "\n",
+      "*** item_type: /search/?searchTerm=DNA+binding\n",
+      "---------- https://test.encodedcc.org//search/?searchTerm=DNA+binding ----------\n",
+      "\u001b[31mAverage es_time: 352.991 ± 54.339 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.531 ± 0.025 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 34.168 ± 10.722 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage wsgi_time: 401.306 ± 58.61 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 788.996 ± 115.49 ms (n=100)\u001b[0m\n",
+      "--------- https://v79rc1-master.demo.encodedcc.org//search/?searchTerm=DNA+binding ---------\n",
+      "\u001b[31mAverage es_time: 309.012 ± 50.516 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.442 ± 0.02 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 25.838 ± 6.634 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 345.825 ± 51.697 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 681.117 ± 102.851 ms (n=100)\u001b[0m\n",
+      "\n",
+      "\n",
+      "*** item_type: /search/?searchTerm=human\n",
+      "------------- https://test.encodedcc.org//search/?searchTerm=human -------------\n",
+      "\u001b[31mAverage es_time: 249.505 ± 31.124 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.525 ± 0.027 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 29.964 ± 8.021 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 287.351 ± 32.164 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 567.346 ± 64.18 ms (n=100)\u001b[0m\n",
+      "------ https://v79rc1-master.demo.encodedcc.org//search/?searchTerm=human ------\n",
+      "\u001b[31mAverage es_time: 212.92 ± 32.219 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.438 ± 0.023 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 24.804 ± 6.531 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 244.6 ± 35.275 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 482.762 ± 70.465 ms (n=100)\u001b[0m\n",
+      "\n",
+      "\n",
+      "*** item_type: /search/?searchTerm=H3K36me3\n",
+      "----------- https://test.encodedcc.org//search/?searchTerm=H3K36me3 ------------\n",
+      "\u001b[31mAverage es_time: 248.062 ± 24.424 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.539 ± 0.023 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 38.939 ± 10.035 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 295.371 ± 28.084 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 582.911 ± 56.039 ms (n=100)\u001b[0m\n",
+      "---- https://v79rc1-master.demo.encodedcc.org//search/?searchTerm=H3K36me3 -----\n",
+      "\u001b[31mAverage es_time: 212.122 ± 23.738 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.441 ± 0.021 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 27.224 ± 6.081 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 247.042 ± 25.751 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 486.828 ± 51.462 ms (n=100)\u001b[0m\n",
+      "\n",
+      "\n",
+      "*** item_type: /search/?searchTerm=CTCF\n",
+      "------------- https://test.encodedcc.org//search/?searchTerm=CTCF --------------\n",
+      "\u001b[31mAverage es_time: 254.143 ± 28.335 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.522 ± 0.02 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 27.405 ± 7.011 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 289.241 ± 30.306 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 571.311 ± 60.455 ms (n=100)\u001b[0m\n",
+      "------ https://v79rc1-master.demo.encodedcc.org//search/?searchTerm=CTCF -------\n",
+      "\u001b[31mAverage es_time: 212.717 ± 28.256 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.431 ± 0.023 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 22.226 ± 6.054 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 241.854 ± 29.208 ms (n=100)\u001b[0m\n",
+      "\u001b[31mAverage total time: 477.229 ± 58.347 ms (n=100)\u001b[0m\n",
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "qa.check_response_time(item_types=[\"/search/?searchTerm=K562\", \"/search/?searchTerm=DNA+binding\", \"/search/?searchTerm=human\", \"/search/?searchTerm=H3K36me3\", \"/search/?searchTerm=CTCF\"], n=100)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Checking response time\n",
+      "\n",
+      "*** item_type: /ENCSR255XZG/\n",
+      "------------------- https://test.encodedcc.org//ENCSR255XZG/ -------------------\n",
+      "\u001b[31mAverage es_time: 13.068 ± 2.72 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.475 ± 0.031 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 114.842 ± 4.813 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 221.894 ± 103.95 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage total time: 350.278 ± 104.227 ms (n=100)\u001b[0m\n",
+      "------------ https://v79rc1-master.demo.encodedcc.org//ENCSR255XZG/ ------------\n",
+      "\u001b[31mAverage es_time: 13.003 ± 5.506 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.486 ± 0.043 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 135.871 ± 104.913 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage wsgi_time: 233.545 ± 126.217 ms (n=100)\u001b[0m\n",
+      "\u001b[33mAverage total time: 382.906 ± 224.928 ms (n=100)\u001b[0m\n",
+      "\n",
+      "\n",
+      "*** item_type: /ENCSR749ILN/\n",
+      "------------------- https://test.encodedcc.org//ENCSR749ILN/ -------------------\n",
+      "\u001b[36mAverage es_time: 6.697 ± 3.32 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.477 ± 0.047 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 35.722 ± 6.491 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage wsgi_time: 61.932 ± 9.362 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage total time: 104.827 ± 16.282 ms (n=100)\u001b[0m\n",
+      "------------ https://v79rc1-master.demo.encodedcc.org//ENCSR749ILN/ ------------\n",
+      "\u001b[36mAverage es_time: 6.561 ± 2.738 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage queue_time: 0.462 ± 0.025 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage render_time: 31.747 ± 5.352 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage wsgi_time: 56.845 ± 6.371 ms (n=100)\u001b[0m\n",
+      "\u001b[36mAverage total time: 95.615 ± 12.547 ms (n=100)\u001b[0m\n",
+      "\n",
+      "\n",
+      "*** item_type: /ENCSR688GVV/\n",
+      "------------------- https://test.encodedcc.org//ENCSR688GVV/ -------------------\n"
+     ]
+    }
+   ],
+   "source": [
+    "qa.check_response_time(item_types=['/ENCSR255XZG/', '/ENCSR749ILN/', '/ENCSR688GVV/', '/ENCSR301HAG/','/ENCSR315NAC/', '/ENCSR856JJB/'], n=100)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true,
+    "scrolled": true
+   },
+   "outputs": [],
+   "source": [
+    "qa.check_response_time(item_types=['/ENCSR480OHP/','/ENCSR000EMB/','/ENCSR323QIP/','/ENCSR718AXQ/','/ENCSR165BGV/','/ENCSR384KAN/','/ENCSR330FXL/','/ENCSR825UNV/','/ENCSR089EOA/'], n=100)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "qa.check_response_time(item_types=['/ENCAB830JLB/','/ENCAB000BKR/','/ENCAB284TTY/','/ENCAB294YUD/','/ENCAB000AOC/','/ENCAB301QZF/','/ENCAB000ANM/','/ENCAB000ANU/','/ENCAB445KMF/','/ENCAB000BAY/'], n=100)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "collapsed": true
+   },
+   "outputs": [],
+   "source": [
+    "qa.check_response_time(item_types=['/ENCBS787TFV/','/ENCBS676QAV/','/ENCBS996IWU/','/ENCBS913XJP/','/ENCBS565NTN/','/ENCBS896YZO/','/ENCBS280NYD/'], n=100)"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.5.1"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}