ngrams api

bigindex/SQL.py

@@ -32,7 +32,8 @@ class SQL:
 			# for item in chunk:
 			# print(item)
 			args_str = ','.join(cursor.mogrify("%s", (x, )) for x in chunk)
-			sql = "INSERT INTO publication (id, year,itemset) VALUES "+args_str+""
+			# sql = "INSERT INTO "+tablename+" (id, year,itemset) VALUES "+args_str+""
+			sql = "INSERT INTO "+tablename+" (id, label) VALUES "+args_str+""
 			# print(sql)
 
 			try:

bigindex/ngrams-api.py

+# pip install  simplejson  git+https://github.com/miguelgrinberg/Flask-Runner.git
+# pip install biopython
+#   more: https://flask-runner.readthedocs.io/en/latest/
+
+# sudo su pksm3
+# export SPARK_HOME="/opt/spark2"
+# export PATH=$SPARK_HOME/bin:$PATH
+# source env/bin/activate
+# python phylum_srv.py -t 0.0.0.0 -p 8080
+
+from flask import Flask, render_template, request , flash , jsonify , url_for
+from flask.ext.runner import Runner #*#
+import simplejson as json
+
+from flask_wtf import Form
+from wtforms import StringField, TextField, IntegerField, DecimalField, validators
+from wtforms.validators import DataRequired
+from flask_wtf.csrf import CsrfProtect
+csrf = CsrfProtect()
+
+import datetime
+import pprint
+
+app = Flask(__name__ , static_url_path='/static' )
+app.secret_key = 's3cr3t'
+csrf.init_app(app)
+runner = Runner(app) #*#
+from bigindex import LoadShit
+import urllib
+
+I = {}
+
+
+@app.route("/close", methods=("GET",))
+def close_contexts():
+	for i in I:
+		I[i].sc.stop()
+		return json.dumps( ["connections","closed"] )
+
+	for i in I:
+		del I[i]
+
+
+# p_["scontext"] (value="blabla")
+# p_["elemfrequency"] (value="1")
+# p_["from_"] (value="1983")
+# p_["to_"] (value="1984")
+# p_["minfpgsupp"] (value="0.0001")
+# p_["minfsetsize"] (value="4")
+# p_["minsetdistance"] (value="0.2")
+# p_["mram"] (value="0.2")
+# p_["ncores"] (value="0.2")
+@csrf.exempt
+@app.route("/ngrams" , methods=("GET", "POST",))
+def test_post():
+	pprint.pprint( request )
+	if request.method == "POST":
+		p_ = {}
+		print( "did a POST" )
+		for i in request.form:
+			print( i , ":", request.form[i] )
+			p_[i] = request.form[i]
+
+		rr = {
+			"hola": "mundo"
+		}
+		return json.dumps( rr )
+		# return json.dumps( ["post","worked","mofos"] )
+
+	return json.dumps( ["regular","get"] )
+	# return jsonify( data=["normal","return"] )
+
+
+
+
+runner.run()

bigindex/postg_mesh.py

+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+
+import sys
+import glob
+import json
+import pprint
+from datetime import datetime
+import time
+import re
+import json
+
+
+
+INPUT     = "mesh.json"
+# OUTPUT    = "folder"
+if len(sys.argv)>1 and sys.argv[1]!=None: INPUT = sys.argv[1]
+# if len(sys.argv)>2 and sys.argv[2]!=None: OUTPUT = sys.argv[2]
+
+
+import psycopg2
+conn = psycopg2.connect("dbname=meshfiltrd user=pksm3")
+c = conn.cursor()
+
+sql_commands = [
+	"DROP TABLE IF EXISTS june2016;",
+	"CREATE TABLE june2016( id INTEGER PRIMARY KEY , label VARCHAR(255) )",
+]
+
+for command in sql_commands:
+	c.execute(  command )
+	conn.commit()
+
+
+
+f = open( INPUT , "r" )
+K = json.load( f )
+f.close()
+
+DATA = []
+DD = {}
+C = 1
+for ID in K:
+	# if C==100: 
+	# 	break
+
+
+	if ID not in DD:
+		DD[ID] = True
+		DATA.append( (ID,K[ID],) )
+
+	C += 1
+
+
+print("")
+print("inserting...",len(DATA))
+from SQL import SQL
+execc = SQL()
+execc.InsertInto_modular( connection=conn , cursor=c , tablename="june2016" , data= DATA )
+
+
+
+print("creating indexes...")
+sql_indexes = [
+	"CREATE INDEX label_idx ON june2016 (label);"
+]
+for command in sql_indexes:
+	c.execute(  command )
+	conn.commit()
+
+
+conn.close()
+
+
+
+
+
+
+
+
+
+# # # # CREATE INDEX # #
+# # import psycopg2
+# # conn = psycopg2.connect("dbname=pubmed user=pksm3")
+# # c = conn.cursor()
+# # print("creating indexes...")
+# # sql_indexes = [
+# # 	"CREATE INDEX year_idx ON publication (year);"
+# # ]
+# # for command in sql_indexes:
+# # 	c.execute(  command )
+# # 	conn.commit()
+# # conn.close()
\ No newline at end of file

static/phylomain.js

@@ -262,6 +262,7 @@ function pubmed_scan( query ) {
             retmax: 0
         },
         success : function(data) { 
+            console.log( data.esearchresult )
             var count =  parseInt( data.esearchresult.count )
             console.log( "AAAAH "+count )
             $("#pubmed_scan-results").html( count+" hits." )