almugabo

## reference_extraction.py
"""
FROM: https://gist.github.com/sobolevnrm/412763ebae5424a92d3239898b615e2a

Process RIS format following the standard at",
http://referencemanager.com/sites/rm/files/m/direct_export_ris.pdf """

import re

ALLOWED_TAGS = {"TY" : "Record start",
                "ER" : "Record end",

## get_photo_unsplash.py
# get photo from unsplash
# depends on python-unsplash
# !pip install python-unsplash

from unsplash.api import Api
from unsplash.auth import Auth
import requests
from PIL import Image
from io import BytesIO

## resnews_template_word.py
# create style


from docx import Document
# create style
from docx.enum.style import WD_STYLE_TYPE
from docx.shared import Inches, Pt

## TO DO
## [1] add an image in a cell

## resnews_templating.py
from string import Template

xDocHead = '''<!DOCTYPE html>
<html><head>
<meta http-equiv="content-type" content="text/html; charset=windows-1252">
    <style>

    .title_orange {
        font-family: Verdana, Geneva, sans-serif;
        font-size: 14px;

## open_patent_services.py
import requests
from base64 import b64encode
import requests
import json

UrlAuth         = 'https://ops.epo.org/3.2/auth/accesstoken'
UrlServiceBase  = 'https://ops.epo.org/3.2/rest-services/published-data'
UrlServiceBaseSearch = UrlServiceBase + '/search/biblio/?q='


## HungarianMethod.py
import pandas as pd
import numpy as np
from scipy.optimize import linear_sum_assignment


def make_assignments(xDF):
    '''
    a simple wrapper around the
    scipy.optimize.linear_sum_assignment
    which implements the Hungarian Algorithm

## genMetaPaths.py
#!/usr/bin/env python
# coding: utf-8
# March 7th, 2019 (by mm)
##  Generating paths (walks)
## inspired by the original py4genMetaPaths.py from
## but also : by stellargraph
## TO DO : create tests

import pandas as pd
import random

## PythonExcelConditionalFormat.py
# CONDITIONAL FORMATTING in Excel with python
# we could use OpenPyXL or xlsxwriter
# Here we use xlsxwriter
#https://xlsxwriter.readthedocs.io/working_with_conditional_formats.html
#https://xlsxwriter.readthedocs.io/example_conditional_format.html#ex-cond-format

import pandas as pd
import xlsxwriter


## misc.py
# a collection of various functionlities

## export json records from pandas

xSQL = '''select * from studies_analysis.qa_oa_syg_joined_dataset limit 5'''
d1 = pd.read_sql(xSQL, xPGCon)

d1.to_json('qa_oa_syg_joined_dataset.json', orient= 'records')


## wikipathway_parse
import requests, base64, xmltodict
xUrl = 'http://webservice.wikipathways.org/getPathway?pwId=WP901'
xq1 = requests.get(xUrl)

xgml_field = xmltodict.parse(xq1.content)['ns1:getPathwayResponse']['ns1:pathway']['ns2:gpml']
base64.b64decode(xgml_field )
	"""
	FROM: https://gist.github.com/sobolevnrm/412763ebae5424a92d3239898b615e2a

	Process RIS format following the standard at",
	http://referencemanager.com/sites/rm/files/m/direct_export_ris.pdf """

	import re

	ALLOWED_TAGS = {"TY" : "Record start",
	"ER" : "Record end",
	# get photo from unsplash
	# depends on python-unsplash
	# !pip install python-unsplash

	from unsplash.api import Api
	from unsplash.auth import Auth
	import requests
	from PIL import Image
	from io import BytesIO
	# create style


	from docx import Document
	# create style
	from docx.enum.style import WD_STYLE_TYPE
	from docx.shared import Inches, Pt

	## TO DO
	## [1] add an image in a cell
	from string import Template

	xDocHead = '''<!DOCTYPE html>
	<html><head>
	<meta http-equiv="content-type" content="text/html; charset=windows-1252">
	<style>

	.title_orange {
	font-family: Verdana, Geneva, sans-serif;
	font-size: 14px;
	import requests
	from base64 import b64encode
	import requests
	import json

	UrlAuth = 'https://ops.epo.org/3.2/auth/accesstoken'
	UrlServiceBase = 'https://ops.epo.org/3.2/rest-services/published-data'
	UrlServiceBaseSearch = UrlServiceBase + '/search/biblio/?q='
	import pandas as pd
	import numpy as np
	from scipy.optimize import linear_sum_assignment


	def make_assignments(xDF):
	'''
	a simple wrapper around the
	scipy.optimize.linear_sum_assignment
	which implements the Hungarian Algorithm
	#!/usr/bin/env python
	# coding: utf-8
	# March 7th, 2019 (by mm)
	## Generating paths (walks)
	## inspired by the original py4genMetaPaths.py from
	## but also : by stellargraph
	## TO DO : create tests

	import pandas as pd
	import random
	# CONDITIONAL FORMATTING in Excel with python
	# we could use OpenPyXL or xlsxwriter
	# Here we use xlsxwriter
	#https://xlsxwriter.readthedocs.io/working_with_conditional_formats.html
	#https://xlsxwriter.readthedocs.io/example_conditional_format.html#ex-cond-format

	import pandas as pd
	import xlsxwriter
	# a collection of various functionlities

	## export json records from pandas

	xSQL = '''select * from studies_analysis.qa_oa_syg_joined_dataset limit 5'''
	d1 = pd.read_sql(xSQL, xPGCon)

	d1.to_json('qa_oa_syg_joined_dataset.json', orient= 'records')
	import requests, base64, xmltodict
	xUrl = 'http://webservice.wikipathways.org/getPathway?pwId=WP901'
	xq1 = requests.get(xUrl)

	xgml_field = xmltodict.parse(xq1.content)['ns1:getPathwayResponse']['ns1:pathway']['ns2:gpml']
	base64.b64decode(xgml_field )