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09_oacct_read_and_publish.py
f6ac3b58106fissn4frontend

09_oacct_read_and_publish.py
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			#!/usr/bin/env python
			# coding: utf-8

			# # Projet Open Access Compliance Check Tool (OACCT)
			#
			# Projet P5 de la bibliothèque de l'EPFL en collaboration avec les bibliothèques des Universités de Genève, Lausanne et Berne : https://www.swissuniversities.ch/themen/digitalisierung/p-5-wissenschaftliche-information/projekte/swiss-mooc-service-1-1-1-1
			#
			# Ce notebook permet de modifier les données extraites des differentes sources et les exporter dans les tables de l'application OACCT.
			#
			# Auteur : Pablo Iriarte, Université de Genève (pablo.iriarte@unige.ch)
			# Date de dernière mise à jour : 08.09.2021

			# In[1]:


			import pandas as pd
			import csv
			import json
			import numpy as np
			import os
			# afficher toutes les colonnes
			pd.set_option('display.max_columns', None)
			# definir le debut des ids
			id_start = 1


			# ## Ajout des rabais pour les revues des licences Read & Publish
			#
			# Journals list by publisher :
			# * https://consortium.ch/elsevier_titlelist_publication
			# * https://consortium.ch/springer_titlelist_publication
			# * https://consortium.ch/wiley_titlelist_publish
			# * https://consortium.ch/tandf_titlelist_publish
			# * https://consortium.ch/sage_titlelist_publish
			# * https://consortium.ch/cup_titlelist_publish
			#
			# Licence term :
			# * Elsevier : 2020-2023
			# * Springer Nature : 2020-2022
			# * Wiley : 2021-2024
			# * Taylor & Francis : 2021-2023
			# * Cambridge University Press (CUP) : 2021-2023
			#
			# CC licences :
			# * Elsevier : CC-BY, CC-BY-NC-ND
			# * Springer Nature : CC-BY, CC-BY-NC
			# * Wiley : CC-BY, CC-BY-NC, CC-BY-NC-ND
			# * Taylor & Francis : CC-BY
			# * Cambridge University Press (CUP) : CC-BY, CC-BY-NC, CC-BY-NC-ND, CC-BY-NC-SA
			#
			# Special conditions :
			# * Cambridge University Press (CUP) : Only the following article types are covered: Research Articles, Review Articles, Rapid Communication, Brief Reports and Case Reports
			#
			#

			# ## Import du fichier des issns

			# In[2]:


			issn = pd.read_csv('sample/issn.tsv', encoding='utf-8', header=0, sep='\t')
			issn


			# In[3]:


			# open publishers
			publisher = pd.read_csv('sample/publisher.tsv', encoding='utf-8', header=0, sep='\t')
			publisher


			# In[4]:


			publisher.loc[publisher['name'] == 'Elsevier']


			# In[5]:


			publisher.loc[(publisher['name'] == 'Springer Verlag') \| (publisher['name'] == 'Nature Research')]


			# In[6]:


			publisher.loc[publisher['name'] == 'Wiley']


			# In[7]:


			publisher.loc[publisher['name'] == 'Taylor and Francis']


			# In[8]:


			publisher.loc[publisher['name'] == 'Cambridge University Press']


			# In[9]:


			# ouvrir la liste d'organisations
			participants = pd.read_csv('agreements/consortium_institutions_participation_read_and_publish.csv', encoding='utf-8', header=0, sep='\t')
			participants


			# In[10]:


			# suppression de Lib4RI qui est une bibliothèque
			participants = participants.loc[participants['Institution'] != 'Lib4RI']
			participants


			# In[11]:


			# ajout de TF et CUP pour tous (TODO : obtenir la liste des bibliothèques pour ces deux licences)
			participants['TF'] = 'x'
			participants['CUP'] = 'x'
			participants


			# In[12]:


			# ouvrir la liste des journaux Elsevier
			elsevier = pd.read_excel('agreements/Elsevier_titlelist_publication.xlsx', skiprows=7)
			elsevier


			# In[13]:


			# ajout du champ version
			elsevier['article_version'] = 'published'
			elsevier


			# In[14]:


			# ajout des dates
			elsevier['valid_from'] = '2020-01-01'
			elsevier['valid_until'] = '2023-12-31'
			elsevier


			# In[15]:


			# ajout du embargo et archiving
			elsevier['embargo_months'] = 0
			elsevier['archiving'] = True
			elsevier


			# In[16]:


			elsevier.iloc[elsevier.shape[0]-1]


			# In[17]:


			# ajout du champ license
			# cc_by, cc_by_nc_nd
			rp = pd.DataFrame()
			elsevier['article_version'] = 'published'
			elsevier['license'] = 'cc_by'
			elsevier['Elsevier'] = 'x'
			rp = rp.append(elsevier, ignore_index=True)
			elsevier['license'] = 'cc_by_nc_nd'
			rp = rp.append(elsevier, ignore_index=True)
			rp


			# In[18]:


			# ouvrir la liste des journaux Springer Nature
			springer = pd.read_excel('agreements/Springer_titlelist_publication.xlsx', skiprows=7)
			springer


			# In[19]:


			# ajout du champ license
			# cc_by, cc_by_nc
			springer['article_version'] = 'published'
			springer['license'] = 'cc_by'
			springer['Springer Nature'] = 'x'
			# ajout des dates
			springer['valid_from'] = '2020-01-01'
			springer['valid_until'] = '2022-12-31'
			# ajout du embargo et archiving
			springer['embargo_months'] = 0
			springer['archiving'] = True


			# In[20]:


			# append
			rp = rp.append(springer, ignore_index=True)
			springer['license'] = 'cc_by_nc'
			rp = rp.append(springer, ignore_index=True)
			rp


			# In[21]:


			# ouvrir la liste des journaux Wiley
			wiley = pd.read_excel('agreements/Wiley_titlelist_publish.xlsx', skiprows=7)
			wiley


			# In[22]:


			# ajout du champ license
			# cc_by, cc_by_nc, cc_by_nc_nd
			wiley['article_version'] = 'published'
			wiley['license'] = 'cc_by'
			wiley['Wiley'] = 'x'
			# ajout des dates
			wiley['valid_from'] = '2021-01-01'
			wiley['valid_until'] = '2024-12-31'
			# ajout du embargo et archiving
			wiley['embargo_months'] = 0
			wiley['archiving'] = True
			rp = rp.append(wiley, ignore_index=True)
			# append avec une autre licence
			wiley['license'] = 'cc_by_nc'
			rp = rp.append(wiley, ignore_index=True)
			# append avec une autre licence
			wiley['license'] = 'cc_by_nc_nd'
			rp = rp.append(wiley, ignore_index=True)
			rp


			# In[23]:


			# ouvrir la liste des journaux TF
			tf = pd.read_excel('agreements/TandF_titlelist_publish.xlsx', skiprows=7)
			tf


			# In[24]:


			# ajout du champ license
			# cc_by, cc_by_nc, cc_by_nc_nd
			tf['article_version'] = 'published'
			tf['license'] = 'cc_by'
			tf['TF'] = 'x'
			# ajout des dates
			tf['valid_from'] = '2021-01-01'
			tf['valid_until'] = '2023-12-31'
			# ajout du embargo et archiving
			tf['embargo_months'] = 0
			tf['archiving'] = True


			# In[25]:


			# append
			rp = rp.append(tf, ignore_index=True)
			rp


			# In[26]:


			# ouvrir la liste des journaux CUP
			cup = pd.read_excel('agreements/CUP_Journals_titlelist_publish.xlsx', skiprows=7)
			cup


			# In[27]:


			# renommer l'ISSN
			cup = cup.rename(columns = {'e-ISSN' : 'ISSN'})
			cup


			# In[28]:


			# ajout du champ license
			# cc_by, cc_by_nc, cc_by_nc_nd, cc_by_nc_sa
			cup['article_version'] = 'published'
			cup['license'] = 'cc_by'
			cup['CUP'] = 'x'
			# ajout des dates
			cup['valid_from'] = '2021-01-01'
			cup['valid_until'] = '2023-12-31'
			# ajout du embargo et archiving
			cup['embargo_months'] = 60
			cup['archiving'] = True


			# In[29]:


			# append
			rp = rp.append(cup, ignore_index=True)
			cup['license'] = 'cc_by_nc'
			rp = rp.append(cup, ignore_index=True)
			cup['license'] = 'cc_by_nc_nd'
			rp = rp.append(cup, ignore_index=True)
			cup['license'] = 'cc_by_nc_sa'
			rp = rp.append(cup, ignore_index=True)
			rp


			# In[30]:


			# test des lignes sans embargo
			rp.loc[rp['embargo_months'].isna()]


			# In[31]:


			# ajout des ISSN-L
			issnl = pd.read_csv('issn/20171102.ISSN-to-ISSN-L.txt', encoding='utf-8', header=0, sep='\t')
			issnl


			# In[32]:


			# renommer les colonnes
			issnl = issnl.rename(columns={'ISSN' : 'issn', 'ISSN-L' : 'issnl'})
			rp = rp.rename(columns={'ISSN' : 'issn'})


			# In[33]:


			# merge
			rp = pd.merge(rp, issnl, on='issn', how='left')
			rp


			# In[34]:


			# cummuler les issns pour le merge
			# rp_1 = rp.loc[rp['issnl'].notna()][['issnl', 'article_version', 'license', 'Elsevier', 'Springer Nature', 'Wiley', 'TF', 'CUP']]
			# rp_1 = rp_1.rename(columns = {'issnl' : 'issn'})
			# rp_2 = rp.loc[rp['issn'].notna()][['issn', 'article_version', 'license', 'Elsevier', 'Springer Nature', 'Wiley', 'TF', 'CUP']]
			# rp_all = rp_1.append(rp_2, ignore_index=True)
			rp_all = rp


			# In[35]:


			# ajouter les champs manquants
			# valeur discount (id 2) à 100% pour les licences read & publish
			# elsevier['amount'] = 100
			# elsevier['symbol'] = '%'
			# elsevier['cost_factor_type'] = 2
			# elsevier['comment'] = 'Source: swissuniversities'
			# elsevier


			# In[36]:


			# merge avec les organisations
			# 'Elsevier', 'Springer Nature', 'Wiley', 'TF', 'CUP'
			participants_elsevier = participants.loc[participants['Elsevier'].notna()][['Elsevier', 'ROR']]
			rp_elsevier = rp_all.loc[rp_all['Elsevier'].notna()]
			rp_1 = pd.merge(rp_elsevier, participants_elsevier, on='Elsevier', how='outer')
			rp_1


			# In[37]:


			rp_elsevier


			# In[38]:


			participants_elsevier


			# In[39]:


			# merge avec les organisations
			# 'Elsevier', 'Springer Nature', 'Wiley', 'TF', 'CUP'
			participants_springer = participants.loc[participants['Springer Nature'].notna()][['Springer Nature', 'ROR']]
			rp_springer = rp_all.loc[rp_all['Springer Nature'].notna()]
			rp_2 = pd.merge(rp_springer, participants_springer, on='Springer Nature', how='outer')
			rp_2


			# In[40]:


			# merge avec les organisations
			# 'Elsevier', 'Springer Nature', 'Wiley', 'TF', 'CUP'
			participants_wiley = participants.loc[participants['Wiley'].notna()][['Wiley', 'ROR']]
			rp_wiley = rp_all.loc[rp_all['Wiley'].notna()]
			rp_3 = pd.merge(rp_wiley, participants_wiley, on='Wiley', how='outer')
			rp_3


			# In[41]:


			rp_wiley


			# In[42]:


			# merge avec les organisations
			# 'Elsevier', 'Springer Nature', 'Wiley', 'TF', 'CUP'
			participants_tf = participants.loc[participants['TF'].notna()][['TF', 'ROR']]
			rp_tf = rp_all.loc[rp_all['TF'].notna()]
			rp_4 = pd.merge(rp_tf, participants_tf, on='TF', how='outer')
			rp_4


			# In[43]:


			# merge avec les organisations
			# 'Elsevier', 'Springer Nature', 'Wiley', 'TF', 'CUP'
			participants_cup = participants.loc[participants['CUP'].notna()][['CUP', 'ROR']]
			rp_cup = rp_all.loc[rp_all['CUP'].notna()]
			rp_5 = pd.merge(rp_cup, participants_cup, on='CUP', how='outer')
			rp_5


			# In[44]:


			# concat des 5
			rp_fin = rp_1.append(rp_2, ignore_index=True)
			rp_fin = rp_fin.append(rp_3, ignore_index=True)
			rp_fin = rp_fin.append(rp_4, ignore_index=True)
			rp_fin = rp_fin.append(rp_5, ignore_index=True)
			rp_fin


			# In[45]:


			# supprimer les doublons et les vides
			rp_fin = rp_fin.dropna(subset=['issn'])
			rp_fin = rp_fin.drop_duplicates(subset=['issn', 'license', 'ROR'])
			rp_fin


			# In[46]:


			# reindex et ajout de l'id avec l'index + 1
			rp_fin = rp_fin.reset_index()
			del rp_fin['index']
			rp_fin = rp_fin.reset_index()
			rp_fin['rp_id'] = rp_fin.index + 1
			rp_fin


			# In[47]:


			rp_fin['embargo_months'].value_counts()


			# In[48]:


			# test des lignes sans embargo
			rp_fin.loc[rp_fin['embargo_months'].isna()]


			# In[49]:


			issn


			# In[50]:


			# merge pour avoir l'issnl
			issn = pd.merge(issn, issnl, on='issn', how='left')
			issn


			# In[51]:


			issn.loc[issn['issnl'].isna()]


			# In[52]:


			# merge dans l'autre sens pour garder que les lignes du fichier
			rp_fin = pd.merge(rp_fin, issn[['id', 'journal', 'issnl']], on='issnl', how='left')
			rp_fin


			# In[53]:


			# test des lignes sans embargo
			rp_fin.loc[rp_fin['embargo_months'].isna() & rp_fin['id'].notna()]


			# In[54]:


			# garder les lignes avec merge
			rp_fin_merge = rp_fin.loc[rp_fin['id'].notna()]
			rp_fin_merge


			# In[55]:


			# supprimer les doublons et les vides
			rp_fin_merge = rp_fin_merge.drop_duplicates(subset=['rp_id'])
			rp_fin_merge


			# In[56]:


			# test des lignes sans journal
			rp_fin_merge.loc[rp_fin_merge['journal'].isna()]


			# In[57]:


			# convertir l'index en id
			del rp_fin_merge['id']
			del rp_fin_merge['index']
			del rp_fin_merge['rp_id']
			rp_fin_merge = rp_fin_merge.reset_index()
			# ajout de l'id avec l'index + 1
			rp_fin_merge['rp_id'] = rp_fin_merge['index'] + 1
			del rp_fin_merge['index']
			rp_fin_merge


			# In[58]:


			# convertir l'index en id
			del rp_fin_merge['rp_id']
			rp_fin_merge = rp_fin_merge.reset_index()
			# ajout de l'id avec l'index + 1
			rp_fin_merge['rp_id'] = rp_fin_merge['index'] + 1
			del rp_fin_merge['index']
			rp_fin_merge


			# In[59]:


			rp_fin_merge['embargo_months'].value_counts()


			# In[60]:


			# test des lignes sans embargo
			rp_fin_merge.loc[rp_fin_merge['embargo_months'].isna()]


			# In[61]:


			# export excel
			rp_fin_merge.to_excel('sample/read_publish_brut_merge.xlsx', index=False)


			# In[62]:


			# export csv
			rp_fin_merge.to_csv('sample/read_publish_brut_merge.tsv', sep='\t', index=False)

rOACCT/import_scripts/09_oacct_read_and_publish.pyf6ac3b58106fissn4frontend

09_oacct_read_and_publish.pyView Options

rOACCT/import_scripts/09_oacct_read_and_publish.py
f6ac3b58106fissn4frontend

09_oacct_read_and_publish.py
View Options