03_oacct_journals.py
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03_oacct_journals.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 d'extraire les données choisis parmis les sources obtenues par API et les traiter pour les rendre exploitables dans l'application OACCT.
	#
	# Auteur : Pablo Iriarte, Université de Genève (pablo.iriarte@unige.ch)
	# Date de dernière mise à jour : 16.07.2021

	# ## Extraction des données des revues
	#
	#
	# ## Corpus initial
	#
	# ISSNs des revues des publication archivées sur l'AoU UNIGE et sur Infoscience EPFL
	#
	# * Fichier des ISSNs de l'AoU exporté le 16.10.2020
	# * Fichier des ISSNs de Infoscience exporté le 28.01.2021
	# * Données extraits à partir du JSON de ISSN.org
	#

	# In[1]:


	import pandas as pd
	import csv
	import json
	import numpy as np
	import os
	# paramètre pour le nombre de journaux dans le sample (0 pour prendre tout)
	journals_sample_n = 1000


	# ## Table OA categories
	#
	# * 1 : UNKNOWN
	# * 2 : Green
	# * 3 : Hybrid
	# * 4 : Full
	# * 5 : Gold
	# * 6 : Diamond

	# In[2]:


	# creation du DF
	col_names = ['id',
	'status',
	'description',
	'subscription',
	'accepted_manuscript',
	'apc',
	'final_version'
	]
	oas = pd.DataFrame(columns = col_names)
	oas


	# In[3]:


	# ajout des valeurs
	oas = oas.append({'id' : 1, 'status' : 'UNKNOWN', 'description' : '', 'subscription' : 0, 'accepted_manuscript' : 0, 'apc' : 0, 'final_version' : 0}, ignore_index=True)
	oas = oas.append({'id' : 2, 'status' : 'Green', 'description' : 'Paywalled access journal, usually allows the archive of submitted or accepted version on institutional repositories (embargo periods may apply)', 'subscription' : 1, 'accepted_manuscript' : 1, 'apc' : 0, 'final_version' : 0}, ignore_index=True)
	oas = oas.append({'id' : 3, 'status' : 'hybrid', 'description' : 'Paywalled access journal, offers several Open Access upon payment of APCs. It allows offten the archive of published version on institutional repositories (embargo periods can apply)', 'subscription' : 1, 'accepted_manuscript' : 1, 'apc' : 1, 'final_version' : 1}, ignore_index=True)
	# oas = oas.append({'id' : 4, 'status' : 'Full', 'description' : 'No subscription, Green or Gold', 'subscription' : 0, 'accepted_manuscript' : 1, 'apc' : 0, 'final_version' : 1}, ignore_index=True)
	oas = oas.append({'id' : 5, 'status' : 'Gold', 'description' : 'Open Access journal (payment of APCs may apply). It allows offten the archive of published version on institutional repositories (embargo periods can apply)', 'subscription' : 0, 'accepted_manuscript' : 1, 'apc' : 1, 'final_version' : 1}, ignore_index=True)
	oas = oas.append({'id' : 6, 'status' : 'Diamond', 'description' : 'Open Access journal (without payment of APCs). It allows offten the archive of published version on institutional repositories (embargo periods can apply)', 'subscription' : 0, 'accepted_manuscript' : 1, 'apc' : 0, 'final_version' : 1}, ignore_index=True)


	# In[4]:


	oas


	# In[5]:


	# esport JSON
	result = oas.to_json(orient='records', force_ascii=False)
	parsed = json.loads(result)
	with open('sample/oa.json', 'w', encoding='utf-8') as file:
	json.dump(parsed, file, indent=2, ensure_ascii=False)


	# In[6]:


	# export csv
	oas.to_csv('sample/oa.tsv', sep='\t', encoding='utf-8', index=False)


	# In[7]:


	# export excel
	oas.to_excel('sample/oa.xlsx', index=False)


	# ## Table Journals

	# In[8]:


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


	# In[9]:


	# ajout des colonnes
	issns.insert(0, 'id', '', False)
	issns


	# In[10]:


	# convertir l'index en id
	issns = issns.reset_index()
	issns


	# In[11]:


	# ajout de l'id avec l'index + 1
	issns['id'] = issns['index'] + 1
	del issns['index']
	issns


	# In[12]:


	# reduction à X journaux pour l'échantillon de test
	if journals_sample_n > 0 :
	issns = issns.loc[:journals_sample_n]
	issns


	# In[13]:


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


	# In[14]:


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


	# In[15]:


	issns = pd.merge(issns, df_issnl, on='issn', how='left')
	issns


	# In[16]:


	# creation du DF
	# 'oa_status' supprimé pour le moment
	col_names = ['id',
	'issn',
	'issnl',
	'title',
	'starting_year',
	'end_year',
	'url',
	'name_short_iso_4'
	]
	journals = pd.DataFrame(columns = col_names)
	journals


	# In[17]:


	# creation du DF
	col_names = ['id', 'iso_code']
	journals_languages = pd.DataFrame(columns = col_names)
	journals_languages


	# In[18]:


	# creation du DF
	# 'oa_status' supprimé
	col_names = ['id', 'iso_code']
	journals_countries = pd.DataFrame(columns = col_names)
	journals_countries


	# In[19]:


	# extraction des informations à partir des données ISSN.org
	for index, row in issns.iterrows():
	myid = row['id']
	myissn = row['issn']
	if (((index/10) - int(index/10)) == 0) :
	print(index)
	# initialisation des variables à extraire
	issnl = np.nan
	title = ''
	keytitle = ''
	starting_year = np.nan
	end_year = np.nan
	myurl = np.nan
	journal_country = np.nan
	journal_language = np.nan
	keytitle_abbr = np.nan
	# export en json
	if os.path.exists('issn/data/' + myissn + '.json'):
	with open('issn/data/' + myissn + '.json', 'r', encoding='utf-8') as f:
	data = json.load(f)
	for x in data['@graph']:
	if ('@id' in x):
	if (x['@id'] == 'resource/ISSN/' + myissn):
	if ('mainTitle' in x):
	title = x['mainTitle']
	else :
	if ('name' in x):
	title = x['name']
	# print(myissn)
	if ('startDate' in x):
	starting_year = x['startDate']
	if ('endDate' in x):
	end_year = x['endDate']
	if ('url' in x):
	urls = x['url']
	if type(urls) is list:
	for url in urls:
	# Filtrer les URLs des archives :
	# www.ncbi.nlm.nih.gov/pmc/*
	# www.pubmedcentral.gov/*
	# pubmedcentral.nih.gov/*
	# bibpurl.oclc.org/*
	# www.jstor.org/*
	# ieeexplore.ieee.org
	# ovidsp.ovid.com
	# et garder le premier des restants
	myurl = url
	if ('ncbi.nlm.nih.gov' not in url
	and 'pubmedcentral' not in url
	and 'bibpurl.oclc.org' not in url
	and 'jstor.org' not in url
	and 'ieeexplore.ieee.org' not in url
	and 'ovidsp.ovid.com' not in url):
	break
	else :
	myurl = x['url']
	if ('spatial' in x):
	countries = x['spatial']
	if type(countries) is list:
	for country in countries:
	if ('https://www.iso.org/obp/ui/#iso:code:3166:' in country):
	journal_country = country[-2:]
	journals_countries = journals_countries.append({'id' : myid, 'iso_code' : journal_country}, ignore_index=True)
	else :
	if ('https://www.iso.org/obp/ui/#iso:code:3166:' in countries):
	journal_country = countries[-2:]
	journals_countries = journals_countries.append({'id' : myid, 'iso_code' : journal_country}, ignore_index=True)
	# langue "inLanguage": "http://id.loc.gov/vocabulary/iso639-2/eng",
	if ('inLanguage' in x):
	languages = x['inLanguage']
	if type(languages) is list:
	for language in languages:
	journal_language = language[-3:]
	journals_languages = journals_languages.append({'id' : myid, 'iso_code' : journal_language}, ignore_index=True)
	else :
	journal_language = languages[-3:]
	journals_languages = journals_languages.append({'id' : myid, 'iso_code' : journal_language}, ignore_index=True)
	if (x['@id'] == 'resource/ISSN/' + myissn + '#KeyTitle'):
	if ('value' in x):
	keytitle = x['value']
	if (x['@id'] == 'resource/ISSN/' + myissn + '#ISSN-L'):
	if ('value' in x):
	issnl = x['value']
	# "@id": "resource/ISSN/1098-0121#AbbreviatedKeyTitle",
	if (x['@id'] == 'resource/ISSN/' + myissn + '#AbbreviatedKeyTitle'):
	if ('value' in x):
	mykeytitle_abbrs = x['value']
	if type(mykeytitle_abbrs) is list:
	for mykeytitle_abbr in mykeytitle_abbrs:
	print(myissn + ' - AbbreviatedKeyTitle is a list ' + mykeytitle_abbr)
	keytitle_abbr = mykeytitle_abbr
	with open('sample/03_journals_issn_multiple_titles.txt', 'a', encoding='utf-8') as g:
	g.write(myissn + ' AbbreviatedKeyTitle is a list ' + mykeytitle_abbr + '\n')
	break
	else :
	keytitle_abbr = mykeytitle_abbrs
	if keytitle != '' :
	title = keytitle
	if title != '' :
	# supprimer le point à la fin
	if (title[-1] == '.'):
	title = title[0:-1]
	# remplacer les caractères spéciaux The
	if type(title) is list:
	for mytitlei in title:
	print(myissn + ' - title is a list ' + mytitlei)
	title = str.replace(mytitlei, 'The ', 'The ')
	with open('sample/03_journals_issn_multiple_titles.txt', 'a', encoding='utf-8') as g:
	g.write(myissn + ' title is a list ' + mytitlei + '\n')
	break
	else :
	title = str.replace(title, 'The ', 'The ')
	else :
	print(row['issn'] + ' - not found')
	with open('sample/03_journals_issn_errors.txt', 'a', encoding='utf-8') as g:
	g.write(row['issn'] + ' not found \n')
	journals.at[index,'id'] = myid
	journals.at[index,'title'] = title
	journals.at[index,'issn'] = myissn
	journals.at[index,'issnl'] = issnl
	journals.at[index,'starting_year'] = starting_year
	journals.at[index,'end_year'] = end_year
	journals.at[index,'url'] = myurl
	journals.at[index,'name_short_iso_4'] = keytitle_abbr


	# In[20]:


	journals


	# In[21]:


	# titres vides
	journals.loc[journals['title'] == '']


	# In[22]:


	# export csv des titres vides
	journals.loc[journals['title'] == ''].to_csv('sample/journals_sans_titre.tsv', sep='\t', encoding='utf-8', index=False)


	# In[23]:


	# export excel des ids
	journals.loc[journals['title'] == ''].to_excel('sample/journals_sans_titre.xlsx', index=False)


	# In[24]:


	# garder les lignes avec titre
	journals = journals.loc[journals['title'] != '']
	journals


	# In[25]:


	journals.shape[0]


	# ## Languages

	# In[26]:


	journals_languages


	# In[27]:


	# ouvrir la table des langues
	languages = pd.read_csv('sample/language.tsv', encoding='utf-8', header=0, sep='\t')
	languages


	# In[28]:


	# renommer les colonnes
	del languages['name']
	languages = languages.rename(columns={'id' : 'language'})


	# In[29]:


	# merge avec languages
	journals_languages = pd.merge(journals_languages, languages, on='iso_code', how='left')
	journals_languages


	# In[30]:


	# concat valeurs avec même id
	journals_languages['language'] = journals_languages['language'].astype(str)
	journals_languages = journals_languages.groupby('id').agg({'language': lambda x: ', '.join(x)})
	journals_languages


	# In[31]:


	# recuperation de l'id des langues
	journals = pd.merge(journals, journals_languages, on='id', how='left')
	journals


	# ## Countries

	# In[32]:


	journals_countries


	# In[33]:


	# ouvrir la table des pays
	country = pd.read_csv('sample/country.tsv', encoding='utf-8', header=0, sep='\t')
	country


	# In[34]:


	# renommer les colonnes
	del country['name']
	country = country.rename(columns={'id' : 'country'})


	# In[35]:


	# merge avec countries
	journals_countries = pd.merge(journals_countries, country, on='iso_code', how='left')
	journals_countries


	# In[36]:


	# concat valeurs avec même id
	journals_countries['country'] = journals_countries['country'].astype(str)
	journals_countries = journals_countries.groupby('id').agg({'country': lambda x: ', '.join(x)})
	journals_countries


	# In[37]:


	# recuperation de l'id des langues
	journals = pd.merge(journals, journals_countries, on='id', how='left')
	journals


	# ### DOAJ

	# In[38]:


	# ajout de DOAJ info
	doaj = pd.read_csv('doaj/journalcsv__doaj_20210312_0636_utf8.csv', encoding='utf-8', header=0)
	doaj


	# In[39]:


	# ajout ISSNL
	doaj['issn'] = doaj['Journal ISSN (print version)']
	doaj.loc[doaj['issn'].isna(), 'issn'] = doaj['Journal EISSN (online version)']
	doaj


	# In[40]:


	doaj = pd.merge(doaj, df_issnl, on='issn', how='left')
	doaj


	# In[41]:


	doaj.columns


	# In[42]:


	doaj['Preservation Services']


	# In[43]:


	doaj['DOAJ Seal']


	# In[44]:


	doaj['issnl']


	# In[45]:


	doaj['APC'].value_counts()


	# In[46]:


	# ajout des infos de DOAJ :
	# Journal title
	# DOAJ Seal
	doaj_for_merge = doaj[['issnl', 'Journal title', 'DOAJ Seal', 'APC']]
	doaj_for_merge


	# In[47]:


	# renommer les colonnes
	doaj_for_merge = doaj_for_merge.rename(columns={'Journal title' : 'doaj_title', 'DOAJ Seal' : 'doaj_seal'})
	doaj_for_merge


	# In[48]:


	# merge avec journals
	journals = pd.merge(journals, doaj_for_merge, on='issnl', how='left')
	journals


	# In[49]:


	# ajouter info sur la presence sur DOAJ ou du seal
	journals.loc[journals['doaj_title'].isna(), 'doaj_status'] = 0
	journals.loc[~journals['doaj_title'].isna(), 'doaj_status'] = 1
	journals.loc[journals['doaj_seal'] == 'Yes', 'doaj_seal'] = 1
	journals.loc[journals['doaj_seal'] == 'No', 'doaj_seal'] = 0
	journals


	# ### LOCKSS

	# In[50]:


	# ajout des infos de preservation LOCKSS, Portico et Licences Nationales
	lockss = pd.read_csv('lockss/keepers-LOCKSS-report.csv', encoding='utf-8', header=0, skiprows=1)
	lockss


	# In[51]:


	# ajout ISSNL
	lockss['issn'] = lockss['eISSN']
	lockss.loc[lockss['eISSN'].isna(), 'issn'] = lockss['ISSN']
	lockss


	# In[52]:


	lockss = pd.merge(lockss, df_issnl, on='issn', how='left')
	lockss


	# In[53]:


	lockss.columns


	# In[54]:


	# test des lignes sans merge
	lockss.loc[lockss['issnl'].isna()]


	# In[55]:


	# utiliser l'ISSN à la place sur ces lignes
	lockss.loc[lockss['issnl'].isna(), 'issnl'] = lockss['issn']


	# In[56]:


	# test des lignes sans merge
	lockss.loc[lockss['issnl'].isna()]


	# In[57]:


	# ajout des infos de LOCKSS :
	# Title
	lockss_for_merge = lockss[['issnl', 'Title']]
	lockss_for_merge


	# In[58]:


	# renommer les colonnes
	lockss_for_merge = lockss_for_merge.rename(columns={'Title' : 'lockss_title'})
	lockss_for_merge


	# In[59]:


	# merge avec journals
	journals = pd.merge(journals, lockss_for_merge, on='issnl', how='left')
	journals


	# In[60]:


	# suppression des doublons
	journals = journals.drop_duplicates(subset=['id'])
	journals


	# In[61]:


	# ajouter info sur la presence sur LOCKSS
	journals.loc[journals['lockss_title'].isna(), 'lockss'] = 0
	journals.loc[~journals['lockss_title'].isna(), 'lockss'] = 1
	journals


	# ### Portico

	# In[62]:


	# ajout des infos de preservation Portico
	portico = pd.read_excel('portico/e-journals.xlsx', sheet_name='Details', skiprows=2)
	portico


	# In[63]:


	# ajout ISSNL
	portico['issn'] = portico['e-ISSN']
	portico.loc[portico['e-ISSN'].isna(), 'issn'] = portico['Print ISSN']
	portico


	# In[64]:


	portico = pd.merge(portico, df_issnl, on='issn', how='left')
	portico


	# In[65]:


	portico.columns


	# In[66]:


	# test des lignes sans merge
	portico.loc[portico['issnl'].isna()]


	# In[67]:


	# utiliser l'ISSN à la place sur ces lignes
	portico.loc[portico['issnl'].isna(), 'issnl'] = portico['issn']


	# In[68]:


	# test des lignes sans merge
	portico.loc[portico['issnl'].isna()]


	# In[69]:


	# ajout des infos de Portico :
	# Status
	portico_for_merge = portico[['issnl', 'Status']]
	portico_for_merge


	# In[70]:


	# garder les lignes "preserved"
	portico_for_merge = portico_for_merge.loc[portico_for_merge['Status'] == 'preserved']
	portico_for_merge


	# In[71]:


	# renommer les colonnes
	portico_for_merge = portico_for_merge.rename(columns={'Status' : 'portico_status'})
	portico_for_merge


	# In[72]:


	# merge avec journals
	journals = pd.merge(journals, portico_for_merge, on='issnl', how='left')
	journals


	# In[73]:


	# suppression des doublons
	journals = journals.drop_duplicates(subset=['id'])
	journals


	# In[74]:


	# ajouter info sur la presence sur portico
	journals.loc[journals['portico_status'].isna(), 'portico'] = 0
	journals.loc[~journals['portico_status'].isna(), 'portico'] = 1
	journals


	# ### Licences Nationales

	# In[75]:


	# ajout des infos de preservation des Licences nationales
	nlch1 = pd.read_excel('licences_nationales/cambridge_Switzerland_NationalLicences_2020-08-17.xlsx')
	nlch1


	# In[76]:


	# ajout des infos de preservation des Licences nationales
	nlch2 = pd.read_excel('licences_nationales/gruyter_Switzerland_NationalLicences_2020-11-30.xlsx')
	nlch2


	# In[77]:


	# ajout des infos de preservation des Licences nationales
	nlch3 = pd.read_excel('licences_nationales/oxford_Switzerland_NationalLicences_2020-09-24.xlsx')
	nlch3


	# In[78]:


	# ajout des infos de preservation des Licences nationales
	nlch4 = pd.read_excel('licences_nationales/springer_Switzerland_NationalLicences_2020-08-12.xlsx')
	nlch4


	# In[79]:


	# concatener les 4
	nlch = pd.concat([nlch1, nlch2, nlch3, nlch4], ignore_index=True)
	nlch


	# In[80]:


	nlch.columns


	# In[81]:


	# ajout ISSNL
	nlch['issn'] = nlch['online_identifier']
	nlch.loc[nlch['online_identifier'].isna(), 'issn'] = nlch['print_identifier']
	nlch


	# In[82]:


	nlch = pd.merge(nlch, df_issnl, on='issn', how='left')
	nlch


	# In[83]:


	# test des lignes sans merge
	nlch.loc[nlch['issnl'].isna()]


	# In[84]:


	# utiliser l'ISSN à la place sur ces lignes
	nlch.loc[nlch['issnl'].isna(), 'issnl'] = nlch['issn']


	# In[85]:


	# test des lignes sans merge
	nlch.loc[nlch['issnl'].isna()]


	# In[86]:


	# ajout des infos de nlch :
	# publication_title
	nlch_for_merge = nlch[['issnl', 'publication_title']]
	nlch_for_merge


	# In[87]:


	# renommer les colonnes
	nlch_for_merge = nlch_for_merge.rename(columns={'publication_title' : 'nlch_title'})
	nlch_for_merge


	# In[88]:


	# merge avec journals
	journals = pd.merge(journals, nlch_for_merge, on='issnl', how='left')
	journals


	# In[89]:


	# ajouter info sur la presence sur portico
	journals.loc[journals['nlch_title'].isna(), 'nlch'] = 0
	journals.loc[~journals['nlch_title'].isna(), 'nlch'] = 1
	journals


	# ### QOAM

	# In[90]:


	# ouverture du fichier
	qoam = pd.read_csv('qoam/qoam_not_zero.tsv', encoding='utf-8', header=0, sep='\t')
	qoam


	# In[91]:


	qoam = pd.merge(qoam, df_issnl, on='issn', how='left')
	qoam


	# In[92]:


	# test des lignes sans merge
	qoam.loc[qoam['issnl'].isna()]


	# In[93]:


	# utiliser l'ISSN à la place sur ces lignes
	qoam.loc[qoam['issnl'].isna(), 'issnl'] = qoam['issn']


	# In[94]:


	# test des lignes sans merge
	qoam.loc[qoam['issnl'].isna()]


	# In[95]:


	# ajout des infos de qoam :
	# publication_title
	qoam_for_merge = qoam[['issnl', 'qoam_av_score']]
	qoam_for_merge


	# In[96]:


	# merge avec journals
	journals = pd.merge(journals, qoam_for_merge, on='issnl', how='left')
	journals


	# In[97]:


	# suppression des doublons
	journals = journals.drop_duplicates(subset=['id'])
	journals


	# ## Finalisation de la table journals

	# In[98]:


	# test des doublons
	journals_doublons = journals[['issn', 'issnl', 'title']].loc[journals.duplicated(subset='issnl')].sort_values(by='issnl')
	journals_doublons


	# In[99]:


	journals_doublons = journals_doublons.loc[journals_doublons['issnl'].notna()]


	# In[100]:


	# merge pour voir les lignes avec doublon
	journals_doublons['doublon_issnl'] = 1
	journals = pd.merge(journals, journals_doublons[['issnl', 'doublon_issnl']], on='issnl', how='left')
	journals.loc[journals['doublon_issnl'] == 1]


	# In[101]:


	journals.loc[journals['doublon_issnl'] == 1].sort_values(by='issnl')


	# In[102]:


	# export csv des doublons
	journals.loc[journals['doublon_issnl'] == 1].sort_values(by='issnl').to_csv('sample/journals_duplicates.tsv', sep='\t', encoding='utf-8', index=False)


	# In[103]:


	# export excel des doublons
	journals.loc[journals['doublon_issnl'] == 1].sort_values(by='issnl').to_excel('sample/journals_duplicates.xlsx', index=False)


	# In[104]:


	# suppression des doublons
	journals = journals.drop_duplicates(subset=['issnl'])
	journals


	# In[105]:


	# ajout du oa_status
	# 6 : Diamond
	# 5 : Gold
	# 4 : Full
	# 3 : Hybrid
	# 2 : Green
	# 1 : UNKNOWN
	journals['oa_status'] = 1
	journals


	# In[106]:


	# status 5 pour les revues DOAJ
	journals.loc[journals['doaj_status'] == 1, 'oa_status'] = 5
	# status 6 pour les revues DOAJ avec APC = 0
	journals.loc[(journals['doaj_status'] == 1) & (journals['APC'] == 'No'), 'oa_status'] = 6
	journals


	# In[107]:


	journals['oa_status'].value_counts()


	# In[108]:


	# export csv brut
	journals.to_csv('sample/journals_brut.tsv', sep='\t', encoding='utf-8', index=False)


	# In[109]:


	# export excel brut
	journals.to_excel('sample/journals_brut.xlsx', index=False)


	# In[110]:


	# export csv des ids
	journals[['id', 'title', 'issn', 'issnl']].to_csv('sample/journals_ids.tsv', sep='\t', encoding='utf-8', index=False)


	# In[111]:


	# export excel des ids
	journals[['id', 'title', 'issn', 'issnl']].to_excel('sample/journals_ids.xlsx', index=False)


	# In[ ]:

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