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Commit 5a0cd77c authored by Maxence Larrieu's avatar Maxence Larrieu
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nakala zenodo added

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/0-collect-data/personnal-keys.json
/0-collect-data/bso/
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0-collect-data/bso-via-hal-dois.txt 0 → 100644
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10.22190/JTESAP1803341W
10.31905/UOQ9LVHZ
10.15454/D3ODJM
10.15454/L7QN45
10.1101/810754
10.26302/SSHADE/EXPERIMENT_OP_20191119_001
10.26302/SSHADE/EXPERIMENT_OP_20200212_001
10.515/lex-2021-0011
10.21336/7f34-8j17
10.1088/1361-665X/aaf0ea
10.57745/GZKUZS
10.1016/j.coastaleng.2021.103917
10.1016/j.ancene.2019.100230.
10.6096/MISTRALS-HyMeX.1438
10.6084/m9.figshare.12295910
10.6084/m9.figshare.14216912
10.1017/pds.2021.443
10.1051/0004-6361/202140963
10.1007/s12351-021-00647-0
10.1109/ICME.2017.8019533
10.6084/m9.figshare.14754468
10.1007/s11747-020-00723-5
10.6084/m9.figshare.7017137.v2
10.1109/WCNC51071.2022.9771695
10.15439/2020F154
10.15778/RESIF.FR
10.5281/zenodo.5913981
10.1080/14786435.2021.1985734
10.1016/j.jinorgbio.2020.111257
10.6073/pasta/b473b048846875b721d139416b8fd882
10.5281/zenodo.4729758
10.1101/756403
0-collect-data/nakala-dois.txt 0 → 100644
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10.34847/nkl.6caam3dp
10.34847/nkl.76abr599
10.34847/nkl.a0fe865m
10.34847/nkl.5bcck3cz
10.34847/nkl.ca709965
10.34847/nkl.ca8dmbdh
10.34847/nkl.a5ae8y33
10.34847/nkl.748eqz51
10.34847/nkl.2c0fj3ai
10.34847/nkl.2bad8uj6
10.34847/nkl.87788ro3
10.34847/nkl.2404plkh
10.34847/nkl.bafagy29
10.34847/nkl.9bd4vqc6
10.34847/nkl.4540o25d
10.34847/nkl.36ac9k92
10.34847/nkl.231c4067
10.34847/nkl.a0db89n9
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10.34847/nkl.aacad5y8
10.34847/nkl.3dbc2mtb
10.34847/nkl.bc2b1071
10.34847/nkl.81dcdekj
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10.34847/nkl.c9e92or4
0-collect-data/nakala-uga-users.txt 0 → 100644
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facquier
nschumacher
acarbonnelle
tfraslin
vgirard1
irequenaruiz
naudas
jfrancony
craphael
lcharles1
rhadbi
echetouane
mlarrieu
egreslou
troulet
mbeligne
acarbonnelle
annegf
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0-collect-data/nakala.py 0 → 100644
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# Récupérer les DOIs de l'UGA présents dans Nakala
## 2023-11-29, Maxence Larrieu
"""
# Particularités
- pas de données d'affiliations, on passe directement par les comptes des déposants qui nous ont été fournis par l'équipe HumaNum
- réponse de l'API dans la navigateur en XML et via requets en json
## Process
- charger les userid
- itérer sur tous les userid
- récupérer les DOIs de tous leurs dépôts
- exlure les actions de création de collection
- extra : recherche aussi de nouveau utilisateurs par l'intémédiaire des droits des dépôts effectués
## question sur le périmètre
- périmètre : est-ce qu'on inclut des personnels comme Thomas Leduc (univ. nantes) mais membre AAU ?
"""
def get_dois_n_users(user_id):
"""
attention logique d'utilisateurs (=compte nakala), pas d'auteur
extrait les DOIs déposées par un user dans Nakala (les collections sont exclues)
user_network : ressortir des userId avec qui les déposant ont partagés des droits de modif. sur leurs dépôts
"""
buffer_dois = []
other_users = []
url_req = "https://api.nakala.fr/search?order=relevance&page=1&size=25&fq=depositor="
req = requests.get(url_req + user_id)
## filtre si la requete n'aboutie pas
if req.status_code != 200 :
return{
"continue" : False,
"content" : r,
"other_users" : False
}
res = req.json()
# iterer sur tous les résultats
for item in res["datas"] :
## exclure les collections, qui ne contiennes pas d'élement "files"
if not item.get("files") :
continue
# récupérer le DOI
buffer_dois.append( item.get("identifier") )
# rechercher d'autres userId
if item.get("rights") :
## pour toutes les personnes à qui on a ajouté des droits
for person in item["rights"] :
## récupérer leurs userid
person_userid = person.get("username")
## si on trouve un autre utilisateurs
if person_userid and person_userid not in nakala_uga_users and person_userid not in other_users :
other_users.append( person_userid )
return{
"continue" : True,
"content" : buffer_dois,
"other_users" : other_users
}
import json, requests
parent_folder = "0-collect-data"
## list to stock datas
nakala_uga_users = []
all_dois = []
other_user_finded = []
## importer les users depuis le fichier txt
with open(parent_folder + '/nakala-uga-users.txt', 'r') as f:
## attention bien stripper quand on import du txt sinon les sauts de ligne sont présents
[nakala_uga_users.append( user.strip() ) for user in f.readlines()]
print("nb d'utilisateur Nakala UGA importés", len(nakala_uga_users))
# ____n____ iterer sur les users uga
for user in nakala_uga_users :
## rechercher les jeux de données
res = get_dois_n_users(user)
if res["continue"] :
print(f"{user}\n\tnb DOI {len(res['content'])}" )
## ajouter les DOIs trouvés
if len(res["content"]) > 0 :
all_dois += res["content"]
## ajouter les personnes
if len(res["other_users"]) > 0 :
#print(f"\nnew person {','.join(res['other_users'])}")
other_user_finded += [x for x in res["other_users"] ]
## ____n____ exporter les DOI au format txt
with open(parent_folder + "/nakala-dois.txt", 'w') as fh :
[fh.write(f"{line}\n") for line in all_dois]
## print les autres utilisateurs trouvés7
print("\n\n nakala user trouvés ")
for elem in other_user_finded :
print(elem)
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10.5281/zenodo.10211920
10.5281/zenodo.10204837
10.5281/zenodo.10204743
10.5281/zenodo.10200663
10.5281/zenodo.10199624
10.5281/zenodo.10142460
10.5281/zenodo.10133203
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10.5281/zenodo.8269855
10.5281/zenodo.10063860
10.5281/zenodo.10062356
10.5281/zenodo.10046054
10.5281/zenodo.10058946
10.5281/zenodo.10049814
10.5281/zenodo.10053093
10.5281/zenodo.10050503
10.5281/zenodo.10050323
10.5281/zenodo.10046806
10.5281/zenodo.10005463
10.5281/zenodo.10005440
10.5281/zenodo.8430044
10.5281/zenodo.8316094
10.1002/esp.5650
10.5281/zenodo.8420459
10.5281/zenodo.8412455
10.5281/zenodo.8384883
10.5281/zenodo.8410346
10.5281/zenodo.8408864
10.5281/zenodo.8408515
10.1021/acs.jpcc.3c01887.
10.5281/zenodo.8392608
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10.5281/zenodo.8379418
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10.5281/zenodo.8353229
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10.5281/zenodo.8341374
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10.5281/zenodo.8272736
10.5281/zenodo.8269693
10.5281/zenodo.8269356
10.5281/zenodo.8269305
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10.5281/zenodo.8226430
10.5281/zenodo.8206446
10.5281/zenodo.8205153
10.5281/zenodo.8144596
10.5281/zenodo.8143305
10.5281/zenodo.7485725
10.5281/zenodo.8139775
10.5281/zenodo.8131976
10.5061/dryad.8gtht76tq
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10.5281/zenodo.8025653
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10.5061/dryad.d51c5b019
10.3897/neobiota.62.52934.suppl2
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0-collect-data/zenodo.py 0 → 100644
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# Récupérer les DOIs de l'UGA depuis Zenodo
## 2023-11-29, Maxence Larrieu
"""
## todo
- recherche itératives par types : dataset, image, video, software, physical object, other OU bien regarder si on requeter aussi dans le champs type directment
## Documentation
* Liste des métadonnées obligatoires lors du dépôts (upload_type, sub_type, publication_date, titre, creators, ) https://developers.zenodo.org/#representation
* Recherche dans l'interfance : https://zenodo.org/search?q=creators.affiliation%3Agrenoble&q=type%3Adataset&l=list&p=1&s=10&sort=bestmatch
* Doc dev API champs de requêtes classsiques https://developers.zenodo.org/#records
* doc champs poussées pour la recherche https://help.zenodo.org/guides/search/
* typologie des dépôts possiblent : publication: Publication, poster: Poster, presentation: Presentation, Dataset: Dataset, image: Image, video: Video/Audio, software: Software, lesson: Lesson, physicalobject: Physical object, other: Other
### Identifier les dépôts :
- utilisation du champs `creators.affiliation` (multi affiliation)
- v2 : chercher aussi au niveau des "contributeurs" : `contributors.affiliation` et au niveau auteur `contributors.orcid`
- v2 : passer par les ORCID des 'auteurs' `creator.orcid`
- v2 : rechercher UGA comme financeur `grants.funder.doi`
## Notes sur la récupération
- exemple résultats de requete : https://zenodo.org/api/records?q=creators.affiliation%3A*grenoble*&type=dataset&page=6&size=100&sort=mostrecent&all_version=False&access_tpoken=4A1P6e4gIkvhpcNpVpI05C9yVCjJIDD3vljILoJ1wlyxT9VA70ZXyPMdjqHB)
- deux DOI identiques sont présent : un à la racine `[hits][doi]` et un autre dans `[hits][metadata][doi]`
- il y a des DOI renseignés par le déposant qui ne sont pas de Zenodo
"""
import pandas as pd, requests, json
parent_folder = "0-collect-data"
print("\n\nzenodo.py is launched")
## import API key. Recquired to req Zenodo API
with open(parent_folder + "/personnal-keys.json") as f :
ACCESS_TOKEN = json.load(f)["ZENODO_KEY"]
def req_zenodo(page_nb) :
"""
retourne les jeux de données UGA depuis Zenodo
page_nb précise le numéro de la page de la requête
"""
r = requests.get(
"https://zenodo.org/api/records",
params = {
"q" : "creators.affiliation:grenoble",
"type" : "dataset",
"page" : page_nb,
"size" : 100,
"sort" : "mostrecent",
"all_version" : False,
"access_tpoken" : ACCESS_TOKEN
}
)
# to debug print(r.url)
## si pb présent dans les résultats
if r.status_code != 200 :
return {
"continue" : False,
"content" : r
}
## s'il n'y a pas de probleme
res = r.json()
return {
"continue" : True,
"content" : res["hits"]
}
## var to initiate the loop
output_dois = []
current_page_number = 0
iterate = True
while iterate :
current_page_number += 1
print("new iteration page =", current_page_number)
res = req_zenodo(current_page_number)
# verifier si la requete a bien fonctionnée
if not res["continue"] :
print("oups, problem with the query")
print(res["content"].status_code ) ## res[content] contient la réponse de la requête
break
# pour la premiere iteration, extraire le nb de DOI a récupérer
if current_page_number == 1 :
nb_dois_to_get = res["content"]["total"]
print("\tfirst iteration. DOIs to get =", nb_dois_to_get )
## parcourir tous les DOIs et les placer dans la liste
## placer le DOI uniquement si une donnée est présente
[output_dois.append( item.get("doi") ) for item in res["content"]["hits"] if item.get("doi")]
## managing the loop
### if I have all the DOIs inside my outputs, then I had finish
if len(output_dois) >= nb_dois_to_get :
iterate = False
## ____z____ exporter la liste de DOI au format txt
with open(parent_folder + "/zenodo-dois.txt", 'w') as f :
[f.write(f"{line}\n") for line in output_dois]
dois-in-datacite.csv 0 → 100644
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run-all-codes.py 0 → 100644
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import os
"""
v2
- revoir gestion de l'arborescence import et export des fichiers (tout passer par des modules ? ) :https://stackoverflow.com/questions/52577047/run-another-python-script-in-different-folder
"""
def execute_python_file(file_path):
"""
excute a py program from a file_path
"""
try :
os.system(f'python {file_path}')
except FileNotFoundError:
print(f"Error: The file '{file_path}' does not exist.")
# file_path = "0-collect-data/nakala.py"
file_path = "0-collect-data/zenodo.py"
execute_python_file (file_path)
\ No newline at end of file
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