Hi,

I have wrote down the following script:

# Récupérer les données du csv contenant la liste des pmid par auteur :
with open("D:/Nancy/Pèse-Savants/Excercice Covid-19/Exercice 3/pmid_par_auteur.csv",'r', encoding='utf-8') as f:   
    # Séparer la liste des auteurs et des pmid en 2 colonnes distinctes :
    with open ("pmid_par_auteur_uniformise.csv", "w", encoding='utf-8') as fu:
        csv_f = csv.reader(f, delimiter = ';')
        for ligne in csv_f: 
            fu.write(ligne[0] + '\n')
auteur_pmid_doi = []
Nettoyer les données encodées en 'utf-8'
with open("pmid_par_auteur_uniformise.csv",encoding='utf-8') as fu:

csv_fu = csv.reader(fu)
for ligne in csv_fu:
    ligne[1] = ligne[1].replace("'", " ")
    ligne[1] = ligne[1].replace("[", " ")
    ligne[1] = ligne[1].replace("]", " ")
    ligne[1] = ligne[1].split(" , ")
    
    pmid_doi = []

    for pmid in ligne[1]:
        time.sleep(0.01)
        try : 
            handle = Entrez.esummary(db="pubmed", id=pmid) 
            record = Entrez.read(handle) 
            record = record[0]['DOI']
        except IndexError :
            print ('Missing DOI')
        except KeyError :
            print ('Missing DOI')
        else :
            pmid_doi.append([pmid, record])
        
    auteur_pmid_doi.append([ligne[0], pmid_doi])

auteur_pmid_doi

When I test my script on a small samle of data, it works well, but when I test it on the big data, i receive the folllowing message erreor: RuntimeError:

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-2-38242e0b715e> in <module>
     25             try :
     26                 handle = Entrez.esummary(db="pubmed", id=pmid)
---> 27                 record = Entrez.read(handle)
     28                 record = record[0]['DOI']
     29             except IndexError :
~\anaconda3\lib\site-packages\Bio\Entrez_init_.py in read(handle, validate, escape)

485

486     handler = DataHandler(validate, escape)

--> 487     record = handler.read(handle)

488     return record

489
~\anaconda3\lib\site-packages\Bio\Entrez\Parser.py in read(self, handle)

343                 handle = BytesIO(_as_bytes(handle.read()))

344         try:

--> 345             self.parser.ParseFile(handle)

346         except expat.ExpatError as e:

347             if self.parser.StartElementHandler:
c:\ci\python_1578510570019\work\modules\pyexpat.c in EndElement()
~\anaconda3\lib\site-packages\Bio\Entrez\Parser.py in endErrorElementHandler(self, name)

694             # error found:

695             value = "".join(self.data)

--> 696             raise RuntimeError(value)

697         # no error found:

698         if self.element is not None:
RuntimeError: Invalid uid

9174794 at position=0

I change des API key and tried the script on another computer but still the same error occurs as result.

May someone help me please?

Thanks in advance.