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Commit 97f3b761 authored by George Marchment's avatar George Marchment
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updated github api request with authentication

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...@@ -45,7 +45,8 @@ class Workflow: ...@@ -45,7 +45,8 @@ class Workflow:
license = None, creativeWorkStatus = None, authors = None, license = None, creativeWorkStatus = None, authors = None,
version = None, keywords = None, producer = None, version = None, keywords = None, producer = None,
publisher = None, processes_2_remove = None, publisher = None, processes_2_remove = None,
processes_annotation = None): processes_annotation = None,
personnal_acces_token = None):
if(not os.path.isfile(file)): if(not os.path.isfile(file)):
nextflow_files = glob.glob(f'{file}/*.nf') nextflow_files = glob.glob(f'{file}/*.nf')
...@@ -54,7 +55,7 @@ class Workflow: ...@@ -54,7 +55,7 @@ class Workflow:
try: try:
file = '/'.join(nextflow_files[0].split('/')[:-1])+"/main.nf" file = '/'.join(nextflow_files[0].split('/')[:-1])+"/main.nf"
with open(file, 'r') as f: with open(file, 'r') as f:
txt= f.read() txt= f.read()
except: except:
file =nextflow_files[0] file =nextflow_files[0]
...@@ -80,6 +81,7 @@ class Workflow: ...@@ -80,6 +81,7 @@ class Workflow:
self.keywords = keywords self.keywords = keywords
self.producer = producer self.producer = producer
self.publisher = publisher self.publisher = publisher
self.personnal_acces_token = personnal_acces_token
if(processes_2_remove==""): if(processes_2_remove==""):
processes_2_remove = None processes_2_remove = None
self.processes_2_remove = processes_2_remove self.processes_2_remove = processes_2_remove
...@@ -172,7 +174,11 @@ class Workflow: ...@@ -172,7 +174,11 @@ class Workflow:
current_directory = os.getcwd() current_directory = os.getcwd()
os.chdir(self.get_repo_adress()) os.chdir(self.get_repo_adress())
try: try:
_ = os.system(f"wget -qO - https://api.github.com/repos/{self.address} > temp_dico_{id(self)}.json") if(self.personnal_acces_token!=None):
command = f'curl --silent --request GET --url "https://api.github.com/repos/{self.address}" --header "Authorization: Bearer {self.personnal_acces_token}" --header "X-GitHub-Api-Version: 2022-11-28" > temp_dico_{id(self)}.json'
else:
command = f'curl --silent --request GET --url "https://api.github.com/repos/{self.address}" > temp_dico_{id(self)}.json'
_ = os.system(command)
with open(f'temp_dico_{id(self)}.json') as json_file: with open(f'temp_dico_{id(self)}.json') as json_file:
self.dico = json.load(json_file) self.dico = json.load(json_file)
os.system(f"rm temp_dico_{id(self)}.json") os.system(f"rm temp_dico_{id(self)}.json")
......
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