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Shifted to sandbox testing server instead of production and added som…
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…e functions to orcid class
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@sri0606
sri0606 committed Sep 7, 2023
1 parent ee14d16 commit e31e727
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Showing 2 changed files with 199 additions and 12 deletions.
207 changes: 197 additions & 10 deletions src/pyorcid/orcid.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,10 +40,16 @@ def __is_access_token_valid(self):
'Content-Type': 'application/json'
}

# Replace with the appropriate test endpoint from the API
test_api_url = f"https://pub.orcid.org/v3.0/{self._orcid_id}"
api_url = ""

response = requests.get(test_api_url, headers=headers)
if self._state == "public":
# Specify the ORCID record endpoint for the desired ORCID iD
api_url = f'https://pub.sandbox.orcid.org/v3.0/{self._orcid_id}'

elif self._state == "member":
api_url = f'https://api.sandbox.orcid.org/v3.0/{self._orcid_id}'

response = requests.get(api_url, headers=headers)
if response.status_code == 404:
# The request was successful, and the token is likely valid
return False
Expand Down Expand Up @@ -72,7 +78,7 @@ def __read_section(self,section="record"):

if self._state == "public":
# Specify the ORCID record endpoint for the desired ORCID iD
api_url = f'https://pub.orcid.org/v3.0/{self._orcid_id}/{section}'
api_url = f'https://pub.sandbox.orcid.org/v3.0/{self._orcid_id}/{section}'

elif self._state == "member":
api_url = f'https://api.sandbox.orcid.org/v3.0/{self._orcid_id}/{section}'
Expand Down Expand Up @@ -237,6 +243,176 @@ def invited_positions(self):
'''
return self.__read_section("invited-positions")

def get_formatted_date(self,date_dict):
"""
Formats a date dictionary into a string (e.g., "MM/YYYY") if all required keys are present and not None.
Args:
date_dict (dict): A dictionary containing 'year', 'month', and 'day' keys.
Returns:
str: The formatted date string or an empty string if any required key is missing or None.
"""
if date_dict is not None:
year = date_dict.get('year', {}).get('value') if date_dict.get('year', {}) else None
month = date_dict.get('month', {}).get('value') if date_dict.get('month', {}) else None
day = date_dict.get('day', {}).get('value') if date_dict.get('day', {}) else None

# Check if all required keys are present and not None
if year is not None and month is not None:
return f"{month}/{year}"
elif year is not None:
return year
else:
return ''
else:
return ''


def __extract_details(self,data, key):
'''
helper function for record_summary()
'''
details = []
summary_key = key+'s'
for summary in data['activities-summary'][summary_key]['affiliation-group']:
for item in summary['summaries']:
key_summary = item[f'{key}-summary']
detail = {
'Department': key_summary.get('department-name', '') if 'department-name' in key_summary else '',
'Role': key_summary.get('role-title', '') if 'role-title' in key_summary else '',
'start-date': self.get_formatted_date(key_summary.get('start-date', {})),
'end-date': self.get_formatted_date(key_summary.get('end-date', {})),
'organization': key_summary.get('organization', {}).get('name', '') if 'organization' in key_summary else '',
'organization-address': ', '.join(filter(None, key_summary.get('organization', {}).get('address', {}).values())) if 'organization' in key_summary and 'address' in key_summary['organization'] else '',
'url': key_summary.get('url', {}).get('value', '') if 'url' in key_summary else '',
}
details.append(detail)
return details

def record_summary(self):
'''
A cleaner version of Orcid record
return : a dictionary of summary view of the full ORCID record
'''
data = self.record()
extracted_data = {
'Name': data['person']['name']['given-names']['value'],
'Biography': data['person']['biography']['content'],
'Emails': [email['email'] for email in data['person']['emails']['email']],
'Keywords': [keyword['content'] for keyword in data['person']['keywords']['keyword']],
}

# Extract education details
education_details = self.__extract_details(data, 'education')
if education_details: extracted_data['Education'] = education_details

# Extract employment details
employment_details = self.__extract_details(data, 'employment')
if employment_details: extracted_data['Employment'] = employment_details

# Extract education details
distinction_details = self.__extract_details(data, 'distinction')
if distinction_details: extracted_data['Distinctions'] = distinction_details

# Extract employment details
Invited_details = self.__extract_details(data, 'invited-position')
if Invited_details: extracted_data['Invited Positions'] = Invited_details

# Extract education details
membership_details = self.__extract_details(data, 'membership')
if membership_details: extracted_data['Memberships'] = membership_details

# Extract service details
service_details = self.__extract_details(data, 'service')
if service_details: extracted_data['Service'] = service_details

# Extract funding details with start and end dates
funding_details = []
for funding_summary in data['activities-summary']['fundings']['group']:
for fund_summary in funding_summary['funding-summary']:
funding_detail = {
'title': fund_summary['title']['title']['value'] if "title" in fund_summary and "title" in fund_summary['title'] else '',
'type': fund_summary['type'] if "type" in fund_summary else '',
'start-date': self.get_formatted_date(fund_summary.get('start-date', {})),
'end-date': self.get_formatted_date(fund_summary.get('end-date', {})),
'organization': fund_summary['organization']['name'] if "organization" in fund_summary and "name" in fund_summary['organization'] else '',
'organization-address': ', '.join(filter(None, fund_summary['organization']['address'].values())) if 'organization' in fund_summary and 'address' in fund_summary['organization'] else '',
'url': fund_summary['url']['value'] if 'url' in fund_summary else '',
}
funding_details.append(funding_detail)
extracted_data['Fundings'] = funding_details

work_details = []
for working_summary in data['activities-summary']['works']['group']:
for work_summary in working_summary['work-summary']:
work_detail = {
'title': work_summary['title']['title']['value'] if "title" in work_summary and "title" in work_summary['title'] else '',
'type': work_summary['type'] if "type" in work_summary else '',
'publication-date': self.get_formatted_date(work_summary.get('publication-date', {})),
'journal title': work_summary['journal-title']['value'] if "journal-title" in work_summary else '',
'organization': work_summary['organization']['name'] if "organization" in work_summary and "name" in work_summary['organization'] else '',
'organization-address': ', '.join(filter(None, work_summary['organization']['address'].values())) if 'organization' in work_summary and 'address' in work_summary['organization'] else '',
'url': work_summary['url']['value'] if 'url' in work_summary else '',
}
work_details.append(work_detail)
extracted_data['Works'] = work_details


return extracted_data

def generate_markdown_file(self, output_file=None):
'''
Generates a markdown file with the ORCID record summary
output_file : the name of the output file
return : None
'''

data = self.record_summary()
if 'Name' in data:
file_name = f"{data['Name']}.md"
else:
file_name = "output.md" # Default file name if 'Name' field is missing

if output_file is not None:
file_name = output_file

with open(file_name, 'w', encoding='utf-8') as markdown_file:
for key, value in data.items():
if key=="Name":
markdown_file.write(f'<center><h1>{value}</h1></center>\n\n')
else:
markdown_file.write(f'## {key}\n\n')
if isinstance(value, list):
for item in value:
markdown_file.write('---')
if isinstance(item, list): # Check if item is a list
for sublist in item:
if isinstance(sublist, dict):
for k, v in sublist.items():
markdown_file.write(f"**{k}**: {v}\n\n")
else:
markdown_file.write(f"{sublist}\n\n")
elif isinstance(item, dict):
for k, v in item.items():
if k == 'Education' or k == 'Employments' or k == 'Fundings' or k == 'Qualifications' or k == 'Professional Activities' or k == 'Works':
markdown_file.write(f'#### {k}\n\n')
for entry in v:
markdown_file.write(f'**Department:** {entry.get("Department", "N/A")}\n\n')
markdown_file.write(f'**Role:** {entry.get("Role", "N/A")}\n\n')
markdown_file.write(f'**Start Date:** {entry.get("start-date", "N/A")}\t\t\t\t')
markdown_file.write(f'**End Date:** {entry.get("end-date", "N/A")}\n\n')
markdown_file.write(f'**Organization:** {entry.get("organization", "N/A")}\t\t\t\t')
markdown_file.write(f'**Organization Address:** {entry.get("organization-address", "N/A")}\n\n')
markdown_file.write(f'**URL:** {entry.get("url", "N/A")}\n\n')
else:
markdown_file.write(f'**{k}:** {v}\n\n')
markdown_file.write('\n')
else:
markdown_file.write(f'{value}\n\n')



## THESE FUNCTIONS ARE FOR TESTING PURPOSES ##
def __test_is_access_token_valid(self):
'''
Expand All @@ -245,7 +421,6 @@ def __test_is_access_token_valid(self):
'''
# Access the environment variable from github secrets
access_token = os.environ["ORCID_ACCESS_TOKEN"]
print(f"Access token for orcid is {access_token}")
if access_token=="":
raise ValueError("Empty value for access token! Please make sure you are authenticated by ORCID as developer.")
# Make a test request to the API using the token
Expand All @@ -254,10 +429,16 @@ def __test_is_access_token_valid(self):
'Content-Type': 'application/json'
}

# Replace with the appropriate test endpoint from the API
test_api_url = f"https://pub.orcid.org/v3.0/{self._orcid_id}"
api_url = ""

response = requests.get(test_api_url, headers=headers)
if self._state == "public":
# Specify the ORCID record endpoint for the desired ORCID iD
api_url = f'https://pub.sandbox.orcid.org/v3.0/{self._orcid_id}'

elif self._state == "member":
api_url = f'https://api.sandbox.orcid.org/v3.0/{self._orcid_id}'

response = requests.get(api_url, headers=headers)
if response.status_code == 404:
# The request was successful, and the token is likely valid
return False
Expand All @@ -280,8 +461,14 @@ def __test_read_section(self,section="record"):
'Content-Type': 'application/json'
}

# # Specify the ORCID record endpoint for the desired ORCID iD
api_url = f'https://pub.orcid.org/v3.0/{self._orcid_id}/{section}'
api_url = ""

if self._state == "public":
# Specify the ORCID record endpoint for the desired ORCID iD
api_url = f'https://pub.sandbox.orcid.org/v3.0/{self._orcid_id}/{section}'

elif self._state == "member":
api_url = f'https://api.sandbox.orcid.org/v3.0/{self._orcid_id}/{section}'

# Make a GET request to retrieve the ORCID record
response = requests.get(api_url, headers=headers)
Expand Down
4 changes: 2 additions & 2 deletions src/pyorcid/orcid_authentication.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -29,8 +29,8 @@ def _get_access_token(self,client_id,client_secret,redirect_uri):
'''

# Set the necessary parameters
auth_url_endpoint = "https://orcid.org/oauth/authorize"
token_url = "https://orcid.org/oauth/token"
auth_url_endpoint = "https://sandbox.orcid.org/oauth/authorize"
token_url = "https://sandbox.orcid.org/oauth/token"

# Step 1: Redirect the user to the authorization URL
params = {
Expand Down

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