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Merge pull request #148 from SynBioDex/tayasherstyukova-readme-update
readme fix
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‎README.md

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@@ -40,82 +40,8 @@ There are several ways to install the converter. The easiest is via pip: `pip in
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**3) Run the Converter**
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Use the code below to run the converter. Converter file needs to be within the same directory as the Excel template.
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The following script asks the user for the name of the input file, version of SBOL to use, and offers the option to sign in to gain access to private repositories.
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```
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# Excel2SBOL Converter
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import excel2sbol.converter as conf
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from datetime import datetime
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import excel_sbol_utils.library2 as exutil2
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import getpass
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import requests
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# Ask the user for the name of the input file
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input_file = input("Please enter the name of the input file: ")
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# Get the current date
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current_date = datetime.now().strftime("%y.%m.%d.%H.%M.%S")
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# Add the current date to the output file name
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output_file = "Output_SBOL_" + current_date + ".xml"
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# Ask the user for the version of SBOL to use
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while True:
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sbol_version = input("Please enter the version of SBOL to use (2 or 3): ")
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if sbol_version in ['2', '3']:
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sbol_version = int(sbol_version)
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break
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else:
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print("Invalid input. Please enter either 2 or 3.")
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# Ask the user if they want to sign in or not to use private repos
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while True:
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signin_permission = input("Do you want to sign in? (y/n): ")
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if signin_permission in ['y', 'n']:
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break
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else:
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print("Invalid input. Please enter either y or n.")
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if signin_permission == 'y':
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for attempt in range(1, 3 + 1):
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domain = input("Please enter the domain name: ")
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domain = domain.rstrip("/")
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try:
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response = requests.get(domain)
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response.raise_for_status()
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print("URL reached successfully")
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break
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except requests.exceptions.RequestException as e:
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print(f"Wrong domain name. Attempt {attempt} of 3.")
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if attempt == 3:
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print("Maximum attempts reached. Exiting the program.")
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exit()
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max_attempts = 3
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for attempt in range(1, max_attempts + 1):
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user_email = input("Please enter your email address: ")
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user_password = getpass.getpass("Please enter your password: ")
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login_response = requests.post(
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f"{domain}/login",
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headers={'Accept': 'plain/text'},
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data={'email': user_email, 'password': user_password}
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)
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if login_response.status_code == 200:
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print("Login successful.")
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conf.converter(input_file, output_file, sbol_version=sbol_version, username=user_email, password=user_password, url=domain)
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break
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else:
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print(f"Login unsuccessful. Attempt {attempt} of {max_attempts}.")
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if attempt == max_attempts:
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print("Maximum login attempts reached. Exiting the program.")
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exit()
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else:
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conf.converter(input_file, output_file, sbol_version=sbol_version)
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```
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[Converter File](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/excel2sbol/tests/test_files/Excel2SBOLConverter.py)
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Tip: the use of `os.getcwd()` and `os.path.join` is reccommended for the creation of the file paths. This is safer from a cybersecurity stand point and provide better operating system interoperability.
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@@ -124,13 +50,13 @@ The SBOL file that is output can then be used by further [SBOL tools](https://sb
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# Example Conversion
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A data-filled [spreadsheet](https://github.com/SynBioDex/Excel-to-SBOL/blob/readme/excel2sbol/resources/templates/Example.xlsm) was converted to an [SBOL file](https://github.com/SynBioDex/Excel-to-SBOL/blob/readme/excel2sbol/tests/test_files/Example.xml).
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A data-filled [spreadsheet](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/excel2sbol/resources/templates/Example.xlsm) was converted to an [SBOL file](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/excel2sbol/tests/test_files/Example.xml).
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**Example Spreadsheet**
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![Example Spreadsheet](https://github.com/SynBioDex/Excel-to-SBOL/blob/readme/images/sample-template.png)
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![Example Spreadsheet](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/images/sample-template.png)
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**Example SBOL**
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![Example SBOL](https://github.com/SynBioDex/Excel-to-SBOL/blob/readme/images/sample-xml.png)
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![Example SBOL](https://github.com/SynBioDex/Excel-to-SBOL/blob/master/images/sample-xml.png)
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‎excel2sbol/tests/test_files/Excel2SBOLConverter.py

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# # Excel2SBOL Converter
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import excel2sbol.converter as conf
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from datetime import datetime
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import excel_sbol_utils.library2 as exutil2
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import getpass
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import requests
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# Ask the user for the name of the input file
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input_file = input("Please enter the name of the input file: ")
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# Get the current date
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current_date = datetime.now().strftime("%y.%m.%d.%H.%M.%S")
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# Add the current date to the output file name
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output_file = "Output_SBOL_" + current_date + ".xml"
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# Ask the user for the version of SBOL to use
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while True:
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sbol_version = input("Please enter the version of SBOL to use (2 or 3): ")
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if sbol_version in ['2', '3']:
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sbol_version = int(sbol_version)
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break
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else:
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print("Invalid input. Please enter either 2 or 3.")
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# Ask the user if they want to sign in or not to use private repos
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while True:
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signin_permission = input("Do you want to sign in? (y/n): ")
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if signin_permission in ['y', 'n']:
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break
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else:
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print("Invalid input. Please enter either y or n.")
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if signin_permission == 'y':
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for attempt in range(1, 3 + 1):
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domain = input("Please enter the domain name: ")
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domain = domain.rstrip("/")
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try:
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response = requests.get(domain)
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response.raise_for_status()
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print("URL reached successfully")
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break
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except requests.exceptions.RequestException as e:
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print(f"Wrong domain name. Attempt {attempt} of 3.")
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if attempt == 3:
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print("Maximum attempts reached. Exiting the program.")
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exit()
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max_attempts = 3
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for attempt in range(1, max_attempts + 1):
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user_email = input("Please enter your email address: ")
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user_password = getpass.getpass("Please enter your password: ")
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login_response = requests.post(
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f"{domain}/login",
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headers={'Accept': 'plain/text'},
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data={'email': user_email, 'password': user_password}
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)
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if login_response.status_code == 200:
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print("Login successful.")
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conf.converter(input_file, output_file, sbol_version=sbol_version, username=user_email, password=user_password, url=domain)
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break
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else:
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print(f"Login unsuccessful. Attempt {attempt} of {max_attempts}.")
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if attempt == max_attempts:
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print("Maximum login attempts reached. Exiting the program.")
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exit()
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else:
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conf.converter(input_file, output_file, sbol_version=sbol_version)
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