• Details
• Requirements
• Usage
• Versions

This programs does:

1. Connect into mysql database and find molecule in 'molecule' table of specific database and find those molecule with missing sds
2. Try to download sds files into a folder in /var/lib/mysql/missing_sds (For Linux environment with LAMP stack)
3. Update those SQL entries with new downloaded sds files

• Python 3.6+
• Linux machine root access to the server hosting Open Enventory (to create a download folder if not existed). If user does not have root account (or sudo), you can:
  1. Change the download_path to a different location that you have read and write permission.
  2. Comment out exit(1) in find_sds.py file

1. Clone this repository:

   git clone https://github.com/khoivan88/oe_find_sds-public.git    #if you have git
   # if you don't have git, you can download the zip file then unzip

2. Change into the directory of the program:

   cd oe_find_sds-public

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NOTE

• This file is made for Linux environment, you should be able to used it on other OS by changing the location of the "download_path"
  • Make sure you use an absolute path
  • For Windows:

    • Use of either forward slashes (/) or backward slashes (\) should be ok!

    • If you use XAMPP (or similar PHP, Apache, SQL package), you can try this path:

      download_path = r'C:/xampp/mysql/data/missing_sds'

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3. (Optional): create virtual environment for python to install dependency: Note: you can change oe_find_sds_venv to another name if desired.

   python -m venv oe_find_sds_venv   # Create virtual environment
   source oe_find_sds_venv/bin/activate    # Activate the virtual environment on Linux
   # oe_find_sds_venv\Scripts\activate    # Activate the virtual environment on Windows

4. Install python dependencies:

   pip install -r requirements.txt

5. Run the program:

   python oe_find_sds/find_sds.py

   • Answer questions for:
     • confirming running under root
     • mySQL root password (typing password will not be shown on screen)
     • the name of the database you want to update (twice to confirm)

See here for the most up-to-date