This program is designed specifically for Open Enventory to fix issue with molecule missing sds (could not be extracted through "Read data from supplier") This programs does:

DETAILS

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

3. Update those sql entries with new downloaded sds files

REQUIREMENTS

• root access to the server hosting Open Enventory

• Python 3+

• This file is made for Linux environment, you should be able

  to used it on other OS with changing the location of the "download_path"

USAGE

After cloning this repo onto the Open Enventory server:

1. Change into directory of the new file:

2. (Optional): create virtual environment for python to install dependency:

3. Install python dependencies:

VERSIONS

Version 5:

• Incorporated result from Fluorochem

• Fixing bug with existing default_safety_sheet_url and default_safety_sheet_mime

  by setting them to NULL

Version 4:

• Testing using cheminfo.org/webservices by extracting catalog number from fluorochem

Version 3:

• Refactor extracting url download into its own method

• Add extracting url download from chemicalsafety.com

Version 2:

• Add asking if user is root and password

• Add asking what database to be modified

• Switch to extracting data from because Chemexper

  has limited requests

This program is designed specifically for Open Enventory to fix issue with molecules missing structures (could not be extracted through "Read data from supplier")

DETAILS

This programs does:

1. Connect into mysql database and find molecule in 'molecule' table

   of specific database and find those molecule with missing structure (smiles)

2. folder "missing_mol_files" needs to be created inside /var/lib/mysql

   with 'mysql' as ownner (chown mysql:mysql)

3. Try to download mol files from various sources into a folder in

   /var/lib/mysql/missing_mol_files

4. Update those sql entries with new downloaded mol_files

REQUIREMENTS

• root access to the server hosting Open Enventory

• Python 3+

• This file is made for Linux environment, you should be able

  to used it on other OS with changing the location of the "download_path"

USAGE

After cloning this repo onto the Open Enventory server:

1. Change into directory of the new file:

2. (Optional): create virtual environment for python to install dependency:

3. Install python dependencies:

VERSIONS

Version 4:

• Using simple download bar with bar=wget.bar_thermometer in wget.download

• Added handling database connection error (wrong password, wrong database)

• Added confirmation for database

Version 5

• Change to https (from http) for ChemicalBook site

Version 6 (2020-01-18):

• Remove this extra step of going into Open Enventory manual by the user using a web browser and doing Batch Processing.

  Why: for versions 5 and before:

  after running this program, YOU STILL NEED TO LOGIN INTO OPEN ENVENTORY ON A WEB BROWSER AS ROOT, GO TO "SETTINGS/BATCH PROCESSING". CHOOSE DATABASE THAT YOU WANT TO UPDATE AND THEN CHOOSE "MOLECULE", "EMPIRICAL FORMULA", "MW", "DEG. OF UNSAT." , "STRUCTURE", "SMILES" AND "FINGERPRINT" AND THEN SUBMIT TO UPDATE THE SQL QUERY. ONLY AFTER THIS, THE STRUCTURE WILL SHOW UP