SDSParser

SDSParser is a Python library and command line tool for extracting chemical data from Safety Data Sheet documents. SDSParser will speed up your data-entry process by eliminating the need to read through Safety Data Sheets to get the data you care about.

For testing purposes, here are some SDS files to download and use:

• Fisher Scientific
• Sigma Aldrich

Motivation

Built out of the need to quickly access chemical data from Safety Data Sheets for data-entry purposes. Each chemical manufacturer will stylize and structure their SDSs a little bit differently. SDSParser can easily be updated to read a new manufacturer format by adding a new set of regular expressions to match the format that that specific manufacturer uses.

Tech/framework used

• pdfminer, a tool for extracting information from PDF documents
• pytesseract, a python wrapper for Google's Tesseract-OCR

Features

Have some physical SDSs you need to scan and get data from? Have no fear, sds_parser will recognize your scanned file as an image and perform optical character recognition (ocr) to extract the text for you.

How to install

pip install SDSParser

Dependencies

SDSParser requires that poppler and tesseract tools are install on your local system and included on your PATH

How to use

Simply initialize SDSParser with an optional list of data fields you wish to extract (e.g. ['manufacturer', 'flash_point']) to the request_keys key-word argument. See sdsparser.request_keys for the proper keys to use. If no keys are requested, all available data fields will be searched.

>>> from sdsparser import SDSParser
>>> request_keys = \
['manufacturer', 'flash_point', 'specific_gravity', 'product_name', 'sara_311', 'nfpa_fire']
>>> parser = SDSParser(request_keys=request_keys)

Here is a list of the keys to use.

>>> import sdsparser
>>> sdsparser.request_keys
[
    'manufacturer',
    'product_name',
    'flash_point',
    'specific_gravity',
    'nfpa_fire',
    'nfpa_health',
    'nfpa_reactivity',
    'sara_311',
    'revision_date',
    'physical_state',
    'cas_number',
]

Call parser.get_sds_data('path/to/ExampleSDS.pdf') and pass in the path to your SDS document to get the sds data.

>>> sds_data = parser.get_sds_data('path/to/SafetyDataSheet.pdf')

.get_sds_data returns a dictionary object mapping request key names to their corresponding matches

>>> sds_data
{
 'manufacturer': 'Sigma-Aldrich',
 'product_name': 'Sodium dodecyl sulfate',
 'flash_point': '338 F',
 'specific_gravity': '3.2',
 'sara_311': 'Data not listed'
 'nfpa_fire': 'No data available'
}

If the heading for the requested data type is not found in the SDS, .get_sds_data will return the string 'Data not listed'. If the heading is found, but no data is found under it, .get_sds_data will return the string 'No data available'.

To see a set of all of the currently supported chemical manufacturers:

>>> import sdsparser
>>> sdsparser.manufacturers
{'the_clorox_company', 'firmenich', 'frutarom', 'symrise', 'exxon_mobil', 'fisher', 'indofine',
'ungerer','formosa_plastics', 'innophos', 'basf', 'citrus_and_allied', 'robertet',
'acros_organics', 'kerry', 'iff', 'treatt', 'excellentia', 'sigma_aldrich', 'takasago',
'givaudan', 'pepsico_inc', 'sc_johnson', 'pfizer', 'reckitt_benckiser', 'alfa_aesar'}

SDSParser-cli

In your terminal

path/to/sds/directory $ sdsparser parse --flash_point --specific_gravity
{'fisher_1.pdf': {'flash_point': 'No data available',
                  'specific_gravity': 'No data available'},
 'fisher_2.pdf': {'flash_point': 'No data available',
                  'specific_gravity': 'No data available'},
 'fisher_3.pdf': {'flash_point': 'No data available',
                  'specific_gravity': '1.84'},
 'fisher_5.pdf': {'flash_point': 'No data available',
                  'specific_gravity': 'No data available'}}

or

path/to/sds/directory $ sdsparser parse --csv
path/to/sds/directory $ cat sds_data.csv
Fisher,Data not listed,No data available,No data available,1,0,0,/312 Hazard CategoriesSee section 2 for more informationCWA (Clean Water Act)Not,26-Jan-2018,Powder,Data not listed
Fisher,"Salicylic acid, sodium salt",No data available,(etc...)

for more information

$ sdsparser --help

or

$ sdsparser parse --help

dev_tools - regex_developer

Easily edit and update existing regular expressions with the help of a local MongoDB server and a GUI for making your changes.

For mongodb installation instructions go here

1. Start by entering into the dev_tools folder, activate your virtalenv and run the command python3.7 regex_developer.py. Login as root to allow mongod to start the local server.

2. Use the top two drop-down menus to select both the manufacturer and regular expression you would like to test.

3. Click 'Get Regex' to populate the input field with the regular expression

4. Click 'Execute' to perform the match with the currently entered regular expression

5. Make changes to your regular expression according to the tabulated output in the terminal, click 'Execute' again.

6. Rinse and repeat.

When you are ready to save your new and improved regular expression, click 'Save Regex'. This will store the text currently in the text input field to the MongoDB database. When you are ready to add your changes to sdsparser, export your regular expressions to /sdsparser/static/regexes.json. This can be accomplished using this command:

• mongoexport -d sdsparser -c sdsRegexes --jsonArray -o regexes1.json --pretty

FAQ

How do I add new manufacturer support?

1. Run the function dev_tools.sds_file_manager.add_new_manufacturer and follow the prompt.

   • This will create two separate directories to store SDSs. sds_pdf_files/ stores SDS pdfs for that particular manufacturer. sds_text_files/ stores the resulting .txt files after text from the pdf files has been extracted. Once the text files have been generated by sds_file_manager, regex_developer can use the text found there to perform regex matching instead of re-extracting the text from the pdf file directly.

2. Move your SDS pdf files to the new directory found in sds_pdf_files.

   • As long as you know the manufacturer for each SDS and that they are all of the same manufacturer, there is no need to rename the files. When regex_developer is started, sds_file_manager will update pdf file names, extract the text from the pdf files and save them to the corresponding directory within sds_text_files/.

3. Start regex_developer and follow the prompt in the console.

   • regex_developer will look for any new directories by comparing directory names with manufacturer names found in mongoDB. If a new directory is found, the user will be asked if they want to add the new manufacturer to mongoDB with the same name as the directory that was found. By choosing yes, the new manufacturer will be added to mongoDB using the default set of regular expressions.

4. The new manufacturer will now be available in the regex developer GUI.

Why are some txt files in sds_text_files suffixed with "_ocr.txt" and some with "_pdf.txt"?

A user named Tom wants to add a new manufacturer named "acme" to sdsparser. After he generates the new directories using dev_tools.sds_file_manager.add_new_manufacturer, he moves 3 "acme" SDSs to the new directory sds_pdf_files/acme/. When he starts up regex_developer, he sees that his 3 SDSs were renamed to amce_1.pdf, amce_2.pdf, amce_3.pdf. He also sees 3 .txt files in sds_text_files/acme/ named acme_1_pdf.txt, acme_2_ocr.txt and acme_3_pdf.txt. acme_1_pdf.txt contains text extracted from amce_1.pdf using standard text extraction methods while acme_2_ocr.txt contains text extracted from amce_2.pdf using optical character recognition. The content found in amce_2.pdf may be corrupted or each page may be an image which doesn't contain any real text.

How do I add new request keys?

TODO

License

MIT © Aris Stepe