TODO plan

[nitish6174]

Database setup

• [x] Function to loop through files in directory and parse
• [x] Determine molecular formula of parsed file
• [x] Determine InChI corresponding to parsed file
• [x] Generate SVG for parsed file
• [x] Setting up molecule document schema
• [x] Setting up parsed file document schema
• [x] Finding extreme values of attributes (for filtering purpose in API)
• [ ] Determine IUPAC and common name using InChI/other info
• [ ] Find and store data/properties about molecule using PubChemPy

API developement

• [x] Fetch all molecular formulas (/api/browse/molecules)
• [x] Fetch all parsed files (/api/browse/files)
• [x] Fetch documents corresponding to a molecular formula (/api/browse/<formula>)
• [x] Get details of a particular parsed file (specified with MongoDB document id) (/api/file/<doc_id>)
• [ ] Search API which supports filtering by various attributes available in parsed files (/api/search/<search_params>)
• [ ] Support for searching by molecule's InChI/InChIKey
• [ ] Support for searching by molecule's name
• [x] Upload a log file (/api/upload)
• [x] Add a log file to data repository (/api/addfile)
• [ ] Add authentication for APIs

Application web front-end

• [x] Page to upload log file and view results instantly
• [x] Page to add a log file(s) to database
• [x] Browse repository by molecular formula
• [ ] Search page
• [x] Page to show details of a particular parsed file
• [x] Button to download particular file data in JSON format (just like given by /api/file/)

Testing

• [ ] Scalability of database
• [ ] Size limit of parsed file which can be inserted as a MongoDB database
• [ ] Invalid parameters/attributes to handle and detect corrupt log files
• [ ] API testing
• [ ] Non-API URLs
• [ ] Front-end testing (using Selenium)

Miscellaneous

• [x] Dockerize the app
• [ ] Add option to map port for flask app and MongoDB
• [ ] Deploy an instance on a public server for user testing
• [ ] Add method to find best view when generating SVG
• [ ] Develop regex-like molecular formula matcher
• [ ] Develop support for structural search

Partially completed (from above list)

• Generate SVG for parsed file : Investigate the crash issue (#4)
• Search : Add filters corresponding to more attributes
• Page to show details of a particular parsed file : Identify more attributes suitable for display in tabular form rather than separately

[ghutchis]

Here are my suggestions of "priority" todo:

Crucial

Testing:

• [ ] Invalid parameters/attributes to handle and detect corrupt log files
• [ ] API testing

• [ ] Scalability of database

  Application web front-end

• [ ] Page to add a log file(s) to database
• [ ] Search page
• [ ] Page to show details of a particular parsed file

Important

API developement

• [ ] Support for searching by molecule's InChI/InChIKey
• [ ] Support for searching by molecule's name
• [ ] Upload a log file (POST API)

Really Nice

• [ ] Determine IUPAC and common name using InChI/other info
• [ ] Add authentication for APIs