Develop Flask web application to execute Trace

[asmirn1]

First, we'll create a very simple web application with 3 pages:

• upload.html, where users can select raw data files and the name for their analysis.
• parameters.html, where users can browse the raw data file and specify parameters for running Trace
• results.html, where users can browse the results of running Trace

Pdf files below show templates for pages base.html and upload.html: Scan-20210625.pdf Scan-20210625 (1).pdf

[asmirn1]

TODO:

• In routes.py, import MasterConfig and update params based on the user-specified values
• Update CENTROID_MS_PATH and PROFILE_MS_PATH in params to lead to the files in uploads folder
• Import mzmlReadRaw, read the raw data file (in the profile mode) and calculate the following parameters:
  • min_mz and max_mz are the minimum and maximum m/z values across all scans. Use numpy.min() and numpy.max() functions.
  • ms_frec is the total number of scans divided by the time space from the first scan to the last scan

[asmirn1]

TODO:

• Display the precalculated values (min_mz, max_mz, ms_freq) on the page parameters.html. Add a separate tab called "Pre-calculated Parameters" to display those parameters.
• When page parameters.html is opening, assign parameter values from params to ParametersForm if ParametersForm doesn't have any values,
• After params is updated, save it to the current session,
• Start executing Trace when the ParametersForm is submitted. To execute Trace, we need to call main(params) from TRACE.py

[asmirn1]

Currently, we seem to be able to execute the Trace algorithms, but we don't see any output. TODO:

• Make mz_min, mz_max, ms_freq part of the ParametersForm so that their look would be consistent with the rest of the parameters
• Specify params.LOGGING_PATH to save the logging information into user's temporary folder in uploads
• Display user's logging file in the right-hand side of our website

[asmirn1]

TODO:

• Change the TRACE logging level to logging.INFO
• Change all calls of logging.critical() to logger.info() in all scripts of TRACE (TRACE.py, scan_cwt_1.py, getImage_2.py, predict_3.py)
• In base.html, we need to display log in some element with a scroll bar. So that users could see the entire log.
• Make sure that TRACE runs all way through. Display a new page when a TRACE run is complete.
• Store variable params in the session instead of individual parameters.

[asmirn1]

Modify the logging area:

• Change the height to fill in all available space. Check bootstrap properties.
• Change the font to <small>
• Call logger = logging.getLogger("TRACE") before using logger in scan_cwt_1.py, etc.

[asmirn1]

TODO:

• On the results page, display a table with values mz, time, height, area, snr, prediction .
• Check why the log file disappears when the Trace is complete.