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Added parser for assay results XML file #1

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holgi merged 11 commits from xmlparsing into master 2 years ago

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holgi commented 2 years ago

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Currently, The csv array files are parsed for the analysis data and the parameters file is also parsed if present. To also get the date an time of the scan, the assay result xml file is also parsed and all (up to three) data sources are combined.

With this change, the assay result xml file will be parsed first and all relevant result data is parsed in this step (besides the parameters file).

If the xml file is not present or could not be parsed, there is a fall back to the csv parser. But this fall back will exclude the parsing of the timestamps, since the xml file is not present.

Parsing the xml file seems to be around 10% faster than parsing the single csv files.

Currently, The csv array files are parsed for the analysis data and the parameters file is also parsed if present. To also get the date an time of the scan, the assay result xml file is also parsed and all (up to three) data sources are combined. With this change, the assay result xml file will be parsed first and all relevant result data is parsed in this step (besides the parameters file). If the xml file is not present or could not be parsed, there is a fall back to the csv parser. But this fall back will exclude the parsing of the timestamps, since the xml file is not present. Parsing the xml file seems to be around 10% faster than parsing the single csv files.

holgi added 11 commits 2 years ago

873091504c renamed the "parser" module to "csv_parser" ...

The "csv_parser" module will be used as a backup if the analysis xml file is not present.

938b063069 removed the "recordtime" module ...

The "recordtime" module uses the assay result xml file for retrieving the Analyses.Datetime value.
This value is only available in the assay result xml.
Since the "parse_csv" module will only be a backup if this xml file is not present, a separate parser for the Analysis.Datetime is not needed anymore

99d0e0fa4e renamed test cases and added a new one for xml parsing

8644a25d78 moved _cleanup_data_columns() function to "columns" module ...

by moving this function it can be easily reused in the upcoming "xml_parser" module

988c7562d9 renamed some functions in "csv_parser" module to have more explicit names

8c591e9f3c removed debug print statement

dd476bb19a added more calls to "clenup_data_columns()" to remove double index columns after merges

819358977e fixed test data for upcoming module xml_parser

9de0a09557 added more example xml data for testing

0a1da70021 added more example data for comparing xml to csv parsing

8169daeb89 Added parser for the assay results xml file ...

The `sensospot_parser.parse_folder()` function now tries to parse the xml file first and will fall back to parsing csv files if an error occurs

holgi referenced this issue from a commit 2 years ago

Merge pull request 'Added parser for assay results XML file' (#1) from xmlparsing into master

holgi merged commit feea2a03ff into master 2 years ago

The pull request has been merged as feea2a03ff.

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