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Ere 306 muster16svg extractor parser implementation #19

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wants to merge 34 commits into from
Closed

Ere 306 muster16svg extractor parser implementation #19

wants to merge 34 commits into from

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OmarMalass
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OmarMalass and others added 30 commits May 31, 2021 10:18
Introduced Muster16SvgExtractorRegexParser:
2751ef5 
- Parsing and cleaning fields with help of regex.
- TODO: parse prescription info.
- Added tests.
Updated date parsing in Muster16SvgExtractorRegexParser.
7ac1cd8 
- Updated tests.
- Moved Regex-Patterns to Parser class.
- Updated tests:
     * reflecting parser changes.
     * added a new test.
     * using SVGExtractor's output as parser's test input.
Supporting date format: dd.MM.yyyy in Muster16SvgExtractorRegexParser.
54e81b5
Missing values handling.
f05c1ca
Prefix parsing.
02b6d10 
* Updated IMuster16FormParser and child classes.
Updated short-ordinal-date parsing:
f0a0406 
* added safe-space when parsing the target year.
Muster16SvgExtractorRegexParser refactoring:
2d3cfca 
* access modifiers and package.
- Structural update:
89105a0 
    * Delegating extraction of nameAndAddress-field subfields to PatientDetailsIntermediateExtractor.
    * Delegating formatting of indivisible fields to Muster16AtomicFormatter.
    * Class FormattingChain enables applying filters in a declarative way.

- Refactoring
Medication Intermediate Parsing:
cf41996 
- MedicationDataIntermediateParser:
    * Initial parsing of the medication entry.
    * Omits redundant lines.
    * Merge related medication lines.
- MedicationLine:
   * The model that the MedicationDataIntermediateParser uses.
- MedicationMatchers:
   * Matches an entry with a medication in the dataset, enabling proper merging of lines and extraction of PZN (TODO).
- DataProvider:
   * Loads and provides medication records from dataset.
- MedicationRecord:
   * Represents a medication entry from the dataset.
- Added tests.
- Refactoring: Moved tests to package: regxer
@OmarMalass
Muster16SvgRegexParser Refactoring & TODO.
9363ab4
@OmarMalass
MedicationString refactoring:
4b07a24 
- Removed parsing logic the class.
- Updated the fields to private final.
@OmarMalass
Introduced FormDataProvider & updated hierarchy.
466a674 
- Added DataProvider interface.
- FormDataProvider: provides medication-forms as FormRecord.
@OmarMalass
Renamed extractor package to delegate
4d28b92
@OmarMalass
Added form and dosage fields to MedicationString + refactoring.
8c491a4
@OmarMalass
Introduced SimilarityCalculator:
dae7fe5 
- Calculates the similarity between the entry string and a medication-record.
@OmarMalass
Completed MedicationMatcher basic implementation:
e451912 
- implemented TODOs.
- integrated SimilarityCalculator.
@OmarMalass
Introduced MedicationParser
2f74874 
- This is the medication-string parsing delegate.
- Completed matching/extraction of PZN, form and size.
- TODO: parse name, dosage, and instructions.
@OmarMalass
Refactoring:
87804a0 
  - Separated delegate package into delegate.medication & delegate.patient.
@OmarMalass
Medication Parsing:
77c20f5 
- Name and dosage parsing and formatting.
- Added tests.
@OmarMalass
Added the python script used to format the medication-dataset.
e50c367
@OmarMalass
Centralized and encapsulated regex patterns.
422cc7b
@OmarMalass
Updated MedicationParserTest
3acf48d
@OmarMalass
Fixed resource loading in DataProvider.
fae9673
@OmarMalass
SVGExtractor fixing resource loading & refactoring.
a7abcee
@OmarMalass
Fixed date matching in Muster16AtomicFormatter
2f37a64
@OmarMalass
Replacing null result values with blank strings.
e4cea0b
@OmarMalass
Integrated MedicationParserDelegate with Muster16SvgRegexParser.
0f165c7
@OmarMalass
Converted patient-name-prefix to a list.
8d65db8
@OmarMalass
Using Muster16SvgRegexParser in Muster16FormDataExtractorService.
9d88757
@OmarMalass
Added patient-name-prefix to PrescriptionBundleBuilder.
2e1bcaf
OmarMalass and others added 4 commits June 13, 2021 19:09
@OmarMalass
Added resources data files.
caddf7b
@OmarMalass
Merge branch 'main' into ERE-306-Muster16SVGExtractorParser-Implement…
c7092bd 
…ation
@OmarMalass
Error fixing:
5c55172 
- Fixed prefix result.
- Disabled tests based on secret samples.
- Removed prefix from bundle.
@OmarMalass
Merge remote-tracking branch 'origin/ERE-306-Muster16SVGExtractorPars…
5f3a5ac 
…er-Implementation' into ERE-306-Muster16SVGExtractorParser-Implementation
ManuelB
ManuelB approved these changes Jun 13, 2021
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This is cool code that can be merged. I especially like the following:

  • usage of a smart approach of string matching using similarity metrics and fuzzywuzzy as implementation
  • the usage of the KBV abbreviations for Darreichungsform
  • Usage of multiple unit tests

@OmarMalass
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@ManuelB Thanks.
As suggested by @cartel1 , the "on-push" workflow is what matters at the moment.
I've merged this locally into main, and I'll close this now.

@OmarMalass OmarMalass closed this Jun 13, 2021
@OmarMalass OmarMalass deleted the ERE-306-Muster16SVGExtractorParser-Implementation branch July 7, 2021 17:16
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@ManuelB ManuelB ManuelB approved these changes

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@OmarMalass @ManuelB