Public-Health-Bioinformatics / LexMapr
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Classification (#93)

* A temporary owl file for terms available for curation.

This is a temporary owl file for terms (currently not available in ontologies) available for further considearion and curation in the ontologies which is used to enable classification in the interim.

* Revamping of classification component based on newer IFSAC+ classification schema.

Includes updated predefined resources.
Addition of some new predefined resources.
Functionality to deal with multi class label values in bucket labels.
Functionality to customize ordering of class labels in the final class assignment.
Updated and newer rules for post-classification refinement of  IFSAC labels.
Excluded "hasBroadSynonym" from the mapping considerations
Functionality to convert the matched component to standard Upper case Ontology Ids
Four new modules for assignment of confidence level in mapping (for future use)

* Update lexmapr/predefined_resources/ifsac-refinement.csv

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_classification.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_helpers.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline_helpers.py

Co-authored-by: ivansg44 <ivan.gill@bccdc.ca>

* Update lexmapr/pipeline.py

Co-authored-by: ivansg44... (continued)

1032 of 1285 relevant lines covered (80.31%)

1.61 hits per line

Relevant lines Covered
1285 RELEVANT LINES 1032 COVERED LINES
1.61 HITS PER LINE
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686 master Classification (#93) * A temporary owl file for terms available for curation. This is a temporary owl file for terms (currently not available in ontologies) available for further considearion and curation in the ontologies which is used to ena... push web-flow travis-ci pending completion  
495 master Add files via upload The revised Interagency Food Safety Analytics Collaboration+ (IFSAC+) schema diagram. push web-flow travis-ci pending completion  
486 master 0.6.1 push ivansg44 travis-ci pending completion  
481 master 0.6.0 * Replacement of ``-f, --format [FORMAT]`` with ``-f, --full`` necessitates 0.6.0 instead of 0.5.2 push ivansg44 travis-ci pending completion  
479 master 0.5.2 push ivansg44 travis-ci pending completion  
442 master Add slides covering classification logic (#83) * Add slides covering classification logic * Removed brief classification slide from ``tutorial_slides.*`` * Attempting to fix Travis CI bug * Attempting to fix Travis CI bug * Attempting... push web-flow travis-ci pending completion  
433 master Merge branch 'master' into development push ivansg44 travis-ci pending completion  
428 master 0.5.0 push ivansg44 travis-ci pending completion  
427 master Merge development into master (#80) * Various small bug fixes (#74) * Do not delimit more than once per row * Also removed InputFileNotFoundError * Let's just use FileNotFoundError * Also raise exception for unreachable code * Re... push web-flow travis-ci pending completion  
392 master Recognize tsv input files (#72) * Recognize tsv input files * Tested * Also added type checking of input files at argparse level * Forgot new test files last commit * 0.4.0 push web-flow travis-ci pending completion  
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