V2.2.2

Minor patch to expose the CSVCTCAdverseEventExtractor in our exports

v2.2.1

What's Changed

• Fixing bugs related to excess whitespace and empty values when using multiple condition codes

Full Changelog: v2.2.0...v2.2.1

v2.2.0

What's Changed

• Multiple condition codes can now be added by separating them with | (e.g. 1234|5678) in the CSV file for the CSVConditionExtractor

Full Changelog: v2.1.0...v2.2.0

v2.1.0

What's Changed

• Cancer Disease Status value set codes updated
• CSV validation updated to allow CSVs with the proper header but no rows of data
• CSV validation updated to handle excess whitespace in the CSV

Full Changelog: v2.0.1...v2.1.0

v2.0.1

Release Notes

• No longer issues an error when the FHIRAdverseEventExtrator is run without a preceding ResearchStudy extractor if the FHIRAdverseEventExtractor configuration includes the study property (#178)
• Exposes two new functions for fetching AdverseEvent resources from context (#178)
• Updates project dependencies (#181)
  • Bump moment from 2.26.0 to 2.29.3
  • Bump minimist from 1.2.5 to 1.2.6
  • Bump follow-redirects from 1.14.7 to 1.15.0

v2.0.0

New Features

• Update extraction to conform to mCODE STU2 (ballot version) (mCODE v1.16.0) (#148 #150 #151 #152 #153 #156)
• Expand fields that can be masked on the Patient resource (#155, #161)
  • Fields that can be masked now are: genderAndSex, mrn, name, address, birthDate, language, ethnicity, race, telecom, multipleBirth, photo, contact, generalPractitioner, managingOrganization, link.
  • The genderAndSex mask option masks Patient.gender and extensions for birth sex (extension url: http://hl7.org/fhir/us/core/STU4/StructureDefinition-us-core-birthsex.html), legal sex (extension url: https://open.epic.com/FHIR/StructureDefinition/extension/legal-sex), and sex for clinical use (extension url: http://open.epic.com/FHIR/StructureDefinition/extension/sex-for-clinical-use).
• Add new configuration property to mask all fields on the Patient resource (#158)
  • To mask all patient fields, use "mask": "all" in the constructorArgs configuration property on a Patient extractor. Additional details here.
• Extract CTC-AE profiled AdverseEvent resource (#164, #165, #166, #167, #168, #171)
• Support CSVs with blank lines and empty values (#169)
• Support specifying a top level directory where all CSV files are stored and a corresponding fileName property to indicate the CSV file name in each extractor's configuration (#170, #172)
• Fix error handling logic for notificationInfo properties (#173)

Code Maintenance Changes

• Update JSON schema for notificationInfo (#157, #160)
• Update how timezones are parsed (#162)
• Clarify Node version documentation (#159)
• Document current mCODE version (#163)
• Dependency updates (#147, #149, #154, #174)

v1.1.0

New Features

• Added ability to specify CSV file paths as URLs
  • CSV read from URL #140
  • Better logging in CSV URL module #141
• Implemented logic for extractor dependencies in configuration file
  • Adding implementation of extractor dependencies #129
• Added validation of CSV configuration file using json-schema
  • Add initial schema for one config property #127
  • Update csv config schema to include all properties #133
  • Add config file validation #135
  • Adding custom schema format for comma separated emails #138
  • Adding email with name custom schema format #139
• Added more verbose validation of FHIR resources in extracted Bundle
  • New FHIR validation logging #136
• Updated Condition ValueSet to expanded version
  • Expand ValueSet for Conditions #144

Bug Fixes

• Update app function to properly initialize logger debug level
  • Fix debug flag bug #134
• Fix file path resolution issues with log files
  • Improve checking for default log file #123

Code Maintenance Changes

• Refactor program halt logic to live in CLI
  • process.exit moved to cli.js #121
• Modify app functions to return extracted data; Modify CLI functions to write data to file
  • Modified app.js to return object instead of writing to file; moved code to write to file to cli.js #126
• Refactor logic for parsing patient CSV ids
  • Add helper for parsing patient CSV ids with BOMs #124
  • Add test for Patient Id CSV with BOM #131
• Refactor separation of app/CLI
  • Created application folder #130
  • Moved config file parsing from app to CLI #142
• Refactor logging functionality
  • Consolidating log functions from app to RunInstanceLogger #132
• Refactor MRN masking functions
  • Move MRN masking to maskPatientData #137
• Add additional exports
  • Update and export CSV config schema #143
• Dependency updates
  • Replaced shajs with crypto #145
  • Bump ws from 7.4.5 to 7.4.6 #125
  • Bump glob-parent from 5.1.1 to 5.1.2 #128

All Pull Requests

• process.exit moved to cli.js #121
• Improve checking for default log file #123
• Add helper for parsing patient CSV ids with BOMs #124
• Bump ws from 7.4.5 to 7.4.6 #125
• Modified app.js to return object instead of writing to file; moved code to write to file to cli.js #126
• Add initial schema for one config property #127
• Bump glob-parent from 5.1.1 to 5.1.2 #128
• Adding implementation of extractor dependencies #129
• Created application folder #130
• Add test for Patient Id CSV with BOM #131
• Consolidating log functions from app to RunInstanceLogger #132
• Update csv config schema to include all properties #133
• Fix debug flag bug#134
• Add config file validation #135
• New FHIR validation logging #136
• Moving MRN masking to maskPatientData #137
• Adding custom schema format for comma separated emails #138
• Adding email with name custom schema format #139
• CSV read from URL #140
• Better logging in CSV URL module #141
• Moved config file parsing from app to CLI #142
• Update and export CSV config schema #143
• Expand ValueSet for Conditions #144
• Replaced shajs with crypto #145

mCODE Extraction Framework v1.0.1

Release Notes

• Strip BOM from CSV input when parsing the patient id CSV file #120
• Normalize null and nil values in CSV to empty strings #119
  • This feature allows the extractors to process most data points in a CSV that are included as "null" or "nil" as an empty string. They are treated the same way an empty data point is treated. For more information, see the Troubleshooting Guide section.

MEF v1.0.0 Release

Release Notes

• Validate CSV files to check for required columns and required values #91
• Support masking all patient data, including MRN when used as an ID reference #92 #98
• Support specifying TLS settings for email notifications in configuration file #94
• Support specifying clinicalSiteSystem in configuration file #99
• Add Treatment Plan Change CSV #102
• Use ResearchStudy ID from context in AdverseEvent search #101
• Loosen required fields for Patient CSV and mark missing required fields #103
• Add function to find all invalid resources in a bundle #104
• Make CSV Module fail gracefully on filter #105
• Ignore Byte Order Markers in CSV files #107
• Add npm start script to run client #106
• Get patient ID from context, return empty bundle when no data received from Module #108
• Clean up sample CSV data #109
• Support case insensitive CSV Columns #110
• Adding references to FHIR Resources in CSV_Templates #111
• Add troubleshooting guide for Byte Order Marker errors #112