patientmatcher - Fixed Publish to PyPI on release action

[4.6.1] - 2025-07-24

Fixed

• Publish to PyPI on release event action

- Python
Published by northwestwitch 7 months ago

patientmatcher - Updated libs and general maintenance

[4.6] 2025-07-24

Added

• Custom issue templates (bug/feature request/other issue) and pull request template
• Release instructions (RELEASE.md)
• Supply chain attestation to Docker files ### Changed
• Install software via uv instead, which supports a pyproject.toml file
• Switched from python 3.8 to python 3.12 on Dockerfile and Dockerfile-server files
• Updated hp.obo.txt and phenotype.hpoa resource files
• Removed requirements.txt and requirements-dev.txt files
• Fixed Dockerfiles to install software via uv
• Suppressed pymongo debug logs
• Updated several libraries on the toml file ### Fixed
• Removed deprecated pkg_resources
• Install missing unicorn lib on Dockerfile-server

- Python
Published by northwestwitch 7 months ago

patientmatcher - Update all actions

[4.5.1] - 2024-09-04

Fixed

• Bump actions/download-artifact from 2 to 4 in /.github/workflows (recommended by security advisory)
• Update version of other actions
• Broken upload to Codecov step in Tests & Coverage GitHub action

- Python
Published by northwestwitch over 1 year ago

patientmatcher - Unfreeze PyMongo lib and support latest MongoDB versions

[4.5] - 2023-11-07

Changed

• Unfreeze PyMongo dependency
• Use MongoDB version 7 in docker-compose.yml
• Execute tests using MongoDB 7

- Python
Published by northwestwitch over 2 years ago

patientmatcher - Display connected nodes on index and fixes

[4.4] - 2023-08-14

Added

• Option to display the description of the connected nodes on the index page ### Fixed
• Build and publish to Docker Hub stage README page badge
• Parsing of phenotype.hpoa file ### Changed
• Updated resource files

- Python
Published by northwestwitch over 2 years ago

patientmatcher - Switch to new phenotype file format phenotype.hpoa

[4.3] - 2023-03-16

Changed

• Abort server startup if phenotypes terms are not correctly parse from resource files ### Fixed
• Parsing and downloading of the HPO definitions in the new format (phenotype.hpoa)
• Replaced deprecated version of Ubuntu in GitHub actions

- Python
Published by northwestwitch almost 3 years ago

patientmatcher - Fixed broken link to phenotype_annotation.tab and improved code quality

[4.2] - 2022-09-23

Changed

• Refactor to avoid code smells reported by SonarCloud ### Fixed
• Broken link to HPO definitions (phenotype_annotation.tab)
• Security hotspots flagged by SonarCloud
• Decreased vulnerability by removing some server log messages
• Problems flagged as bugs by SonarCloud
• Server startup debug message showing correct number of parsed diseases

- Python
Published by northwestwitch over 3 years ago

patientmatcher - Automatic update of phenotype resources

[4.1] - 2022-06-27

Added

• Documentation on how to update phenotype resource files ### Changed
• Download automatically phenotype resources when a non-demo app starts

- Python
Published by northwestwitch over 3 years ago

patientmatcher - Removed support for async requests and dedicated documentation pages

[4.0] - 2022-05-18

Added

• GitHub action to auto-deploy documentation when a new release is created ### Fixed
• Ports used to serve the app in docker-compose howto ### Changed
• Removed support for asynchronous requests to the server
• Moved documentation to mkdocs pages (https://clinical-genomics.github.io/patientMatcher)

- Python
Published by northwestwitch almost 4 years ago

patientmatcher - Improved GitHub actions and updated resource files

[3.4] - 2022-04-29

Added

• Created codecov config file in app's root folder ### Fixed
• Updated deprecated codecov action from v1. to v.2
• Upgraded the version of Black lib to latest (22.3.0) in GitHub action
• Link to the GitHub repo on the top-left corner of index page
• Remove HTTP-related security issues ### Changed
• Updated resource files (HPO and OMIM definitions)

- Python
Published by northwestwitch almost 4 years ago

patientmatcher - Database name in crash report email and updated citation reference

[3.3] - 2022-03-09

Changed

• Citation file, pointing to newly published paper ### Added
• Name of database in crash report email, to understand if crashed app is stage or prod app
• Citation button on index page
• Double helix favicon to index page

- Python
Published by northwestwitch almost 4 years ago

patientmatcher - Fixed admin error notifications and landing page's colors and icons

[3.2] - 2022-01-21

Changed

• Colors and icons of landing page ### Fixed
• Admin error log email handling and relative test

- Python
Published by northwestwitch about 4 years ago

patientmatcher - Improved support for email notifications

[3.1.2] - 2022-01-17

Fixed

• Set MAILSUPPRESSSEND to False and MAILDEBUG to True whenever app config has a MAILSERVER param

- Python
Published by northwestwitch about 4 years ago

patientmatcher - Fixed parsing of non-strings env variables when creating the app

[3.1.1] - 2022-01-15

Fixed

• Parsing of numerical and boolean env vars when creating the app

- Python
Published by northwestwitch about 4 years ago

patientmatcher - Code refactoring for speeding up tests and mocking Ensembl web services

[3.1] - 2022-01-13

Changed

• Speed-up CI tests by caching installation of libs and splitting tests into randomized groups using pytest-test-groups
• Mock Ensembl services (gene conversions and liftover) used all tests
• Mock the download of files containing phenotype resources in tests

- Python
Published by northwestwitch about 4 years ago

patientmatcher - Maintenance and standard cli options

[3.0] - 2021-12-27

added

• Index (landing page) reachable at endpoint /
• Include software version in matching emails body ### Fixed
• Restore saving of all matching attempts into database, also those with no results
• Parsing of admins emails list when provided using env vars
• Heartbeat endpoint to return True or False if the app is prod or staging app ### Changed
• Refactor command line params and options to be compliant with the GNU coding standards

- Python
Published by northwestwitch about 4 years ago

patientmatcher - Better support for running a production server via Docker

[2.13] - 2021-12-13

added

• GitHub action to push staging branches from pull requests to Docker Hub
• Created another Dockerfile to run the app via gunicorn
• Modified GitHub actions to push Dockerfile-server image (stage) to Docker Hub when a pull request is opened or modified ### Changed
• Docker base image to run the app via Docker and Gunicorn in a prod environment
• Created another Dockerfile to run the app via gunicorn
• Extended config file functionality to collect all required params from environment variables
• Modified README to describe the two distinct Dockerfiles
• Modified the docker-compose to provide an example on how to use the two Dockerfiles
• Modified GitHub actions to push both Dockerfile and Dockerfile-server images (prod) to Docker Hub when a new release is created
• Improved initial debug messages reporting database connection info ### Fixed
• Freeze PyMongo lib to version<4.0 to keep supporting previous MongoDB versions
• Deprecated werkzeug.contrib preventing running the docker app in prod environment

- Python
Published by northwestwitch about 4 years ago

patientmatcher - Removed dead code and added GitHub Action to find it

[2.12] - 2021-11-24

Fixed

• Removed unused imports ### added
• Vulture GitHub action to flag unused code with 90% confidence ### Changed
• Scan only changed files with Vulture action

- Python
Published by northwestwitch over 4 years ago

patientmatcher - Update patient contact info and minor fixes

[2.11] - 2021-11-16

Fixed

• Fix some deprecated code causing warnings during automatic tests
• Do not duplicate mailto schema when contact href is an email with correct schema ### Changed
• Improve views code by reusing a controllers function when request auth fails ### Added
• Bulk replace patients' contact info using the command line
• Documentation on how to update patients' contact info using the command line
• Contact href string validation (schemas: http, https, mailto) when saving or updating patients

- Python
Published by northwestwitch over 4 years ago

patientmatcher - Increase MongoDB connection serverSelectionTimeoutMS

[2.10.2] - 2021-11-12

Fixed

• Increase MongoDB connection serverSelectionTimeoutMS to 30K (defeult value accorfing to MongoDB socumentation)

- Python
Published by northwestwitch over 4 years ago

patientmatcher - Fix params passed from the cli to the custom FlaskGroup

[2.10.1] - 2021-10-12

Fixed

• Params passed from the command line to the custom FlaskGroup

- Python
Published by northwestwitch over 4 years ago

patientmatcher - Improved database connectivity and tests

[2.10] - 2021-10-12

Added

• Software purpose and short description of developers and Stockholm MME node in README ### Changed
• Improve docker-compose file with 2 demo connected nodes
• Replaced vepo/mongo with the official MongoDB image mongo:4.4.9 in docker-compose files
• Created a mongo-init script for database authentication in docker-compose docker-compose_auth_server_with_2_nodes.yml development file
• Modified docker-compose file to connect to database without authentication
• Modified the pytest_codecov GitHub action file to connect to database matrix (MongoDB 3.2, 4.4, 5.0) without authentication
• Some cli commands don't instantiate a complete app object
• Fixed the code to connect to a MongoDB replica set ### Fixed
• Removed unused --ensembl_genes parameter from add demodata command in all docker-compose file

- Python
Published by northwestwitch over 4 years ago

patientmatcher - Improve tests and fix Gene symbol to Ensembl ID bug

[2.9] - 2021-09-22

Added

Changed

• Save Ensembl ids for demo patient data genes automatically
• Mock the Ensembl REST API converting gene symbols to Ensembl IDs in tests
• Changed the tests for the gene conversion Ensembl APIs to use mocks APIs
• Do not download resources when testing the update resources command
• Use the requests lib instead of urllib.request to interrogate the Ensembl APIs
• Split cli tests into 4 dedicated files (testadd, testremove, testupdate, testcommands) ### Fixed
• Syntax in the disclaimer
• Validate the Ensembl gene ID against the Ensembl API when multiple IDs are returned by converting a HGNC symbol.

- Python
Published by northwestwitch over 4 years ago

patientmatcher - Publish package to PyPI on new release action and small fixes

[2.8] - 2021-09-17

Added

• .cff citation file and doi badge on readme page
• GitHub action to publish repo to PyPI when a new release is created ### Changed ### Fixed
• Fixed in README file the server port used by the web server container launched from docker-compose
• Provide a content type description for long_description in setup file

- Python
Published by northwestwitch over 4 years ago

patientmatcher - Improved test environment using Docker Compose

[2.7] - 2021-09-07

Added

• A demo docker-compose file with a MME server connected to 2 other nodes under /containers ### Changed ### Fixed
• Assign 2 different ids to the demo connected nodes in docker-compose

- Python
Published by northwestwitch over 4 years ago

patientmatcher - Removed patient-similarity dependency and improved demo features

[2.6] - 2021-08-11

Added

• Email logging of errors howto in readme
• Inclusive-language check using woke github action ### Changed
• Removed coveralls badge and added codecov badge
• Required downloading of hp.obo.txt and phenotype_annotation.tab.txt to run a non-test app
• Integrate HPO parsing and handling into the software (decouple from Patient-similarity for HPO)
• Integrate OMIM parsing and handling into the software (decouple from Patient-similarity for OMIM)
• Use app port 9020 instead of 5000 in docker-compose
• Use MongoDB port 27013 instead of 27017 in docker-compose
• Subnet address used in bridge of docker-compose file
• Integrate HPOIC (HPO info content) creation in HPO extensions (decouple from Patient-similarity for HPOIC)
• All collections are removed and recreated on add demodata rerun
• Demo client with token DEMO is created when add demodata command is run
• Remove patient-similarity dependency and replace needed functions with internal code ### Fixed
• downloading phenotype_annotation.tab file from Monarch Initiative
• document keys when a demo client is created with the command pmatcher add demodata

- Python
Published by northwestwitch over 4 years ago

patientmatcher - Admin error notifications

[2.5] - 2021-01-20

Added

• Notify admins via email when app crashes ### Changed
• Use codecov instead of coveralls in github actions
• Send notification emails using TLS instead of SSL ### Fixed

- Python
Published by northwestwitch about 5 years ago

patientmatcher - Fixed Liftover bug when no end coordinate is not provided

[2.4.1] - 2020-01-07

Fixed

• Liftover crashing when no end coordinate is not provided

- Python
Published by northwestwitch about 5 years ago

patientmatcher - Liftover variants when matching patients

[2.4] - 2020-12-30

Added

• Code for performing coordinate liftover using Ensembl REST API
• Variant liftover when comparing genotype features ### Changed
• Using coloredlogs for app logs ### Fixed
• removed unused docker folder

- Python
Published by northwestwitch about 5 years ago

patientmatcher - Fix app database connection and improve Docker files

[2.3.1] - 2020-12-04

Added

Changed

• Install requirements in setup
• Improved Dockerfile and docker-compose files ### Fixed
• Connection string to database when creating the app

- Python
Published by northwestwitch about 5 years ago

patientmatcher - Handle gene conversion and matching when Ensembl Rest API is down

[2.3] - 2020-12-01

Changed

• Pulling Docker images in docker-compose from clinicalgenomics Docker Hub
• Switched from Travis CI to github actions

Changed

• Display error message and raise exception when Ensembl Rest API is needed but offline
• New Dockerfile and instructions to run on docker
• Github action to build and push Docker image when a new software release is created
• Try to match patients based on gene symbol (gene._geneName) if gene.id doesn't match

Fixed

• Do not crash trying to convert genes when Ensembl REST API isn't available

- Python
Published by northwestwitch about 5 years ago

patientmatcher - Dependencies update

[2.2] - 2020-10-19

Added

• Codeowners document

Fixed

• Avoid pymongo-related deprecated code
• Unblock pytest and mongomock dependencies

- Python
Published by northwestwitch over 5 years ago

patientmatcher - Updated HPO link and opened metrics

[2.1]

Modified

• Open up metrics endpoint for any request (no token needed)

Fixed

• Update HPO file name to reflect resource on compbio.charite.de/jenkins

- Python
Published by northwestwitch almost 6 years ago

patientmatcher - Gene IDs as Ensembl IDs

Modified

• Ensembl gene IDs to describe gene IDs
• Allow matching when external patients have entrez gene IDs or HGNC symbols
• Display contact email in notification emails
• Save to database only matches with results or error messages

- Python
Published by northwestwitch over 6 years ago

patientmatcher - Fix missing patient id in results

[1.3] - 2019-10-31

Fixes

• Handle better external matching errors
• Fix a bug introduced in version 1.2.0 (missing patient id in results)

- Python
Published by northwestwitch over 6 years ago

patientmatcher - Remove Host from external request headers

Avoid compatibility issues

- Python
Published by northwestwitch over 6 years ago

patientmatcher - Introduced patient score threshold for filtering match results

[1.2.0] - 2019-10-29

Added

• Introduced SCORE_THRESHOLD parameter as a minimum patient score threshold for returned results

Modified

• Command line returns app version

- Python
Published by northwestwitch over 6 years ago

patientmatcher - Fixed bug in phenotype matching

[1.1.1] - 2019-04-25

Modified

• Fixed bug in phenotype matching when no OMIM or no HPO terms are available

- Python
Published by northwestwitch almost 7 years ago

patientmatcher - Patient similarity against all patients in database

[1.1.0] - 2019-04-25

Modified

• patient-similarity against all patients in database if query patient has HPO term

- Python
Published by northwestwitch almost 7 years ago

patientmatcher - patient-similarity integration

[1.0.0] - 2019-04-18

Added

• patient-similarity integration for phenotype scoring

- Python
Published by northwestwitch almost 7 years ago