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CHANGELOG.md

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[4.5] - 2023-11-07

Changed

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

[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

[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

[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

[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

[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

[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)

[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

[3.2] - 2022-01-21

Changed

  • Colors and icons of landing page

Fixed

  • Admin error log email handling and relative test

Added

  • Double helix favicon to index page

[3.1.2] - 2022-01-17

Fixed

  • Set MAIL_SUPPRESS_SEND to False and MAIL_DEBUG to True whenever app config has a MAIL_SERVER param

[3.1.1] - 2022-01-15

Fixed

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

[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

[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

[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

[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

[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

[2.10.2] - 2021-11-12

Fixed

  • Increase MongoDB connection serverSelectionTimeoutMS to 30K (default value according to MongoDB documentation)

[2.10.1] - 2021-10-12

Fixed

  • Params passed from the command line to the custom FlaskGroup

[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

[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 (test_add, test_remove, test_update, test_commands)

Fixed

  • Syntax in the disclaimer
  • Validate the Ensembl gene ID against the Ensembl API when multiple IDs are returned by converting a HGNC symbol.

[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

[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

[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

[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

[2.4.1] - 2021-01-07

Added

Changed

Fixed

  • Liftover crashing when no end coordinate is not provided

[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

[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

[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

[2.2] - 2020-10-19

Added

  • Codeowners document

Fixed

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

[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

[2.0] - 2019-11-17

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

[1.4] - 2019-11-06

Modified

  • Allow gene search using ensembl gene IDs

[1.3] - 2019-10-31

Fixed

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

[1.2.1] - 2019-10-30

Modified

  • Remove Host from external request headers for compatibility issues

[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

[1.1.1] - 2019-04-25

Modified

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

[1.1.0] - 2019-04-25

Modified

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

[1.0.0] - 2019-04-18

Added

  • patient-similarity integration for phenotype scoring