Version v2.10.0

This version:

• Adds the ability to export a dataset as a series of text files suitable for ingestion by cBioPortal at /private/export;
• Adds type exception for public overview count;
• Updates django from 2.2.27 to 2.2.28

Version v2.9.1

Patch release: replaces icontains lookup with iexact lookup for string search in extra_properties.

Version v2.9.0

This version:

• Adds genome_assembly_id field to ExperimentResult model with the following options: GRCh37, GRCh38, GRCm38, GRCm39. Adds this field to schemas and ingest function.

• Adds "missing" property for all public fields in the public overview: the field contains a count of all individuals that don't have information in this field present.

• Adds two migrations for mcode and phenopackets related to text updates in the schema. Those changes are not related to the database schema.

Version v2.8.0

This version:

• Adds the following public API endpoints:

  /api/public - to perform a search, returns a count of individuals that fit the search,
  /api/public_overview - returns overview that contains counts for each field of interest,
  /api/public_search_fields - returns information about public fields that can be used for searching.

  The fields are specified in config.json file that must be provided by a project.
  If config.json file is not provided by a project then the above endpoints return a message saying that there is no public data in this project. The example.config.json file can be found in the /katsu/chord_metadata_service/ directory.

• Implements threshold for a response object for all public fields: if the response count is less or equal to the threshold value then the response contains a message that insufficient data is available.

• Adds filters for /api/public:

  The filters are set for the following fields of the Individual model:

  • sex (sex, e.g. sex=female)
  • age (age_range_min and age_range_max, e.g. age_range_min=20&age_range_max=30)
  • extra_properties (extra_properties): takes a string formatted as a list of objects.

  Examples of extra properties searches:
  search for items that are type of string:
  extra_properties=[{"smoking": "Non-smoker"},{"death_dc": "deceased"},{"covidstatus": "positive"}]

  search for items that contain date ranges:
  extra_properties=[{"date_of_consent": {"after": "2020-03-01", "before": "2021-05-01"}}]

  search for items thta contain numeric ranges:
  extra_properties=[{"lab_test_result_value": {"rangeMin": 5, "rangeMax": 900}}]

  All fields that are specified in extra_properties will be picked up for a search from the config.json. What kind of filtering is performed on those fields is defined by their type in config.json (e.g. number or string, isRange)

• Adds two new fields to the Individual model:

  • age_numeric field to store age as a number
  • age_unit to store unit measuring age
    There is now a function that converts ISO8601 age duration string recorded in the age field to a numeric value in years, for example: "P56Y3M7D" is converted to 56.27 value.

• Adds migrations with a function that populates new age fields with new values.

• Updates ingestion function: converts iso duration string and saves it to age_numeric field.

Version v2.7.0

The version adds:

• ARGO renderers for the following mcode elements:

  • individual
  • genetic specimen
  • cancer condition
  • tnm staging
  • cancer related procedure
  • medication statement

• Genomics report and related elements to ingestion

• More tests for mcode genetic data elements ingestion

• .bw and .bb file extensions for bed files

Version v2.6.0

This version adds:

• new endpoint for mcode data overview: /api/mcode_overview
• filtering by dataset and authorized dataset titles for all phenopackets and mcode elements
• new CanDIG Dataset Authentication middleware
• docker file for standalone Katsu deployment
• bigBed file extension in ingest workflow

Version v2.5.0

This release:

• adds three new autocomplete endpoints:

  • biosample sample tissue, e.g.:
    /api/biosample_sampled_tissue_autocomplete?q=blo
  • phenotypic feature type. e.g.:
    /api/phenotypic_feature_type_autocomplete?q=abnormal
  • disease term, e.g.:
    /api/disease_term_autocomplete?q=carci

  Returns a list of strings containing partial match (case-insensitive ).

• allows reading Postgres password from a file if it's stored in "POSTGRES_PASSWORD_FILE"

Version v2.4.1

Patch release that fixes a bug in experiment ingestion.

Version v2.4.0

This release adds a new data type readset to allow running ingestion workflow in order to copy available files over to the DRS service.
Currently supported file extensions are .cram, .bam and .bigWig.

Version v2.3.1

Patch release that improves/fixes mcode data ingestion.