* refactoring of service library loading
- the main `bycon/__init__.py` now pre-loads the `byconServices` libraries
* renaming of `services` to `byconServices`
- for the web server the `byconServices` files are still copied to `services`
2024-09-19 (v.1.9.4)
* `byconaut` => `bycon refactoring
- move of many "mature" utility functions from `byconaut` into the `bycon`
repository following the previous `services` move
* `housekeepers`
* `importers`
* move of the `ontologymaps` and `publications` collections from `progenetix`
to `_byconServicesDB`
- clearer separation between "Beacon core" and "additional services"
use admin
db.runCommand(
{
renameCollection: 'progenetix.ontologymaps',
to : '_byconServicesDB.ontologymaps'
}
);
db.runCommand(
{
renameCollection: 'progenetix.publications',
to : '_byconServicesDB.publications'
}
);
2024-09-13 (v.1.9.3)
* services moved to bycon from byconaut
2024-09-12 (v.1.9.2)
* mostly `byconaut` additions (housekeeping scripts etc. and map plot fix)
2024-08-13 (v.1.9.1)
* modifications to the VRS Adjacency based format for fusions
- Example [progenetix.org/beacon/biosamples/pgxbs-kftvgifa/g_variants](https://progenetix.org/beacon/biosamples/pgxbs-kftvgifa/g_variants?includeHandovers=false)
* modifications to the `ISCNdefuser` script in `byconaut` for testing fusions
2024-08-07 (v.1.9.0)
* adding the new `Adjunction ` variant format based on VRS v2.0pre
- query method `variantFusionRequest` (using `mate_...` parameters etc.)
* update of the `byconaut` variantsImporter etc.
* general refactoring of datatable import for fields containing objects
- now allows list of ordered parameters for the concatenated values, as well
as type definitions
- for details please look at `datatable_mappings.yaml`
* rewrite of the `RefactoredValues` class in `bycon_helpers`
2024-07-30 (v.1.8.9)
* rewrite of query stack as `ByconDatasetResults` class
- including fix of `analyses` reporting: Now no aggregation towards biosamples
anymore
- no "non-aggregate" retrieval methods yet; might be added later
* change of variant id query; now not in separate query type
* multi-variant query responses are now aggregated towards response entity (e.g.
all variants have to occurr in same individual or - usually - biosample)
* TODO: check multi-variant queries for multi-analyses responses ...
2024-07-17 (v.1.8.8)
* We removed of the server URL rewrites to services for e.g. `output=table`
pragmas. One has to use the specific endpoints (that have existed since Ocober 2023)
and entities, e.g.:
- old: `https://progenetix.org/beacon/individuals/?filters=pgx:cohort-oneKgenomes&datasetIds=progenetix&output=table`
- now: `https://progenetix.org/services/sampletable/?datasetIds=progenetix&filters=pgx:cohort-oneKgenomes&response_entity_path_id=individuals`
2024-07-10 (v.1.8.7)
* fixed wrong `meta.returned_granularity`
* changed the [`map` schema](https://progenetix.org/beacon/map/) in line with todays's discussions an
[pull request 134](https://github.com/ga4gh-beacon/beacon-v2/pull/134)
* moved the post-processing of exported variants list to a new `VariantsResponse`
class and adjusted some of the optional parameters by editing the `ByconVariant().vrsVariant()`
class/method
2024-07-08 (v.1.8.6)
* more work on cleaning up the table formats and `byconaut` tools
* fix of `response_entity_path_id=analyses` for `services/sampletables`
* some Progenetix data content cleanup (e.g. TNM and stage removal from `info.tnm`)
* cleaner standard schema definitions for export/documentation (`genomicVariations`
will need more work...)
2024-06-24 (v.1.8.5)
* bug fix: `variantMinSize` wasn't evaluated if also `variantMaxSize` was given
* `byconaut`: change in datastructure of status maps and frequencies
- we have abandoned the "max value ..." concepts which weren't used anyway
and switched to bin coverage and frequency values for high level changes
additionally to the all CNV values
- this allows now a simple overplotting of high level gains and losses over
the low level/combined CNV histograms
2024-06-19 (v.1.8.4)
* changed the values for individual.sex from PATO to EFO (see the [Progenetix data notes](https://docs.progenetix.org/changelog/#2024-06-18-switching-ontology-use-for-individualsex))
* changed the default for `includeResultsetResponses` from `ALL` to `HIT`, in
line w/ the Beacon standard definition
- now empty resultsets won't appear in the list
- the Progenetix / Beaconplus fron-ends call an `ALL` value...
2024-06-11 (v.1.8.3)
* restructuring of the whole entity / path ... interpolation - now
`set_entities()` and `initialize_bycon_service()` are part of `bycon`
`__init__.py`
* now evaluates the `includeResultsetResponses` parameters (default: `ALL`)
so that e.g. only `HIT` responses can be returned in a network context
- `__acknowledge_HIT` removes all `exists: false` resultsets
- `__acknowledge_MISS` removes all `exists: true` resultsets
* bug fix: removal of the accidential filtering_terms scopes
(service entities)
2024-06-06 (v.1.8.2)
* removed server side pagination; this should be implemented by clients based
on the numbers from the response summary
* FIX: pagination did not work correctly when requesting
pavges > 1 using a handover id (due to a "double pagination" at query and response preparation times)
2024-05-27 (v.1.8.1)
* re-organized the `local` config location
* fixed the correct entity use for non-standard (services...) in test mode
* changed behaviour: results are now shuffled before storing which leads to different
result page contents for the same query when applying pagination (_i.e._ not always
the same first 100 etc. samples are returned)
* more fixes for geographic map output after recent code rewrite