Releases | Open Source Science

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v 1.9.5 French Demo

This pre-release has numerous changes to code and a few visible interface changes. This is DH version 1.9.5, which will be released as 2.0.0 soon.

Internationalization: This DH version 1.9.5 and upcoming 2.0 version has the internationalization feature present in two parts:

1) User interface: A language menu will control the language that the DataHarmonizer interface is presented in. The translation file for all of this language is present in the DataHarmonizer github repo, in the web/translations/translations.json file. Canadian government approved translators have provided our first translation into French. Other translated languages are welcome!

2) Schema content: Every language field aspect of each LinkML data schema (and its templates) can be translated into a given language as well, appearing in the templates column header help, and in menu selections, and even in data saved in a given language. i.e. if one selects picklist items while using the interface in french, they are saved in french. Ones' selections are converted back into english if one flips the user interface back into english.

Note that if a schema has no translation, its content will remain in the default language regardless of what language a user is interacting with DataHarmonizer in.

To see how the multilingual schema content works, our test case is with the CanCoGeN specification, whose language variants can be found in the locales/ subfolder, in this case "locales/fr/schema.yaml" for the french translation, which gets converted into a schema.json file in the standalone distribution of DataHarmonizer. The schema.yaml file has only the language sensitive fields in it (title, description, comment, examples etc.) and is an "overlayed" onto the main, default - language provided in the template / schema home folder.

Menu datastructure: A second change (useful perhaps to programmers) is that there is a better structure to the menu.js which holds basic information used to construct a stand-alone DataHarmonizer's menu of templates.

JSON Data load/save: Finally, we've upgraded our data structure for saving JSON data to accommodate a few needs:

A new LinkML "Container" format that enables several tables of data to be saved and loaded in one file. This is a prerequisite for the 1-many editing functionality coming down the pipe.
A sparse JSON save that only saves key value pairs where values are not empty.
The schema URI and version are included in the file data for easier recognition.

- JavaScript
Published by ddooley about 1 year ago

https://github.com/cidgoh/dataharmonizer - DH2 beta release

Download the distribution as DataHarmonizer-v2.0.0-beta.zip attached below.

Includes all of the changes of #333 and has incorporated the features of #318.

Addresses the following issues: - #430 - #431 - #434 - #435

Incorporates translated CANCOGEN schema.

The beta release is meant to shorten the feedback loops for the Data Harmonizer. The internationalization features were a "package deal" and so were difficult to roll out as one milestone.

However, a beta release will give users access to partially completed milestones, which will give the developers feedback more often. It will also help them identify bugs more quickly.

This could be also a nightly build which can be shared with users.

- JavaScript
Published by kennethbruskiewicz about 2 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v1.6.5

What's Changed

Merge root and induced slot definitions into new object by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/383
Pgp issue 9etc by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/386
Add help sidebar component by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/393
New generic pathogen template by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/394
update to grdi schema by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/396
GRDI SOP 7.6 by @cmrn-rhi in https://github.com/cidgoh/DataHarmonizer/pull/397
Unified date, time, and datetime input widgets by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/395
added clarifications to new template docs (fixes #400) by @cpauvert in https://github.com/cidgoh/DataHarmonizer/pull/401
Add ability to import and export data in container object format by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/399
Allow users to upload templates by @ivansg44 in https://github.com/cidgoh/DataHarmonizer/pull/403
Update to Handsontable 13.0.1 to enable batch() quick render. by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/409
388 clickable links by @kennethbruskiewicz in https://github.com/cidgoh/DataHarmonizer/pull/405
Mpox rename by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/411
413 compress image assets by @kennethbruskiewicz in https://github.com/cidgoh/DataHarmonizer/pull/414
Monkeypox template rename + FlatpickrEditor field paste fix by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/415
Fix date editor keyboard copy by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/416
More date editor keyboard copy bug fixes by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/417
Mpox rename by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/418
multiselect html p tag input fix by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/422
Reintroduce missing remove / add row commands by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/424
GRDI template update by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/425
Refactor validation code and support LinkML rules by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/420
Use existing todos conventions for min/max constraints by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/426
Let required attribute to take precedence over recommended for header style by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/428

New Contributors

@cpauvert made their first contribution in https://github.com/cidgoh/DataHarmonizer/pull/401
@kennethbruskiewicz made their first contribution in https://github.com/cidgoh/DataHarmonizer/pull/405

Full Changelog: https://github.com/cidgoh/DataHarmonizer/compare/v1.4.7...v1.6.5

- JavaScript
Published by pkalita-lbl about 2 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v1.4.7

What's Changed

AMBR template update by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/380
Add columnHelpEntries constructor option by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/381

Full Changelog: https://github.com/cidgoh/DataHarmonizer/compare/v1.4.6...v1.4.7

- JavaScript
Published by pkalita-lbl over 3 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v1.4.6

What's Changed

extra monkeypox template field cull by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/377
ambr template update by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/378
Use dynamic import for Getting Started content by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/379

Full Changelog: https://github.com/cidgoh/DataHarmonizer/compare/v1.4.5...v1.4.6

- JavaScript
Published by pkalita-lbl over 3 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v1.4.5

What's Changed

test file update by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/357
fix to pulldown list indentation, and monkeypox vocab. by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/356
Provenance template by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/358
Clear existing Jump To click handler before adding it by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/361
fix to multi-select validation by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/362
Make Toolbar Get Latest Release a dynamic link by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/363
Toolbar & Readme updates by @cmrn-rhi in https://github.com/cidgoh/DataHarmonizer/pull/364
Update pgp 1.3.9 by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/365
version bump by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/366
Ambr specification by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/368
Add support for unique_keys field in LinkML classes by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/371
ambr and CanCoGeN schema updates by @ddooley in https://github.com/cidgoh/DataHarmonizer/pull/372
README - manuscript information by @cmrn-rhi in https://github.com/cidgoh/DataHarmonizer/pull/374
Add utility methods for parsing and formatting multivalued cell values by @pkalita-lbl in https://github.com/cidgoh/DataHarmonizer/pull/376

Full Changelog: https://github.com/cidgoh/DataHarmonizer/compare/v1.4.0...v1.4.5

- JavaScript
Published by pkalita-lbl over 3 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v1.4.0

Adds ability to save and load datasets in .json format.

- JavaScript
Published by ddooley over 3 years ago

https://github.com/cidgoh/dataharmonizer - Pathogen Genomics Package 1.3.5

Includes DataHarmonizer v1.3.5 as well as:

- JavaScript
Published by ddooley almost 4 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer-1.3.4

Monkeypox update

Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- CanCOGeN (SC2) | 1.0.0 | | | DEXA (One Health) | 1.0.0 | | | GISAID (SC2) | 1.0.0 | | | GRDI | 1.0.0 | | | Monkeypox | 2.2.1 | | "cheek" added to anatomical part pick list, gene names for PCR testing restructured and additional target added | Monkeypox-international | 2.2.1 | | "cheek" added to anatomical part pick list | PHA4GE (SC2) | 1.0.0 | | |

- JavaScript
Published by ddooley almost 4 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v1.3.3

Mainly a Monkeypox specification update. Fix for validating provenance also included.

Template Name | Template Version x.y.z | x changes (field) | y changes (values/IDs) -- | -- | -- | -- CanCOGeN (SC2) | 1.0.0 | | DEXA (One Health) | 1.0.0 | | GISAID (SC2) | 1.0.0 | | GRDI | 1.0.0 | | Monkeypox | 2.1.1 | Major changes: new fields added (Sample collection, Host information, Host exposure/vaccination/reinfection information, Sequencing,Bioinformatics); exports updated; recommended status changed for some fields | new pick lists added aligned to WHO and PHAC case report forms Monkeypox-international | 2.1.1 | Major changes: new fields added (Sample collection, Host information, Host exposure/vaccination/reinfection information, Sequencing,Bioinformatics); exports updated; recommended status changed for some fields | new pick lists added aligned with WHO and PHAC case report forms PHA4GE (SC2) | 1.0.0 | |

- JavaScript
Published by ddooley almost 4 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v1.3.2

This is an update for the Monkeypox Canada and International Templates.

DataHarmonizer Version | Release Date | Template Name | Template Versionx.y.z | x changes (field) | y changes (values/IDs) | z changes (defs/formats/examples) -- | -- | -- | -- | -- | -- | -- 1.3.2 | 2022-07-13 | | | | | | | CanCOGeN (SARS-CoV-2) | 1.0.0 | | | | | DEXA (One Health) | 1.0.0 | | | | | GISAID (SARS-CoV-2) | 1.0.0 | | | | | GRDI-AMR2 | 1.0.0 | | | | | Monkeypox | 1.1.0 | | added anatomical parts | | | Monkeypox-international | 1.1.0 | | added anatomical parts | | | PHA4GE (SARS-CoV-2) | 1.0.0 | | |

- JavaScript
Published by ddooley almost 4 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v1.3.1

This includes a new Monkyepoxinternational data collection template. All templates have been set to version 1.0.0 . Previously templates did not have their own versions, but rather relied upon DataHarmonizer's main version number to be distinguished. Now template version information is held separately in the schemacore.yaml file and downstream in schema.yaml and schema.js.

- JavaScript
Published by ddooley almost 4 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v1.0.0

A big release involving switch to the LinkML schema data structure for representing templates (https://linkml.io/). Full details coming shortly in Wiki.

As well, this release includes a Monkeypox data collection specification.

LifeLabs (Ontario) included in "sample collected by" pick list.

- JavaScript
Published by ddooley almost 4 years ago

https://github.com/cidgoh/dataharmonizer - DH-LinkML v6.5

This is a pre-release of the upcoming DataHarmonizer LinkML version, which will have templates that run entirely of of a LinkML YAML schema, rather than the current data.js JSON schema. The functionality will be identical for existing DataHarmonizer clients.

- JavaScript
Published by ddooley about 4 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer v0.15.5

"sample collected by" value added to CanCOGeN template Dexa, GRDI and GISAID templates moved from "drafts" to main template list

- JavaScript
Published by ddooley about 4 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer-v0.15.4

New fields/terms added to CanCoGen Covid19 specification Additions include: border testing fields multi-select for sample type fields exposure setting vocabulary "sample collected by" organization names test dataset specific for new release

- JavaScript
Published by ddooley about 4 years ago

https://github.com/cidgoh/dataharmonizer - DataHarmonizer-0.15.3

NML Vocabulary update includes two new travel related fields. See https://github.com/cidgoh/DataHarmonizer/issues/289 The optional (not required, not recommended) field of specimen processing details [GENEPIO:0100311] has been added.

- JavaScript
Published by ddooley about 4 years ago