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.

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.

DataHarmonizer v1.6.5

What's Changed

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

New Contributors

• @cpauvert made their first contribution in #401
• @kennethbruskiewicz made their first contribution in #405

Full Changelog: v1.4.7...v1.6.5

DataHarmonizer v1.4.7

What's Changed

• AMBR template update by @ddooley in #380
• Add columnHelpEntries constructor option by @pkalita-lbl in #381

Full Changelog: v1.4.6...v1.4.7

DataHarmonizer v1.4.6

What's Changed

• extra monkeypox template field cull by @ddooley in #377
• ambr template update by @ddooley in #378
• Use dynamic import for Getting Started content by @pkalita-lbl in #379

Full Changelog: v1.4.5...v1.4.6

DataHarmonizer v1.4.5

What's Changed

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

Full Changelog: v1.4.0...v1.4.5

DataHarmonizer v1.4.0

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

Pathogen Genomics Package 1.3.5

Includes DataHarmonizer v1.3.5 as well as:

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	3.2.1	LIMS export field updated (PH_SEQUENCE_SUBMITTER)
Monkeypox-international	3.3.1	Environmental material field added	Environmental terms added, Additional hosts added to Host pick lists
PHA4GE (SC2)	1.0.0

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

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