* Adds support for concept identifiers in auto completion. Fixes small messup with setError message dialog in autocompletion

* Adds query string parameter q/query to specify a TranQL query. Adds URL with query param to import/export interface for sharing. Fixes a couple css problems.

* Adds barebones interactive shell implementation. Overhauls find tool in favor of a Elasticlunr prototype

* Heavily extends on the functionality of the interactive shell. Adds intermediary prototype to shell for two-way communication. Adds basic functionality to intermediary, such as importing external modules and reading promises synchronously.

* Adds rudimentary multiline capability in shell thorugh the usage of \n. Adds some functionality to the shell intermediary.

* Adds an editor mode to the interactive shell for use with more complex programs

* Adds program tabs to script editor

* Minor changes to shell

* Adds resizing to overflowing tabs in script editor. Adds python syntax highlighting to script editor

* Basic (semifunctional) elasticlunr find tool searching

* Adds ability to use custom functions in where clause + unit test

* Ensures proper parsing of functions and lists + extends relevant units tests

* Adds named/keyword arguments to functions + adds corresponding unit test

* UDFs added .Refactor CustomFuntion (now CustomFunctions)

* Refactoring TranQL pyodide into module

* UDF format modified to be more expressive. Major refactor of App modals. A couple other things I'm forgetting

* Added promise utility to TranQLApp. Added graph operations to KnowledgeGraph. Pyodide loading and stuff does not occur until the shell is opened

* Quick fix to TranQLApp->render

* Adds variable support to lists. Fixes bug in expand_nodes where if a concept had multiple nodes and its first node was a variable, it would only generate questions for the variable

* Adds ability to use vars as function arguments

* Fixes commit to wrong branch

* Adds promise wrapper to pyodide_module

* adds (semi-functoinal) manifest for pip and reverts change to tranql_ast expand_nodes for now

* Removes interactive shell/pyodide

* Changes find tool to expand tokens for better results

* Lots of changes to find tool

* adds highlighting to find tool

* Remove context menu & add hover styles to find tool

* Adds github pages?

* test pages

* Adds more to pages

* Hopefully fixes pages theme

* Adds things to GitHub pages

* Adds example notebook directly into pages

* Adds UDFs info/comments & more functions

* Adds example docs to GitHub Pages. Adds __init__.py to tranql which never got committed

* Adds function docs to GitHub Pages

* Fixes error modal typo

* Adds history viewer prototype. Might be better to just sort cache viewer by timestamp.

* Adds ONTO sibling function

* Adds comment for failing unit test documenting a known bug which the test aims to prevent

* Changes expand_nodes to fix bug/unit test (NCATS-Tangerine#122).

* Set theme jekyll-theme-time-machine

* Adds documentation on how to add a function in udfs.py

* Set theme jekyll-theme-cayman

* Adds documentation on how to add a function in udfs.py. Changes jekyll theme in config back to just-the-docs

* Fixes some issues with the find tool. Comments out the history viewer.

Co-authored-by: frostyfan109 <[email protected]>
Co-authored-by: frostyfan109 <[email protected]>
Co-authored-by: frostyfan109 <[email protected]>

…es, and hence causing all graph grabbing, this was overlooked in initial merge.

…all capable KPs.

* Backplane overhaul to enable centrizied of configuration and conversion between trapi versions

* Backplane overhaul to enable centrizied of configuration and conversion between trapi versions

* Addition of roger, update tranql frontend to talk to backplane always to ensure trapi configs are universal.
Updating tests to those changes

* docker image version bump

* gnbr and indigo

* Tests were that were using local server  to use mock servers

* icees update to latest bl lookup changes

* update tests to match biolink:PascalConceptType in tests

* Trapi 1.0 overhaul

* Trapi 1.0 schema update.

* update unit test files to Trapi 1.0

* Dependency corrections

* adding web_prefix conf for web api

* adding web_prefix conf for web api

* minor version added

* adding web_prefix conf for web api

* adding web_prefix conf for web api

* minor version added

* bumping plater version

Add UI conversion from TRAPI 1.0 to TRAPI 0.9.

* ui web prefix jinja way.
and adds reasoner to redis results.

* changes window.origin to window.href as root location of tranql to play well with prefixed proxy deployments.

* Parameterizes docker file to support building a branch for CI/CD.
Allows npm to build index file as a jinja template to web_prefix for static assets is allowed when serving
from flask. (This has no effect on local development)

* Update Dockerfile

…ATS-Tangerine#145)

- tranql app image should base off of tranql-base image that is build for a specific branch. In CI these two images are built in seq, and tranql-base for develop will checkout develop ,
- by default tranql-base is built for master and tranql-app will build off of tranql-base:latest.

…S-Tangerine#147)

…rsion-bump

Plater version bump

Using config for faster parsing instead of a new tranql object

…dis password

…onsidering start and end nodes ,

2. sometimes numeric values cause errors , so tree.toString ensures that doesn't happen

Feature/redis schema

…-repo

Update Dockerfile

…from clause . Redis timeout placed

…et to empty dict

Bugfix/schema and timeout

…/cicd-improvements

…ranql into feature/cicd-improvements

- Dockerfile , need to override some conf on the chart so doing install makes dir location hard. for instance we mount tranql/conf/schema.yaml with redis server info, locating that in site-packages is hard

Feature/cicd improvements

Co-authored-by: Yaphetkg <[email protected]>

Adds make commands for local development

* upgrade bmt  concept model, and tests to remove chemical substance

* Updates schema.yaml to be redis dependent.
Adds make commands for local development

* Make schema.yaml path configurable via env var

Co-authored-by: Yaphetkg <[email protected]>

Upgrades React, react-force-graph, react-bootstrap, react-codemirror2, classnames, & qs.

Upgrades react-filepond/filepond, react-icons, react-split-pane, recharts, & json5

Fills/mocks unsupported features required by the TranQL app in jsdom. Adds a basic test that should never fail as an example.

Replaces domjs jest testing in feature/dependency-updates with end-to-end testing using Puppeteer driver. Adds two temporary tests for prototyping

…side of React (i.e. in unit tests

Resolves bezier-js dependency conflict between CRA and react-force-graph. See issue #282 in react-force-graph.

…ee graph

…e a globally-specified website URL

…e test

…s of completions. Adds an autocomplete tests for context-aware select prediction. Polishes mocking system

…completion test

Moves lengthy autocompletion logic into its own file. Moves main toolbar initialization data into AppToolbar under Toolbar.js. Moves settings modal into SettingsModal.js. Moves example queries used by help modal into static file.

…leViewer.js

…ars. Jenkins sets web testing env variables. make test.npm runs tests a single time (without watching).