Release 0.3 (#8)

* Merging Griffin's changes (NCATS-Tangerine#118)

* 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 <urnancx@gmail.com>
Co-authored-by: frostyfan109 <urnansupersux@gmail.com>
Co-authored-by: frostyfan109 <31631417+frostyfan109@users.noreply.github.com>

* when using schema the expand nodes function fails to set starting nodes, and hence causing all graph grabbing, this was overlooked in initial merge.

* Udfs functions for parents and sibilings looking up wrong keys fix

* Error modal not closing properly fix

* docker image version bump for new dev image

* Update for planner, to fail iff no results can be found after trying all capable KPs.

* docker version bump

* Varnish docker image to slim debian version

* Trapi updates (NCATS-Tangerine#122)

* 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 (NCATS-Tangerine#126)

* Trapi 1.0 overhaul

* Trapi 1.0 schema update.

* update unit test files to Trapi 1.0

* Dependency corrections

* Web prefix (NCATS-Tangerine#129)

* adding web_prefix conf for web api

* adding web_prefix conf for web api

* minor version added

* Convert renciorg refs to helxplatform refs.

* Web prefix (NCATS-Tangerine#133)

* 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.

* Web prefix for UI (NCATS-Tangerine#139)

* 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

* Parameterizes docker file to support building a branch for CI/CD. (NCATS-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.

* Configure message not being called filters out important nodes. (NCATS-Tangerine#147)

* skip and limit additions for cypher queries

* plater lib version bump

* test for skip and limit options on redis

* fixes test , upgrades plater

* strips / from main url (NCATS-Tangerine#154)

* Adding db to schema so it shows up on UI auto complete

* Refactoring merge endpoint.
Using config for faster parsing instead of a new tranql object

* Modify schema factory sending tranql config so its able to resolve redis password

* Parsing tweaks for 1. Suggesting concepts only base on context, i.e considering start and end nodes ,
2. sometimes numeric values cause errors , so tree.toString ensures that doesn't happen

* merge for trapi 1.0

* test overhaul for merge and schema supporting redis

* Score as summation of publication counts on each edge

* score test disable

* Support for max connections

* fixing api test for score

* Adding Makefile, Jenkinsfile, consolidated Docker, tranql src dir

* Makefile and Jenkinsfile

* Starting to organize & cleanup tests

* Makefile

* Test cleanup

* Bumping version

* Makefile

* Testing jenkins file

* Temp changing jenkins control flow

* Update Dockerfile

* Structural changes for simplified deployment

* Jenkins and Makefile

* using first message query graph fixed, now questions are also merged.

* root question as query graph for merged answers when using schema on from clause . Redis timeout placed

* schema to updated dynamically after redis is populated, and some tests

* test for empty schema tweak

* import at top

* plater version bump

* when grabbing trapi option, if tranql query parser does not set it, set to empty dict

* Fixing merge conflicts

* bump plater version

* requirements to fix tests

* Removing travis file

* - Update requirements.txt , just the required libs
- 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

* upgrade bmt  concept model, and tests to remove chemical substance (#6)

Co-authored-by: Yaphetkg <yaphetkg@renci.org>

* Feature/local development (#7)

* 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 <yaphetkg@renci.org>

* Update _version.py

Co-authored-by: frostyfan109 <urnancx@gmail.com>
Co-authored-by: frostyfan109 <urnansupersux@gmail.com>
Co-authored-by: frostyfan109 <31631417+frostyfan109@users.noreply.github.com>
Co-authored-by: yaphetkg <kebedey@renci.com>
Co-authored-by: Chuck Bennett <cnbennett3@gmail.com>
Co-authored-by: cnbennett3 <53792237+cnbennett3@users.noreply.github.com>
Co-authored-by: Steven <scox@renci.org>
Co-authored-by: Carl Schreep <schreepc@renci.org>
Co-authored-by: Yaphetkg <yaphetkg@renci.org>
Co-authored-by: Carl Schreep <cschreep@users.noreply.github.com>

.dockerignore

@@ -0,0 +1,20 @@
+npm-debug.log
+.github/
+.pytest_cache
+docker/
+docs/
+kubernetes/
+varnish-cache/
+web/node_modules/
+
+*.egg-info/
+
+.env
+.gitignore
+.python-version
+.travis.yml
+docker-compose.yml
+Dockerfile
+Jenkinsfile
+
+*.log

.gitignore

@@ -0,0 +1,148 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+.idea/
+
+# NPM
+**/web/node_modules
+**/web/build
+
+# Filesystem
+.DS_Store

Dockerfile

@@ -0,0 +1,26 @@
+FROM python:3.7.3-alpine
+
+RUN apk add build-base git libxslt-dev linux-headers make nodejs npm zeromq zeromq-dev
+
+ENV USER tranql
+ENV HOME /home/$USER
+
+RUN addgroup -S $USER && adduser -S $USER -G $USER -s /bin/bash -h $HOME
+
+USER $USER
+WORKDIR $HOME
+
+ENV PATH=$HOME/.local/bin:$PATH
+ENV PUBLIC_URL={{web_prefix}}
+ENV BACKPLANE=http://tranql-backplane.renci.org
+
+COPY --chown=$USER . tranql/
+
+WORKDIR $HOME/tranql/src/tranql/web
+RUN npm install
+RUN npm run build
+
+WORKDIR $HOME/tranql
+RUN pip install --user --upgrade pip
+RUN pip install --user -r requirements.txt
+ENV PYTHONPATH=$HOME/tranql/src/

Jenkinsfile

@@ -0,0 +1,41 @@
+pipeline {
+    agent {
+        kubernetes {
+            cloud 'kubernetes'
+            label 'agent-docker'
+            defaultContainer 'agent-docker'
+        }
+    }
+    stages {
+        stage('Install') {
+            steps {
+                sh '''
+                python3 -m pip install --user --upgrade pip
+                python3 -m pip install --user -r requirements.txt
+                python3 -m pip install --user .
+                '''
+            }
+        }
+        stage('Test') {
+            steps {
+                sh '''
+                make test
+                '''
+            }
+        }
+        stage('Publish') {
+            when {
+                buildingTag()
+            }
+            environment {
+                DOCKERHUB_CREDS = credentials('rencibuild_dockerhub_machine_user')
+            }
+            steps {
+                sh '''
+                echo $DOCKERHUB_CREDS_PSW | docker login -u $DOCKERHUB_CREDS_USR --password-stdin
+                make build
+                '''
+            }
+        }
+    }
+}

MANIFEST.in

@@ -1,4 +1,5 @@
 recursive-include * *.txt
 recursive-include * *.json
 recursive-include * *.yaml
-recursive-include * *.yml
+recursive-include * *.yml
+graft src/tranql/web/build

Makefile

@@ -0,0 +1,74 @@
+PYTHON       = /usr/bin/env python3
+VERSION_FILE = ./src/tranql/_version.py
+VERSION      = $(shell cut -d " " -f 3 ${VERSION_FILE})
+DOCKER_REPO  = docker.io
+DOCKER_OWNER = helxplatform
+DOCKER_APP	 = tranql
+DOCKER_TAG   = ${VERSION}
+DOCKER_IMAGE = ${DOCKER_OWNER}/${DOCKER_APP}:$(DOCKER_TAG)
+TEST_REDIS_DUMP_FILE = "https://stars.renci.org/var/kgx_data/v3.0/roger-mini.rdb"
+
+
+.DEFAULT_GOAL = help
+
+.PHONY: help clean install test build image publish
+
+#help: List available tasks on this project
+help:
+	@grep -E '^#[a-zA-Z\.\-]+:.*$$' $(MAKEFILE_LIST) | tr -d '#' | awk 'BEGIN {FS = ": "}; {printf "\033[36m%-20s\033[0m %s\n", $$1, $$2}'
+
+#clean: Remove old build artifacts and installed packages
+clean:
+	rm -rf build
+	rm -rf dist
+	rm -rf src/tranql.egg-info
+	${PYTHON} -m pip uninstall -y tranql
+	${PYTHON} -m pip uninstall -y -r requirements.txt
+
+#install.python: Install python application along with required development packages
+install.python:
+	${PYTHON} -m pip install --upgrade pip
+	${PYTHON} -m pip install -r requirements.txt
+	${PYTHON} -m pip install .
+
+#install.npm: Builds the NPM modules
+install.npm:
+	cd src/tranql/web; npm install; npm run build
+
+#install: Install application
+install: install.python install.npm
+
+#test.python: Run all python tests
+test.python:
+	#${PYTHON} -m pytest --doctest-modules src
+	${PYTHON} -m pytest tests
+
+#test.npm: Run all NPM tests
+test.npm:
+	echo "test NPM"
+
+#test: Run all tests
+test: test.python test.npm
+
+#build: Build Docker image
+build:
+	echo "Building docker image: ${DOCKER_IMAGE}"
+	docker build -t ${DOCKER_IMAGE} -f Dockerfile .
+	echo "Successfully built: ${DOCKER_IMAGE}"
+
+#publish: Build and push docker image
+publish:
+	docker tag ${DOCKER_IMAGE} ${DOCKER_REPO}/${DOCKER_IMAGE}
+	docker push ${DOCKER_REPO}/${DOCKER_IMAGE}
+
+#download: Downloads example dataset for redis
+download:
+	mkdir -p redis_data/
+	if [ ! -f "./redis_data/dump.rdb" ] ; then \
+	wget ${TEST_REDIS_DUMP_FILE} -O redis_data/dump.rdb; \
+	fi
+
+#run.local: seeds redis with data, builds web page and runs tranql docker container
+run.local: download
+	docker-compose up -d
+	cd src/tranql/web; npm start;

QUICKSTART.md

@@ -0,0 +1,18 @@
+## Setting up server
+
+Note: For building react app nodejs and npm are required.
+
+1. Install node js dependencies.
+```shell
+make install.npm
+```
+2. Runs Tranql in a docker container, with reload enabled for the web server. UI is not reloaded on change but one can start 
+cd
+```shell
+make run.local 
+```
+
+3. Browse to 
+    1. [Tranql UI](http://localhost:8001) 
+    2. [Openapi Swagger UI](http://localhost:8001/apidocs)
+    3. [Tranql UI served from Nodejs](http://localhost:3000) 

dev-schema.yaml

@@ -0,0 +1,16 @@
+---
+doc : |
+  The Translator schema aggregates reasoner schemas. Reasoner schemas
+  describe transitions between biolink-model types. These transitions are
+  expressed as predicates, also from the biolink-model.
+schema:
+  redis:
+    doc: |
+      Roger is a knowledge graph built by aggregeting several kgx formatted knowledge graphs from several sources.
+    url: "redis:test"
+    redis: true
+    redis_connection_params:
+      host: redis_graph
+      port: 6379
+        # SET USERNAME and PASSWORD
+        # via ROGER_USERNAME , ROGER_PASSWORD Env vars (i.e capitialize service name)