Merge branch 'master' of https://github.com/NCATS-Tangerine/reasoner-…

…tools

.travis.yml

@@ -20,7 +20,7 @@ env:
 
 # command to run tests
 script:
-  - pytest -p no:warnings -v greent/test/
+  - pytest -p no:warnings -vv --cov=greent --cov-report term --cov-config=greent/test/.coveragerc greent/test
 
 #after_success:
-#  - coveralls
+  - coveralls

README.md

@@ -24,6 +24,7 @@ The above two files should be considered in tandem.
 
 Add unit test cases to greent/test/test_ontology.py
 
+<<<<<<< HEAD
 
 - TO RUN:
 $pip install -r greent/requirements.txt
@@ -45,6 +46,37 @@ pytest -p no:warnings -vv greent/test/test_ontology.py
 - Run a single unit test:
 pytest greent/test/test_ontology.py -k <test_name>
 pytest greent/test/test_ontology.py -k test_label
+=======
+
+- TO RUN:
+$cd reasoner-tools
+$pip install -r greent/requirements.txt
+
+$gunicorn onto_gunicorn:app --workers 1 --pythonpath=$PWD/greent/api
+Navigate in your browser to http://127.0.0.1:8000/apidocs.
+
+
+- TO TEST:
+$cd reasoner-tools
+
+Note: If you're running a local server, edit the onto URL in greent/greent.conf to point to 127.0.0.1:8000.
+$export greent_conf=greent/greent.conf
+$export PYTHONPATH=$PWD:$PWD/greent/api
+
+- To run all unit tests:
+pytest greent/test/test_ontology.py
+    
+- Remove warnings and get more information as tests run:
+pytest -p no:warnings -vv greent/test/test_ontology.py
+    
+- Run a single unit test:
+pytest greent/test/test_ontology.py -k <test_name>
+pytest greent/test/test_ontology.py -k test_label
+
+- Do code coverage for onto:
+pytest --cov=greent --cov-report term --cov-config=greent/test/.onto_coveragerc greent/test/test_ontology.py
+
+>>>>>>> 0424988eb5ad9f09bdef9af5574875b96b31848b
 ```
 
 ## BioNames API
@@ -73,6 +105,7 @@ $pip install -r greent/requirements.txt
 
 $PYTHONPATH=$PWD python3 builder/api/naming.py
 - Navigate in your browser to localhost:5000/apidocs.
+<<<<<<< HEAD
 
 
 - TO TEST:
@@ -87,4 +120,27 @@ pytest -p no:warnings -vv greent/test/test_bionames.py
 - Run a single unit test:
 pytest greent/test/test_bionames.py -k <test_name>
 pytest greent/test/test_bionames.py -k test_lookup_router
+=======
+
+
+- TO TEST:
+$cd reasoner-tools
+Note:  If you're running a local server, edit the bionames URL in greent/greent.conf to point to localhost:5000
+$export greent_conf=greent/greent.conf
+$export PYTHONPATH=$PWD:$PWD/builder/api
+    
+- To run all unit tests:
+pytest greent/test/test_bionames.py
+    
+- Remove warnings and get more information as tests run:
+pytest -p no:warnings -vv greent/test/test_bionames.py
+    
+- Run a single unit test:
+pytest greent/test/test_bionames.py -k <test_name>
+pytest greent/test/test_bionames.py -k test_lookup_router
+
+- Do code coverage for bionames:
+pytest --cov=greent --cov-report term --cov-config=greent/test/.bionames_coveragerc greent/test/test_bionames.py
+
+>>>>>>> 0424988eb5ad9f09bdef9af5574875b96b31848b
 ```

bin/bionames

@@ -0,0 +1,74 @@
+#!/bin/bash
+
+################################################################
+##
+## BioNames is a generic facility which aggregates bio-ontology 
+##   lookup services. It retrieve names from IDs or IDs based 
+##   on Natural Language names.
+## 
+##   This is the Bash command line interface (CLI) for BioNames.
+##   
+##   author: Chuck Bennett
+##   version: 0.1
+##   usage:
+##      
+##     exec: 
+##      
+##       onto exec
+##       ex: bionames exec
+##      
+##     test:
+##      
+##       onto test
+##       ex: bionames test
+##
+##     test_cov:
+##
+##       onto test_cov
+##       ex: bionames test_cov
+##       
+################################################################
+set -e
+
+##
+## Configure paths.
+##
+export CURDIR=$(pwd)
+export REASONERTOOLS=${CURDIR%/bin}
+export BIONAMES_ROOT=$REASONERTOOLS/builder/api
+export GREENT=$REASONERTOOLS/greent
+export TESTDIR=$GREENT/test
+export PYTHONPATH=$REASONERTOOLS:$BIONAMES_ROOT
+export GREENT_CONF=$GREENT/greent.conf
+
+export COVERAGE_DEBUG="sys,config"
+export COVERAGE_DEBUG_FILE=$CURDIR/pytestconfig.log
+
+##
+## Run the BioNames server
+##
+exec () {
+    PYTHONPATH=$PYTHONPATH python3 $BIONAMES_ROOT/naming.py
+}
+
+##
+## Run tests on the BioNames server.
+##
+test () {
+    pytest -p no:warnings -vv $TESTDIR/test_bionames.py
+}
+
+##
+## Run tests with code coverage.
+##
+test_cov () {
+    cd ..
+    pytest -p no:warnings -vv --cov=$GREENT --cov-report term --cov-config=$TESTDIR/.bionames_coveragerc $TESTDIR/test_bionames.py
+    # Same test using coverage tool:
+    #coverage run --rcfile=$TESTDIR/.bionames_coveragerc -m pytest -p no:warnings -vv $TESTDIR/test_bionames.py
+    #coverage report --rcfile=$TESTDIR/.bionames_coveragerc
+}
+
+$*
+
+exit 0

bin/comp

@@ -0,0 +1,105 @@
+#!/bin/bash
+
+export CURDIR=$(pwd)
+export REASONERTOOLS=${CURDIR%/bin}
+export DOCKER=$REASONERTOOLS/docker
+
+build () {
+    local mod=$1
+    if [ -z "$mod" ]; then
+        echo module name required
+    fi
+    docker build --no-cache $DOCKER/$mod -t renciorg/green-$mod
+}
+push () {
+    local mod=$1
+    if [ -z "$mod" ]; then
+        echo module name required
+    fi
+    docker push renciorg/green-$mod
+}
+clean () {
+    images () {
+        for i in $(sudo docker images | awk '{ print $3 }' | grep -vi image); do echo $i; sudo docker rmi -f $i; done
+    }
+    $*
+}
+
+all () {
+    build base
+    push base
+    build onto_gunicorn
+    push onto_gunicorn
+    build bionames
+    push bionames
+}
+
+all_bionames () {
+    build base
+    push base
+    build bionames
+    push bionames
+}
+
+all_onto_gunicorn () {
+    build base
+    push base
+    build onto_gunicorn
+    push onto_gunicorn
+}
+kill () {
+    local mod=$1
+    if [ -z "$mod" ]; then
+        echo module name required
+    fi
+    docker kill -s 9 $mod
+}
+shell () {
+        local mod=$1
+    if [ -z "$mod" ]; then
+        echo module name required
+    fi
+    docker exec -it $mod bash
+}
+monit () {
+    set -x
+    docker run \
+           --name monit \
+           --rm \
+           renciorg/green-monit-base $*
+    set +x
+}
+tranql () {
+    set -x
+    docker run \
+           --name tranql \
+           --rm \
+           --publish=8101:8101 \
+           renciorg/green-tranql
+    set +x
+}
+onto_gunicorn () {
+    set -x
+    local_dir=$1
+    docker run \
+           --env GIT_PULL=true \
+           --name ont \
+           --rm \
+           --publish=5001:5359 \
+           -v ${local_dir}:/data renciorg/green-onto_gunicorn
+    set +x
+}
+bionames () {
+    set -x
+    local_dir=$1
+    docker run \
+           --env GIT_PULL=true \
+           --name bio \
+           --rm \
+           --publish=5001:5354 \
+           -v ${local_dir}:/data renciorg/green-bionames
+    set +x
+}
+
+
+$*

bin/onto

@@ -0,0 +1,74 @@
+#!/bin/bash
+
+################################################################
+##
+## Onto aggregates lookup services that provide generic facts 
+##   about ontologies. It leverages the Uberongraph RDB (a 
+##   SPARQL-queried Uberongraph database available at 
+##   https://stars-app.renci.org/uberongraph/#query) for data.
+## 
+##   This is the Bash command line interface (CLI) for Onto.
+##   
+##   author: Chuck Bennett
+##   version: 0.1
+##   usage:
+##      
+##     exec: 
+##      
+##       onto exec
+##       ex: onto exec
+##      
+##     test:
+##      
+##       onto test
+##       ex: onto test
+##
+##     test_cov:
+##
+##       onto test_cov
+##       ex: onto test_cov
+##       
+################################################################
+set -e
+
+##
+## Configure paths.
+##
+export CURDIR=$(pwd)
+export REASONERTOOLS=${CURDIR%/bin}
+export GREENT=$REASONERTOOLS/greent
+export TESTDIR=$GREENT/test
+export PYTHONPATH=$GREENT/api:$REASONERTOOLS
+export GREENT_CONF=$GREENT/greent.conf
+
+export COVERAGE_DEBUG="sys,config"
+export COVERAGE_DEBUG_FILE=$CURDIR/pytestconfig_onto.log
+
+##
+## Run the onto gunicorn server
+##
+exec () {
+    gunicorn onto_gunicorn:app --workers 1 --pythonpath=$PYTHONPATH
+}
+
+##
+## Run tests.
+##
+test () {
+    pytest -p no:warnings -vv $TESTDIR/test_ontology.py
+}
+
+##
+## Run tests with code coverage.
+##
+test_cov () {
+    cd $REASONERTOOLS
+    pytest -p no:warnings -vv --cov=$GREENT --cov-report term --cov-config=$TESTDIR/.onto_coveragerc $TESTDIR/test_ontology.py
+    # Same test using coverage tool:
+    #coverage run --rcfile=greent/test/.onto_coveragerc -m pytest -p no:warnings -vv greent/test/test_ontology.py
+    #coverage report --rcfile=greent/test/.onto_coveragerc
+}
+
+$*
+
+exit 0

docker/base/Dockerfile

@@ -0,0 +1,13 @@
+FROM python:3.6.5
+ADD . /code
+WORKDIR /code
+
+RUN git clone https://github.com/NCATS-Tangerine/reasoner-tools.git
+
+RUN pip install -r reasoner-tools/greent/requirements.txt
+
+RUN apt-get update
+RUN apt-get install telnet
+RUN apt-get install -y emacs24
+
+CMD ["PYTHONPATH=reasoner-tools", "python", "reasoner-tools/greent/rosetta.py", "--debug", "--test"]

docker/bionames/Dockerfile

@@ -0,0 +1,13 @@
+FROM renciorg/green-base:latest
+
+ADD ./bionames_smartapi.sh .
+ADD ./synonym.py /usr/local/lib/python3.6/site-packages/pronto/synonym.py
+
+RUN chmod +x bionames_smartapi.sh
+
+ENV APP_PORT 5001
+ENV NUM_WORKERS 2
+ENV DATA_DIR /data
+ENV GIT_PULL false
+
+CMD ["./bionames_smartapi.sh"]