python3 conversion, url checking methods

.coveragerc

@@ -0,0 +1,13 @@
+[run]
+omit = 
+    # omit code not under our control
+    UIService/UIServiceServer.py
+    UIService/authclient.py
+    UIService/__init__.py
+
+[report]
+omit = 
+    # omit code not under our control
+    UIService/UIServiceServer.py
+    UIService/authclient.py
+    UIService/__init__.py

.gitignore

@@ -2,3 +2,4 @@ test_local
 sdk.cfg
 *.pyc
 *.bak-*
+_attic

.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "python.linting.pylintEnabled": true,
+    "python.pythonPath": "/opt/local/bin/python3.6"
+}

Dockerfile

@@ -1,68 +1,70 @@
-FROM alpine:3.8 as builder
+FROM alpine:3.12 as builder
 MAINTAINER KBase Developer
 
 # The build stage needs just enough to run the KBase SDK tools.
-# 
 
 # update system and system dependencies
-RUN apk upgrade --update-cache --available \
-    && apk add --update --no-cache \
-        apache-ant=1.10.4-r0 \
-        bash=4.4.19-r1 \
-        git=2.18.0-r0 \
-        linux-headers=4.4.6-r2 \
-        make=4.2.1-r2 \
-        openjdk8=8.171.11-r0 \
-        python2=2.7.15-r0
-
-RUN mkdir -p /kb \
-    && git clone --depth=1 https://github.com/kbase/kb_sdk /kb/kb_sdk \
-    && cd /kb/kb_sdk \
-    && make
+RUN apk upgrade --update-cache --available && \
+    apk add --update --no-cache apache-ant bash git linux-headers make openjdk8
+
+# Currently need this special install for python3. oh, python.
+RUN apk add --no-cache python3 && \
+    python3 -m ensurepip && \
+    rm -r /usr/lib/python*/ensurepip && \
+    pip3 install --upgrade pip setuptools && \
+    if [ ! -e /usr/bin/pip ]; then ln -s pip3 /usr/bin/pip ; fi && \
+    if [[ ! -e /usr/bin/python ]]; then ln -sf /usr/bin/python3 /usr/bin/python; fi && \
+    rm -r /root/.cache
+
+RUN mkdir -p /kb && \
+    git clone --depth=1 https://github.com/kbase/kb_sdk /kb/kb_sdk && \
+    cd /kb/kb_sdk && \
+    make
 
 COPY ./ /kb/module
 
-RUN mkdir -p /kb/module/work/cache \
-    && chmod -R a+rw /kb/module \
-    && cd /kb/module \
-    && PATH=$PATH:/kb/kb_sdk/bin make install
+RUN mkdir -p /kb/module/work/cache && \
+    chmod -R a+rw /kb/module && \
+    cd /kb/module && \
+    PATH=$PATH:/kb/kb_sdk/bin make install
 
 # Final image
 
-FROM alpine:3.8
+FROM alpine:3.12
 MAINTAINER KBase Developer
 
 # update system and system dependencies
-RUN apk upgrade --update-cache --available \
-    && apk add --update --no-cache \
-        bash=4.4.19-r1 \
-        g++=6.4.0-r8 \
-        git=2.18.0-r0 \
-        libffi-dev=3.2.1-r4 \
-        linux-headers=4.4.6-r2 \
-        make=4.2.1-r2 \
-        openssl-dev=1.0.2o-r2 \
-        py2-pip=10.0.1-r0 \
-        python2=2.7.15-r0 \
-        python2-dev=2.7.15-r0
+RUN apk upgrade --update-cache --available && \
+    apk add --update --no-cache bash g++ git libffi-dev linux-headers make openssl-dev
+
+# Currently need this special install for python3. oh, python.
+RUN apk add --no-cache python3 python3-dev py3-setuptools && \
+    python3 -m ensurepip && \
+    rm -r /usr/lib/python*/ensurepip && \
+    pip3 install --upgrade pip setuptools && \
+    if [ ! -e /usr/bin/pip ]; then ln -s pip3 /usr/bin/pip ; fi && \
+    if [[ ! -e /usr/bin/python ]]; then ln -sf /usr/bin/python3 /usr/bin/python; fi && \
+    rm -r /root/.cache
 
 # install python dependencies for the service runtime.
 RUN pip install --upgrade pip && \
     pip install \
-        cffi==1.11.5 \
-        jinja2==2.10 \
-        jsonrpcbase==0.2.0 \
-        ndg-httpsclient==0.5.1 \
-        pymongo===3.7.1 \
-        python-dateutil==2.7.3 \
-        pytz==2018.5 \
-        requests==2.19.1 \
-        uwsgi==2.0.17.1
-
+    cffi==1.14.3 \
+    coverage==4.5.4 \
+    jinja2==2.11.2 \
+    jsonrpcbase==0.2.0 \
+    ndg-httpsclient==0.5.1 \
+    git+https://github.com/nose-devs/nose@master \
+    python-dateutil==2.8.1 \
+    pytz==2020.1 \
+    requests==2.24.0 \
+    uwsgi==2.0.19.1
+
 RUN addgroup --system kbmodule && \
     adduser --system --ingroup kbmodule kbmodule
 
-COPY --from=builder --chown=kbmodule:kbmodule /kb/module /kb/module
+COPY --from=builder /kb/module /kb/module
+RUN chown -R kbmodule:kbmodule /kb/module
 
 WORKDIR /kb/module
 

Makefile

@@ -52,7 +52,9 @@ build-test-script:
 	@echo 'export KB_AUTH_TOKEN=`cat /kb/module/work/token`' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
 	@echo 'export PYTHONPATH=$$script_dir/../$(LIB_DIR):$$PATH:$$PYTHONPATH' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
 	@echo 'cd $$script_dir/../$(TEST_DIR)' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
-	@echo 'python -m nose --with-coverage --cover-package=$(SERVICE_CAPS) --cover-html --cover-html-dir=/kb/module/work/test_coverage --nocapture  --nologcapture .' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
+	@echo 'echo "Running tests"' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
+	@echo 'echo `pwd`' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
+	@echo 'python -m nose --with-coverage --cover-package=$(SERVICE_CAPS) --cover-html --cover-html-dir=/kb/module/work/test_coverage --nocapture  --nologcapture --cover-config-file=$$script_dir/../$(TEST_DIR)/coverage.cfg .' >> $(TEST_DIR)/$(TEST_SCRIPT_NAME)
 	@chmod +x $(TEST_DIR)/$(TEST_SCRIPT_NAME)
 
 docker-image-dev:

README.md

@@ -1,32 +1,48 @@
-
 # UIService
+
 ---
 
 A [KBase](https://kbase.us) module generated by the [KBase SDK](https://github.com/kbase/kb_sdk).
 
-## Local development
+## Using ui-service
+
+See the spec file, UIService.spec, for api and type definitions.
+
+## Getting started with testing and development
+
+See [Developer Docs](docs/development.md)
 
-old way:
+## Tests
+
+## Local development with kbase-ui
+
+To make the image locally:
 
 ```
-PATH=$PATH:`pwd`/../../kb_sdk/bin
-kb-sdk test
-bash scripts/run-bash.sh
-bash scripts/start_server.sh
+make docker-image-dev
 ```
 
-new way:
+Then to run it:
 
 ```
-make docker-image-dev
 make run-docker-image-dev
 ```
 
+This will start the container attached to the Docker custom network used by kbase-ui.
+
+Then in kbase-ui, start it with the dynamic-services option, like
+
+```
+kbase-ui start-dev env=dev build=dev build-image=f dynamic-services="ui-service"
+```
+
 ## Pure local image build
 
 kb_sdk's ModuleTester.java contains the code to build the docker image. All it does, as far as building goes, is construct a simple docker build bash command string. (It also manages images, etc.)
 
+```
 docker build --rm -t TARGET_IMAGE_NAME REPO_PATH
+```
 
 where TARGET_IMAGE_NAME is test/MODULE:latest
 
@@ -40,47 +56,14 @@ docker build --rm -t test/ui-service:dev
 
 If you are starting from a cold docker cache the initial build may take several minutes: the kbase base image is rather huge.
 
-## Actually...
-
-To make the image locally: 
-
-```
-make docker-image-dev
-```
-
-Then to run it:
-
-```
-make run-docker-image-dev
-```
-
-This will start the container attached to the Docker custom network 
-
-## Work in Progress Instructions
+## Testing
 
-In the current incarnation, when the service starts it creates the sqlite database schema, and populates initial data therein. This includes the admin user, ui_service_admin. A token for this user may be used to add alerts.
+After running `kb-sdk test` the first time, which generates `test_local`:
 
-See the scripts ```test/manual```. Running the script 'send.sh' with an argument set to the base name for an accompanying json file will send the associated json-rpc payload.
-
-E.g.
+-   For test_local/test.cfg set the test_token to a valid login token.
+-   Generate an ssl self signed certificate and place into test_local/workdir: `test-ssl.crt` and `test-ssl.key`.
 
 ```bash
-KB_TOKEN=XXXMYTOKENXXX bash send.sh add-alert
-```
-
-## Development
-
-### install mongo image 
-
-I use Kitematic to get the latest in the 3 series (currently 3.7.9) - the 2 series which kbase uses is not supported in the official distribution.
-
-Change these settings:
-
-- enable kbase-dev network
-- map directories to SPRINT/mongo/db and SPRINT/mongo/configdb
-
-### Add ui_service user and database
-
-mongo localhost:PORT
-
-where port is the port reported in Kitematic (it changes with every container startup)
+mkdir test_local/workdir
+openssl req -x509 -nodes -days 365 -newkey rsa:2048 -keyout test_local/workdir/test-ssl.key -out test_local/workdir/test-ssl.crt -subj "/C=US/ST=California/L=Berkeley/O=LBNL/OU=KBase/CN=ci.kbase.us"
+```