Fix npm install on quay.io

.github/workflows/lint_test.yml

@@ -8,7 +8,7 @@ jobs:
       uses: actions/checkout@v2
     - uses: actions/setup-python@v1
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install flake8
       run: pip install flake8
     - name: Flake8
@@ -33,7 +33,7 @@ jobs:
       uses: actions/checkout@v2
     - uses: actions/setup-python@v1
       with:
-        python-version: 3.6
+        python-version: 3.8
     - name: Update apt cache
       run: sudo apt-get update
     - name: Install python-ldap deps

Makefile

@@ -81,7 +81,7 @@ test-js: eslint
 
 eslint: check-node-modules
 	@echo -n 'Linting javascript...                                        '
-	$(NODEDIR)/.bin/eslint --config $(BASEDIR)/.eslintrc.yml "$(BASEDIR)/askomics/react/src/**"
+	$(NODEDIR)/.bin/eslint --config $(BASEDIR)/.eslintrc.yml "$(BASEDIR)/askomics/react/src/**" || { echo "ERROR"; exit 1; }
 	@echo "Done"
 
 test-python: pylint pytest
@@ -94,7 +94,7 @@ pytest: check-venv
 pylint: check-venv
 	@echo -n 'Linting python...                                            '
 	. $(ACTIVATE)
-	flake8 $(BASEDIR)/askomics $(BASEDIR)/tests --ignore=E501,W504
+	flake8 $(BASEDIR)/askomics $(BASEDIR)/tests --ignore=E501,W504 || { echo "ERROR"; exit 1; }
 	@echo "Done"
 
 serve: check-venv build-config create-user
@@ -126,32 +126,32 @@ check-node-modules:
 
 build-config:
 	@echo -n 'Building config file...                                      '
-	bash cli/set_config.sh
+	bash cli/set_config.sh || { echo "ERROR"; exit 1; }
 	@echo 'Done'
 
 create-user:
 	@echo -n 'Creating first user...                                       '
 	. $(ACTIVATE)
-	bash cli/set_user.sh
+	bash cli/set_user.sh || { echo "ERROR"; exit 1; }
 	@echo 'Done'
 
 update-base-url: check-venv
 	@echo 'Updating base url...'
 	. $(ACTIVATE)
-	bash cli/update_base_url.sh
+	bash cli/update_base_url.sh || { echo "ERROR"; exit 1; }
 	@echo 'Done'
 
 clear-cache: check-venv
 	@echo 'Clearing abstraction cache...'
 	. $(ACTIVATE)
-	bash cli/clear_cache.sh
+	bash cli/clear_cache.sh || { echo "ERROR"; exit 1; }
 	@echo 'Done'
 
 build: build-js
 
 build-js: check-node-modules
 	@echo 'Building askomics.js...                                        '
-	$(NPM) run --silent $(NPMOPTS)
+	$(NPM) run --silent $(NPMOPTS) || { echo "ERROR"; exit 1; }
 	@echo '                                                             Done'
 
 install: install-python install-js
@@ -161,22 +161,22 @@ fast-install:
 
 install-python: check-python
 	@echo -n 'Building python virtual environment...                       '
-	$(PYTHON) -m venv $(VENVDIR)
+	$(PYTHON) -m venv $(VENVDIR) || { echo "ERROR"; exit 1; }
 	@echo 'Done'
 	@echo -n 'Sourcing Python virtual environment...                       '
-	. $(ACTIVATE)
+	. $(ACTIVATE) || { echo "ERROR"; exit 1; }
 	@echo 'Done'
 	@echo -n 'Upgrading pip...                                             '
-	$(PIP) install --upgrade pip > /dev/null
+	$(PIP) install --upgrade pip > /dev/null || { echo "ERROR"; exit 1; }
 	@echo 'Done'
 	@echo 'Installing Python dependencies inside virtual environment... '
-	$(PIP) install -e . > /dev/null
-	PIPENV_VERBOSITY=-1 $(PIPENV) install $(PIPENVOPTS)
+	$(PIP) install -e . > /dev/null || { echo "ERROR"; exit 1; }
+	PIPENV_VERBOSITY=-1 $(PIPENV) install $(PIPENVOPTS) || { echo "ERROR"; exit 1; }
 	@echo '                                                             Done'
 
 install-js: check-npm
 	@echo  'Installing javascript dependencies inside node_modules...    '
-	$(NPM) install --silent
+	$(NPM) install || { echo "ERROR"; exit 1; }
 	@echo '                                                             Done'
 
 clean: clean-js clean-python

Pipfile

@@ -5,7 +5,7 @@ name = "pypi"
 
 [packages]
 werkzeug = "==0.16.1"
-flask = "==1.1.4"
+flask = "<2"
 flask-reverse-proxy-fix = "*"
 validate-email = "*"
 gunicorn = "*"

askomics/libaskomics/SparqlQueryLauncher.py

@@ -220,7 +220,7 @@ def insert_data(self, ttl, graph, metadata=False):
         TYPE
             query result
         """
-        triples = self.get_triples_from_graph(ttl) if metadata else ttl.serialize(format='nt').decode("utf-8")
+        triples = self.get_triples_from_graph(ttl) if metadata else ttl.serialize(format='nt')
 
         query = '''
         INSERT {{

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM askomics/flaskomics-base:4.0.0-alpine3.9 AS builder
+FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.14 AS builder
 MAINTAINER "Xavier Garnier <xavier.garnier@irisa.fr>"
 
 COPY . /askomics
@@ -7,10 +7,10 @@ WORKDIR /askomics
 RUN make clean-config fast-install build
 
 # Final image
-FROM alpine:3.9
+FROM alpine:3.14
 
 WORKDIR /askomics
-RUN apk add --no-cache make python3 bash git libc-dev libstdc++ nodejs nodejs-npm openldap-dev
+RUN apk add --no-cache make python3 bash git libc-dev libstdc++ nodejs-current npm openldap-dev
 COPY --from=builder /askomics .
 
 EXPOSE 5000

docker/DockerfileAll

@@ -1,5 +1,5 @@
 # Build AskOmics
-FROM askomics/flaskomics-base:4.0.0-alpine3.9 AS askomics_builder
+FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.14 AS askomics_builder
 MAINTAINER "Xavier Garnier <xavier.garnier@irisa.fr>"
 
 COPY . /askomics
@@ -14,7 +14,7 @@ FROM xgaia/corese:20.6.11 AS corese_builder
 FROM askomics/virtuoso:7.2.5.1 AS virtuoso_builder
 
 # Final image
-FROM alpine:3.8
+FROM alpine:3.14
 
 ENV MODE="prod" \
     NTASKS="5" \
@@ -35,7 +35,7 @@ RUN apk add --no-cache openssl py-pip && \
     apk --no-cache add --update openjdk11 --repository=http://dl-cdn.alpinelinux.org/alpine/edge/community && \
     mkdir /corese && \
     apk add --no-cache redis sqlite && \
-    apk add --no-cache make python3 bash git libc-dev libstdc++ nodejs nodejs-npm openldap-dev
+    apk add --no-cache make python3 bash git libc-dev libstdc++ nodejs-current nodejs openldap-dev
 
 COPY --from=virtuoso_builder /usr/local/virtuoso-opensource /usr/local/virtuoso-opensource
 COPY --from=virtuoso_builder /virtuoso /virtuoso

docker/DockerfileCelery

@@ -1,4 +1,4 @@
-FROM askomics/flaskomics-base:4.0.0-alpine3.9 AS builder
+FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.14 AS builder
 MAINTAINER "Xavier Garnier <xavier.garnier@irisa.fr>"
 
 COPY . /askomics
@@ -7,7 +7,7 @@ WORKDIR /askomics
 RUN make clean-config fast-install
 
 # Final image
-FROM alpine:3.9
+FROM alpine:3.14
 
 WORKDIR /askomics
 RUN apk add --no-cache make python3 bash git libc-dev libstdc++ openldap-dev

tests/test_api_file.py

@@ -600,5 +600,4 @@ def test_serve_file(self, client):
         response = client.client.get('/api/files/ttl/1/jdoe/{}'.format(filename))
 
         assert response.status_code == 200
-        # print(response.data.decode("utf-8"))
         assert response.data.decode("utf-8") == content