diff --git a/.circleci/config.yml b/.circleci/config.yml
index d001c2ae43b3fdf3fbaef100a6faab60ad234a2a..03531b3ccb9573854e904e44fccec484b870b1fc 100644
--- a/.circleci/config.yml
+++ b/.circleci/config.yml
@@ -1,36 +1,38 @@
---
-version: 2
+# Sample advanced CircleCI configuration: https://github.com/transcom/mymove/blob/master/.circleci/config.yml
+
+version: 2.1
jobs:
build:
working_directory: ~/src
docker:
- - image: hbpmip/docker-compose-for-ci:17.06-1
+ - image: hbpmip/docker-compose-for-ci:18.09-1
environment:
- CIRCLECI: true
steps:
- setup_remote_docker:
- version: 17.06.0-ce
+ version: 18.06.0-ce
- checkout
+ - restore_cache:
+ keys:
+ - pre-commit-dot-cache-{{ checksum ".pre-commit-config.yaml" }}
- run:
name: "Install requirements"
command: |
docker --version
- pip install --upgrade pre-commit
pre-commit install
- run:
name: "Validate code quality"
command: |
pre-commit run --all-files
+ - save_cache:
+ key: pre-commit-dot-cache-{{ checksum ".pre-commit-config.yaml" }}
+ paths:
+ - ~/.cache/pre-commit
- run:
name: "Build project"
- command: |
- PATH=$PATH:/$HOME/.captain/bin/ ./build.sh
+ command: ./build.sh
- run:
name: "Test project"
- command: |
- PATH=$PATH:/$HOME/.captain/bin/ ./tests/test.sh
-
- notify:
- webhooks:
- - url: 'https://webhook.atomist.com/atomist/circle'
+ command: ./tests/test.sh
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index e89de63d8be89a26361446031b2aca7d8cb2f12e..4424d57a3de2fa2a9cc2decb1ca06a0d4e178170 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -1,9 +1,14 @@
repos:
- repo: git://github.com/pre-commit/pre-commit-hooks
- sha: v0.7.1
+ rev: v2.1.0
hooks:
- id: trailing-whitespace
- id: end-of-file-fixer
+ exclude: .bumpversion.cfg
- id: check-merge-conflict
- #- id: check-added-large-files - disabled, bug in v0.9.5?
+ - id: check-added-large-files
- id: check-yaml
+ - id: check-json
+ - id: pretty-format-json
+ args: ["--autofix"]
+ exclude: slack.json
diff --git a/build.sh b/build.sh
index beb4b5d032cd389c1e2aa43e740ab4906390577a..998db65551e95df3684d84995e3455e0bea6cf8a 100755
--- a/build.sh
+++ b/build.sh
@@ -18,9 +18,9 @@ get_script_dir () {
cd "$(get_script_dir)"
-if [[ $NO_SUDO || -n "$CIRCLECI" ]]; then
+if [[ "$NO_SUDO" || -n "$CIRCLECI" ]]; then
DOCKER="docker"
-elif groups $USER | grep &>/dev/null '\bdocker\b'; then
+elif groups "$USER" | grep &>/dev/null '\bdocker\b'; then
DOCKER="docker"
else
DOCKER="sudo docker"
@@ -36,3 +36,23 @@ docker build --build-arg BUILD_DATE=$(date -Iseconds) \
--tag "$IMAGE:latest" \
--tag "$IMAGE:$VERSION" \
.
+
+BUGSNAG_KEY=""
+eval $(grep -e "^\\s*BUGSNAG_KEY" Dockerfile | tr '\\' ' ')
+
+if [[ -n "$BUGSNAG_KEY" ]]; then
+ curl https://build.bugsnag.com/ \
+ --header "Content-Type: application/json" \
+ --data "{
+ \"apiKey\": \"$BUGSNAG_KEY\",
+ \"appVersion\": \"$VERSION\",
+ \"releaseStage\": \"dev\",
+ \"builderName\": \"$USER\",
+ \"sourceControl\": {
+ \"provider\": \"github\",
+ \"repository\": \"https://github.com/LREN-CHUV/portal-backend\",
+ \"revision\": \"$VCS_REF\"
+ },
+ \"metadata\": {}
+ }"
+fi
diff --git a/src/main/java/eu/hbp/mip/akka/AkkaClusterHealthCheck.java b/src/main/java/eu/hbp/mip/akka/AkkaClusterHealthCheck.java
index 932599223fbf1c160485174faaf76da04db6b864..8f4b05f99c871469534d1bb66b0f8fb2a86e0906 100644
--- a/src/main/java/eu/hbp/mip/akka/AkkaClusterHealthCheck.java
+++ b/src/main/java/eu/hbp/mip/akka/AkkaClusterHealthCheck.java
@@ -23,4 +23,4 @@ public class AkkaClusterHealthCheck implements HealthIndicator {
return Health.up().build();
}
-}
\ No newline at end of file
+}
diff --git a/src/main/resources/application.conf b/src/main/resources/application.conf
index 333813a1dedc7f79090e077f1d826763ea6521f8..1377464947d56b9bd2546a5756339f2d19145606 100644
--- a/src/main/resources/application.conf
+++ b/src/main/resources/application.conf
@@ -1,3 +1,2 @@
# No specific configuration for Portal backend
# All configuration is related to Akka
-
diff --git a/src/main/resources/data/exareme_algorithms.json b/src/main/resources/data/exareme_algorithms.json
index f1601397d77487b7623c9e2661d188feb3c8a6cc..3ea4bdf19b7f2a779ecd70ab3385ef9b96c8533d 100644
--- a/src/main/resources/data/exareme_algorithms.json
+++ b/src/main/resources/data/exareme_algorithms.json
@@ -1,22 +1,6 @@
[
{
"code": "WP_VARIABLES_HISTOGRAM",
- "label": " Histogram",
- "type": ["statistics"],
- "environment": "Exareme",
- "description": "Histograms",
- "parameters": [{
- "code": "nobuckets",
- "label": "nobuckets",
- "default_value": 4,
- "type": "int",
- "constraints": {
- "min": 1,
- "max": null
- },
- "description":
- "The number of clusters. Typical values range from 2 to 10."
- }],
"constraints": {
"variable": {
"binominal": true,
@@ -24,15 +8,29 @@
"polynominal": true,
"real": true
}
- }
+ },
+ "description": "Histograms",
+ "environment": "Exareme",
+ "label": " Histogram",
+ "parameters": [
+ {
+ "code": "nobuckets",
+ "constraints": {
+ "max": null,
+ "min": 1
+ },
+ "default_value": 4,
+ "description": "The number of clusters. Typical values range from 2 to 10.",
+ "label": "nobuckets",
+ "type": "int"
+ }
+ ],
+ "type": [
+ "statistics"
+ ]
},
{
"code": "PIPELINE_ISOUP_REGRESSION_TREE_SERIALIZER",
- "label": " Regression Tree",
- "type": ["statistics"],
- "environment": "Exareme",
- "description": "Regression Tree Serializer",
- "parameters": [],
"constraints": {
"variable": {
"binominal": true,
@@ -40,15 +38,17 @@
"polynominal": true,
"real": true
}
- }
+ },
+ "description": "Regression Tree Serializer",
+ "environment": "Exareme",
+ "label": " Regression Tree",
+ "parameters": [],
+ "type": [
+ "statistics"
+ ]
},
{
"code": "PIPELINE_ISOUP_MODEL_TREE_SERIALIZER",
- "label": "Model Tree",
- "type": ["statistics"],
- "environment": "Exareme",
- "description": "Model Tree Serializer",
- "parameters": [],
"constraints": {
"variable": {
"binominal": true,
@@ -56,70 +56,82 @@
"polynominal": true,
"real": true
}
- }
+ },
+ "description": "Model Tree Serializer",
+ "environment": "Exareme",
+ "label": "Model Tree",
+ "parameters": [],
+ "type": [
+ "statistics"
+ ]
},
{
"code": "WP_LINEAR_REGRESSION",
- "label": "Linear regression",
- "type": ["statistics"],
- "environment": "Exareme",
+ "constraints": {
+ "variable": {
+ "binominal": false,
+ "integer": true,
+ "polynominal": false,
+ "real": true
+ }
+ },
"description": "Linear Regression using Exareme services",
+ "environment": "Exareme",
+ "label": "Linear regression",
"parameters": [
{
"code": "design",
"default_value": "factorial",
- "description":
- "The type of multi-factors design. Choose 'factorial' to enable interactions analysis or 'additive' for a model without no interaction at all.",
+ "description": "The type of multi-factors design. Choose 'factorial' to enable interactions analysis or 'additive' for a model without no interaction at all.",
"label": "design",
"type": "enumeration",
- "values": ["factorial", "additive"]
+ "values": [
+ "factorial",
+ "additive"
+ ]
}
],
+ "type": [
+ "statistics"
+ ]
+ },
+ {
+ "code": "K_MEANS",
"constraints": {
+ "covariables": {
+ "max_count": null,
+ "min_count": "1"
+ },
+ "groupings": {
+ "max_count": 0,
+ "min_count": 0
+ },
+ "mixed": false,
"variable": {
- "binominal": false,
+ "binominal": true,
"integer": true,
- "polynominal": false,
+ "polynominal": true,
"real": true
}
- }
- },
- {
- "code": "K_MEANS",
- "label": "K_MEANS",
- "type": ["statistics"],
- "environment": "Exareme",
+ },
"description": "k-Means using Exareme services",
+ "environment": "Exareme",
+ "label": "K_MEANS",
"parameters": [
{
"code": "k",
- "label": "k",
- "default_value": 5,
- "type": "int",
"constraints": {
- "min": 1,
- "max": null
+ "max": null,
+ "min": 1
},
- "description":
- "The number of clusters. Typical values range from 2 to 10."
+ "default_value": 5,
+ "description": "The number of clusters. Typical values range from 2 to 10.",
+ "label": "k",
+ "type": "int"
}
],
- "constraints": {
- "variable": {
- "real": true,
- "integer": true,
- "binominal": true,
- "polynominal": true
- },
- "groupings": {
- "min_count": 0,
- "max_count": 0
- },
- "covariables": {
- "min_count": "1",
- "max_count": null
- },
- "mixed": false
- }
+ "type": [
+ "statistics"
+ ]
}
]