Merge pull request #2 from lca1/dev

MedCo v0.2.1

Makefile

@@ -2,17 +2,29 @@ EXCLUDE_LINT = "_test.go"
 
 # generate/update go server based on swagger specifications
 swagger-gen:
-	swagger validate ./swagger/swagger.yml
+	swagger validate ./swagger/medco-connector-server.yml
 	swagger generate server \
+		--server-package=restapi/server \
+		--model-package=restapi/models \
 		--principal=models.User \
-		--target=./swagger/ \
-		--spec=./swagger/swagger.yml \
+		--target=./ \
+		--spec=./swagger/medco-connector-server.yml \
 		--name=medco-connector
+	swagger validate ./swagger/medco-cli-client.yml
+	swagger generate client \
+		--client-package=restapi/client \
+		--existing-models=github.com/lca1/medco-connector/restapi/models \
+		--skip-models \
+		--principal=models.User \
+		--target=./ \
+		--spec=./swagger/medco-cli-client.yml \
+		--name=medco-cli \
+		--default-scheme=https
 
 test_lint:
 	@echo Checking linting of files
 	@{ \
-		go install golang.org/x/lint/golint; \
+		GO111MODULE=off go get -u golang.org/x/lint/golint; \
 		el=$(EXCLUDE_LINT); \
 		lintfiles=$$( golint ./... | egrep -v "$$el" ); \
 		if [ -n "$$lintfiles" ]; then \

cmd/medco-cli-client/main.go

@@ -0,0 +1,105 @@
+package main
+
+import (
+	medcoclient "github.com/lca1/medco-connector/medco/client"
+	"github.com/sirupsen/logrus"
+	"github.com/urfave/cli"
+	"os"
+	"strings"
+)
+
+func main() {
+
+	cliApp := cli.NewApp()
+	cliApp.Name = "medco-cli-client"
+	cliApp.Usage = "Command-line query tool for MedCo."
+	cliApp.Version = "0.2.1" // todo: dynamically get version from build process
+
+	// from env / config: whatever is in the config of GB : debug,
+	// cli: whatever is user input
+
+	// --- global app flags
+	cliApp.Flags = []cli.Flag{
+		cli.StringFlag{
+			Name:  "user, u",
+			Usage: "OIDC user login",
+		},
+		cli.StringFlag{
+			Name:  "password, p",
+			Usage: "OIDC password login",
+		},
+		cli.StringFlag{
+			Name:  "token, t",
+			Usage: "OIDC token",
+		},
+		cli.BoolFlag{
+			Name:  "disableTLSCheck",
+			Usage: "Disable check of TLS certificates",
+		},
+	}
+
+	// --- search command flags
+	//searchCommandFlags := []cli.Flag{
+	//	cli.StringFlag{
+	//		Name:  "path",
+	//		Usage: "File containing the query definition",
+	//
+	//	},
+	//}
+
+	//--- query command flags
+	queryCommandFlags := []cli.Flag{
+		cli.StringFlag{
+			Name:  "resultFile, r",
+			Usage: "Output file for the result CSV. Printed to stdout if omitted.",
+			Value: "",
+		},
+		cli.BoolFlag{
+			Name:  "bypassPicsure",
+			Usage: "Bypass PIC-SURE and query directly the MedCo connectors",
+		},
+	}
+
+	// --- app commands
+	cliApp.Commands = []cli.Command{
+	//{
+	//	Name:    "search",
+	//	Aliases: []string{"s"},
+	//	Usage:   "Browse the MedCo tree ontology",
+	//	Action:  encryptIntFromApp,
+	//	Flags:   searchCommandFlags,
+	//	ArgsUsage: "",
+	//
+	//},
+		{
+			Name:    "query",
+			Aliases: []string{"q"},
+			Usage:   "Query the MedCo network",
+			Flags: queryCommandFlags,
+			ArgsUsage: "[patient_list|count_per_site|count_per_site_obfuscated|count_per_site_shuffled|" +
+				"count_per_site_shuffled_obfuscated|count_global|count_global_obfuscated] [query string]",
+			Action:  func(c *cli.Context) error {
+				return medcoclient.ExecuteClientQuery(
+					c.GlobalString("token"),
+					c.GlobalString("user"),
+					c.GlobalString("password"),
+					c.Args().First(),
+					strings.Join(c.Args().Tail(), " "),
+					c.String("resultFile"),
+					c.GlobalBool("disableTLSCheck"),
+					c.Bool("bypassPicsure"),
+				)
+			},
+		},
+
+	}
+
+	//cliApp.Before = func(c *cli.Context) error {
+	//	log.SetDebugVisible(c.GlobalInt("debug"))
+	//	return nil
+	//}
+	err := cliApp.Run(os.Args)
+	if err != nil {
+		logrus.Error(err)
+	}
+}

deployment/Dockerfile

@@ -1,14 +1,13 @@
-FROM golang:1.11 as build
+FROM golang:1.12 as build
 
 COPY ./ /src
 
-# compile and install medco-connector
+# compile and install medco-connector-server
 WORKDIR /src
-RUN CGO_ENABLED=0 go build -v ./... && \
-    CGO_ENABLED=0 go install -v ./...
+RUN CGO_ENABLED=0 go install -v ./cmd/medco-connector-server/...
 
 # -------------------------------------------
-FROM golang:1.11-alpine as release
+FROM golang:1.12-alpine as release
 
 COPY deployment/docker-entrypoint.sh /usr/local/bin/
 RUN apk update && apk add bash && rm -rf /var/cache/apk/* && \
@@ -18,21 +17,25 @@ COPY --from=build /go/bin/medco-connector-server /go/bin/
 
 # swagger server configuration
 ENV HOST=0.0.0.0 \
-    PORT=1999
+    PORT=1999 \
+    SERVER_HTTP_WRITE_TIMEOUT_SECONDS=600
 
 # run-time environment
 ENV I2B2_HIVE_URL=http://i2b2:8080/i2b2/services \
     I2B2_LOGIN_DOMAIN=i2b2medco \
     I2B2_LOGIN_PROJECT=MedCo \
     I2B2_LOGIN_USER=e2etest \
     I2B2_LOGIN_PASSWORD=e2etest \
+    I2B2_WAIT_TIME_SECONDS=300 \
     LOG_LEVEL=5 \
     UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml \
     UNLYNX_GROUP_FILE_IDX=0 \
+    UNLYNX_TIMEOUT_SECONDS=300 \
     JWKS_URL=http://keycloak:8080/auth/realms/master/protocol/openid-connect/certs \
     OIDC_JWT_ISSUER=http://keycloak:8080/auth/realms/master \
     OIDC_CLIENT_ID=medco \
-    OIDC_JWT_USER_ID_CLAIM=preferred_username
+    OIDC_JWT_USER_ID_CLAIM=preferred_username \
+    MEDCO_OBFUSCATION_MIN=5
 
 EXPOSE 1999
-ENTRYPOINT ["docker-entrypoint.sh"]
+ENTRYPOINT docker-entrypoint.sh medco-connector-server --write-timeout=${SERVER_HTTP_WRITE_TIMEOUT_SECONDS}s

deployment/client.Dockerfile

@@ -0,0 +1,30 @@
+FROM golang:1.12.5 as build
+
+COPY ./ /src
+
+# compile and install medco-cli-client
+WORKDIR /src
+RUN CGO_ENABLED=0 go install -v ./cmd/medco-cli-client/...
+
+# -------------------------------------------
+FROM golang:1.12.5-alpine as release
+
+COPY deployment/docker-entrypoint.sh /usr/local/bin/
+RUN apk update && apk add bash && rm -rf /var/cache/apk/* && \
+    chmod a+x /usr/local/bin/docker-entrypoint.sh
+
+COPY --from=build /go/bin/medco-cli-client /go/bin/
+
+# run-time environment
+ENV LOG_LEVEL=5 \
+    UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml \
+    UNLYNX_GROUP_FILE_IDX=0 \
+    OIDC_CLIENT_ID=medco \
+    CLIENT_QUERY_TIMEOUT_SECONDS=660 \
+    PICSURE2_API_HOST=picsure:8080/pic-sure-api-2/PICSURE \
+    PICSURE2_API_BASE_PATH="" \
+    PICSURE2_API_SCHEME=https \
+    PICSURE2_RESOURCES=MEDCO_testnetwork_0_a,MEDCO_testnetwork_1_b,MEDCO_testnetwork_2_c \
+    OIDC_REQ_TOKEN_URL=http://keycloak:8080/auth/realms/master/protocol/openid-connect/token
+
+ENTRYPOINT ["docker-entrypoint.sh", "medco-cli-client"]

deployment/docker-compose.yml

@@ -8,17 +8,43 @@ services:
     ports:
       - "1999"
     environment:
+      - SERVER_HTTP_WRITE_TIMEOUT_SECONDS=600
       - I2B2_HIVE_URL=http://i2b2:8080/i2b2/services
       - I2B2_LOGIN_DOMAIN=i2b2medco
       - I2B2_LOGIN_PROJECT=MedCo
       - I2B2_LOGIN_USER=e2etest
       - I2B2_LOGIN_PASSWORD=e2etest
+      - I2B2_WAIT_TIME_SECONDS=300
       - LOG_LEVEL=5
       - UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml
       - UNLYNX_GROUP_FILE_IDX=0
+      - UNLYNX_TIMEOUT_SECONDS=300
       - JWKS_URL=http://keycloak:8080/auth/realms/master/protocol/openid-connect/certs
       - OIDC_JWT_ISSUER=http://keycloak:8080/auth/realms/master
       - OIDC_CLIENT_ID=medco
       - OIDC_JWT_USER_ID_CLAIM=preferred_username
+      - MEDCO_OBFUSCATION_MIN=5
     volumes:
       - ./configuration-profile:/medco-configuration
+
+  medco-cli-client:
+    image: medco/medco-cli-client:dev
+    build:
+      context: ../
+      dockerfile: deployment/client.Dockerfile
+    environment:
+      - LOG_LEVEL=5
+      - UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml
+      - UNLYNX_GROUP_FILE_IDX=0
+      - OIDC_CLIENT_ID=medco
+      - CLIENT_QUERY_TIMEOUT_SECONDS=660
+      - PICSURE2_API_HOST=localhost
+      - PICSURE2_API_BASE_PATH=/pic-sure-api-2/PICSURE
+      - PICSURE2_API_SCHEME=http
+      - PICSURE2_RESOURCES=MEDCO_testnetwork_0_a,MEDCO_testnetwork_1_b,MEDCO_testnetwork_2_c
+      - OIDC_REQ_TOKEN_URL=http://localhost/auth/realms/master/protocol/openid-connect/token
+    volumes:
+      - ~/MedCo/repositories/medco-deployment/configuration-profiles/dev-local-3nodes:/medco-configuration
+    network_mode: host
+    command: >-
+      todo: default e2e query command;

deployment/docker-entrypoint.sh

@@ -7,4 +7,4 @@ if [[ `ls -1 /medco-configuration/srv*-certificate.crt 2>/dev/null | wc -l` != 0
     update-ca-certificates
 fi
 
-exec medco-connector-server
+exec $@

go.mod

@@ -1,27 +1,32 @@
 module github.com/lca1/medco-connector
 
 require (
-	github.com/PuerkitoBio/purell v1.1.1 // indirect
-	github.com/go-openapi/analysis v0.18.0 // indirect
-	github.com/go-openapi/errors v0.18.0
-	github.com/go-openapi/jsonpointer v0.18.0 // indirect
-	github.com/go-openapi/jsonreference v0.18.0 // indirect
-	github.com/go-openapi/loads v0.18.0
-	github.com/go-openapi/runtime v0.18.0
-	github.com/go-openapi/spec v0.18.0
-	github.com/go-openapi/strfmt v0.18.0
-	github.com/go-openapi/swag v0.18.0
-	github.com/go-openapi/validate v0.18.0
-	github.com/google/uuid v1.1.1 // indirect
+	github.com/asaskevich/govalidator v0.0.0-20190424111038-f61b66f89f4a // indirect
+	github.com/docker/go-units v0.4.0 // indirect
+	github.com/go-openapi/analysis v0.19.0 // indirect
+	github.com/go-openapi/errors v0.19.0
+	github.com/go-openapi/jsonpointer v0.19.0 // indirect
+	github.com/go-openapi/jsonreference v0.19.0 // indirect
+	github.com/go-openapi/loads v0.19.0
+	github.com/go-openapi/runtime v0.19.0
+	github.com/go-openapi/spec v0.19.0
+	github.com/go-openapi/strfmt v0.19.0
+	github.com/go-openapi/swag v0.19.0
+	github.com/go-openapi/validate v0.19.0
 	github.com/jessevdk/go-flags v1.4.0
-	github.com/lca1/medco-unlynx v0.0.0-20190326092154-e12359adb567
-	github.com/lca1/unlynx v0.0.0-20190312131415-2e3533f65afe
-	github.com/lestrrat-go/jwx v0.0.0-20190415045601-bee008e7f2ee
-	github.com/lestrrat-go/pdebug v0.0.0-20180220043849-39f9a71bcabe // indirect
-	github.com/mailru/easyjson v0.0.0-20190221075403-6243d8e04c3f // indirect
-	github.com/pkg/errors v0.8.1 // indirect
-	github.com/sirupsen/logrus v1.4.0
-	github.com/smartystreets/goconvey v0.0.0-20190330032615-68dc04aab96a // indirect
-	go.dedis.ch/onet/v3 v3.0.0
-	golang.org/x/net v0.0.0-20190311183353-d8887717615a
+	github.com/konsorten/go-windows-terminal-sequences v1.0.2 // indirect
+	github.com/lca1/medco-loader v0.2.1
+	github.com/lca1/medco-unlynx v0.2.1
+	github.com/lca1/unlynx v1.3.1
+	github.com/lestrrat-go/jwx v0.9.0
+	github.com/mailru/easyjson v0.0.0-20190403194419-1ea4449da983 // indirect
+	github.com/pkg/errors v0.8.1
+	github.com/r0fls/gostats v0.0.0-20180711082619-e793b1fda35c
+	github.com/sirupsen/logrus v1.4.2
+	github.com/smartystreets/assertions v1.0.0 // indirect
+	github.com/urfave/cli v1.20.0
+	go.dedis.ch/onet/v3 v3.0.14
+	golang.org/x/crypto v0.0.0-20190605123033-f99c8df09eb5 // indirect
+	golang.org/x/net v0.0.0-20190606173856-1492cefac77f
+	golang.org/x/sys v0.0.0-20190606203320-7fc4e5ec1444 // indirect
 )