Merge pull request #1 from lca1/dev

MedCo v0.2.0

Makefile

@@ -1,10 +1,23 @@
-validate:
-	swagger validate ./swagger.yml
+EXCLUDE_LINT = "_test.go"
 
-gen: validate
+# generate/update go server based on swagger specifications
+swagger-gen:
+	swagger validate ./swagger/swagger.yml
 	swagger generate server \
-		--target=./ \
-		--spec=./swagger.yml \
+		--principal=models.User \
+		--target=./swagger/ \
+		--spec=./swagger/swagger.yml \
 		--name=medco-connector
 
-.PHONY: install gen validate
+test_lint:
+	@echo Checking linting of files
+	@{ \
+		go install golang.org/x/lint/golint; \
+		el=$(EXCLUDE_LINT); \
+		lintfiles=$$( golint ./... | egrep -v "$$el" ); \
+		if [ -n "$$lintfiles" ]; then \
+		echo "Lint errors:"; \
+		echo "$$lintfiles"; \
+		exit 1; \
+		fi \
+	}

deployment/Dockerfile

@@ -0,0 +1,38 @@
+FROM golang:1.11 as build
+
+COPY ./ /src
+
+# compile and install medco-connector
+WORKDIR /src
+RUN CGO_ENABLED=0 go build -v ./... && \
+    CGO_ENABLED=0 go install -v ./...
+
+# -------------------------------------------
+FROM golang:1.11-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-connector-server /go/bin/
+
+# swagger server configuration
+ENV HOST=0.0.0.0 \
+    PORT=1999
+
+# 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 \
+    LOG_LEVEL=5 \
+    UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml \
+    UNLYNX_GROUP_FILE_IDX=0 \
+    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
+
+EXPOSE 1999
+ENTRYPOINT ["docker-entrypoint.sh"]

deployment/docker-compose.yml

@@ -0,0 +1,24 @@
+version: '3.5'
+services:
+  medco-connector:
+    image: medco/medco-connector:dev
+    build:
+      context: ../
+      dockerfile: deployment/Dockerfile
+    ports:
+      - "1999"
+    environment:
+      - I2B2_HIVE_URL=http://i2b2:8080/i2b2/services
+      - I2B2_LOGIN_DOMAIN=i2b2medco
+      - I2B2_LOGIN_PROJECT=MedCo
+      - I2B2_LOGIN_USER=e2etest
+      - I2B2_LOGIN_PASSWORD=e2etest
+      - LOG_LEVEL=5
+      - UNLYNX_GROUP_FILE_PATH=/medco-configuration/group.toml
+      - UNLYNX_GROUP_FILE_IDX=0
+      - 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
+    volumes:
+      - ./configuration-profile:/medco-configuration

deployment/docker-entrypoint.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+set -Eeuo pipefail
+
+# trust the certificates of other nodes
+if [[ `ls -1 /medco-configuration/srv*-certificate.crt 2>/dev/null | wc -l` != 0 ]]; then
+    /bin/cp -f /medco-configuration/srv*-certificate.crt /usr/local/share/ca-certificates/
+    update-ca-certificates
+fi
+
+exec medco-connector-server

go.mod

@@ -1,13 +1,27 @@
 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/jessevdk/go-flags v1.4.0
-	golang.org/x/net v0.0.0-20190301231341-16b79f2e4e95
+	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
 )

i2b2/common_models.go

@@ -0,0 +1,164 @@
+package i2b2
+
+import (
+	"encoding/xml"
+	"errors"
+	"github.com/lca1/medco-connector/util"
+	"strconv"
+	"time"
+)
+
+// NewRequest creates a new ready-to-use i2b2 request, with a nil message body
+func NewRequest() Request {
+	now := time.Now()
+	return Request{
+		XMLNSMSG:    "http://www.i2b2.org/xsd/hive/msg/1.1/",
+		XMLNSONT:    "http://www.i2b2.org/xsd/cell/ont/1.1/",
+		XMLNSPDO:    "http://www.i2b2.org/xsd/hive/pdo/1.1/",
+		XMLNSCRCPDO: "http://www.i2b2.org/xsd/cell/crc/pdo/1.1/",
+		XMLNSCRCPSM: "http://www.i2b2.org/xsd/cell/crc/psm/1.1/",
+
+		MessageHeader: MessageHeader{
+			I2b2VersionCompatible: "0.3",
+			Hl7VersionCompatible: "2.4",
+			SendingApplicationApplicationName: "MedCo Connector",
+			SendingApplicationApplicationVersion: "0.2",
+			SendingFacilityFacilityName: "MedCo",
+			ReceivingApplicationApplicationName: "i2b2 cell",
+			ReceivingApplicationApplicationVersion: "1.7",
+			ReceivingFacilityFacilityName: "i2b2 hive",
+			DatetimeOfMessage: now.Format(time.RFC3339),
+			SecurityDomain: util.I2b2LoginDomain,
+			SecurityUsername: util.I2b2LoginUser,
+			SecurityPassword: util.I2b2LoginPassword,
+			MessageTypeMessageCode: "EQQ",
+			MessageTypeEventType: "Q04",
+			MessageTypeMessageStructure: "EQQ_Q04",
+			MessageControlIDSessionID: now.Format(time.RFC3339),
+			MessageControlIDMessageNum: strconv.FormatInt(now.Unix(), 10),
+			MessageControlIDInstanceNum: "0",
+			ProcessingIDProcessingID: "P",
+			ProcessingIDProcessingMode: "I",
+			AcceptAcknowledgementType: "messageId",
+			ApplicationAcknowledgementType: "",
+			CountryCode: "CH",
+			ProjectID: util.I2b2LoginProject,
+		},
+		RequestHeader: RequestHeader{
+			ResultWaittimeMs: strconv.Itoa(util.I2b2TimeoutSeconds* 1000),
+		},
+	}
+}
+
+// NewRequestWithBody creates a new ready-to-use i2b2 request, with a message body
+func NewRequestWithBody(body MessageBody) (req Request) {
+	req = NewRequest()
+	req.MessageBody = body
+	return
+}
+
+// Request is an i2b2 XML request
+type Request struct {
+	XMLName        xml.Name `xml:"msgns:request"`
+	XMLNSMSG       string `xml:"xmlns:msgns,attr"`
+	XMLNSPDO       string `xml:"xmlns:pdons,attr"`
+	XMLNSONT       string `xml:"xmlns:ontns,attr"`
+	XMLNSCRCPDO    string `xml:"xmlns:crcpdons,attr"`
+	XMLNSCRCPSM    string `xml:"xmlns:crcpsmns,attr"`
+
+	MessageHeader  MessageHeader `xml:"message_header"`
+	RequestHeader  RequestHeader `xml:"request_header"`
+	MessageBody    MessageBody   `xml:"message_body"`
+}
+
+// Response is an i2b2 XML response
+type Response struct {
+	XMLName        xml.Name `xml:"response"`
+	MessageHeader  MessageHeader `xml:"message_header"`
+	RequestHeader  RequestHeader `xml:"request_header"`
+	ResponseHeader ResponseHeader `xml:"response_header"`
+	MessageBody    MessageBody   `xml:"message_body"`
+}
+
+func (response *Response) checkStatus() error {
+	if response.ResponseHeader.ResultStatus.Status.Type != "DONE" {
+		return errors.New(response.ResponseHeader.ResultStatus.Status.Text)
+	}
+	return nil
+}
+
+// MessageHeader is an i2b2 XML header embedded in a request or response
+type MessageHeader struct {
+	XMLName               xml.Name `xml:"message_header"`
+
+	I2b2VersionCompatible string   `xml:"i2b2_version_compatible"`
+	Hl7VersionCompatible  string   `xml:"hl7_version_compatible"`
+
+	SendingApplicationApplicationName string `xml:"sending_application>application_name"`
+	SendingApplicationApplicationVersion string `xml:"sending_application>application_version"`
+
+	SendingFacilityFacilityName string `xml:"sending_facility>facility_name"`
+
+	ReceivingApplicationApplicationName string `xml:"receiving_application>application_name"`
+	ReceivingApplicationApplicationVersion string `xml:"receiving_application>application_version"`
+
+	ReceivingFacilityFacilityName string `xml:"receiving_facility>facility_name"`
+
+	DatetimeOfMessage string `xml:"datetime_of_message"`
+
+	SecurityDomain string `xml:"security>domain"`
+	SecurityUsername string `xml:"security>username"`
+	SecurityPassword string `xml:"security>password"`
+
+	MessageTypeMessageCode string `xml:"message_type>message_code"`
+	MessageTypeEventType string `xml:"message_type>event_type"`
+	MessageTypeMessageStructure string `xml:"message_type>message_structure"`
+
+	MessageControlIDSessionID   string `xml:"message_control_id>session_id"`
+	MessageControlIDMessageNum  string `xml:"message_control_id>message_num"`
+	MessageControlIDInstanceNum string `xml:"message_control_id>instance_num"`
+
+	ProcessingIDProcessingID   string `xml:"processing_id>processing_id"`
+	ProcessingIDProcessingMode string `xml:"processing_id>processing_mode"`
+
+	AcceptAcknowledgementType      string `xml:"accept_acknowledgement_type"`
+	ApplicationAcknowledgementType string `xml:"application_acknowledgement_type"`
+	CountryCode                    string `xml:"country_code"`
+	ProjectID                      string `xml:"project_id"`
+}
+
+// RequestHeader is an i2b2 XML header embedded in a request
+type RequestHeader struct {
+	XMLName          xml.Name `xml:"request_header"`
+	ResultWaittimeMs string   `xml:"result_waittime_ms"`
+}
+
+// ResponseHeader is an i2b2 XML header embedded in a response
+type ResponseHeader struct {
+	XMLName xml.Name `xml:"response_header"`
+	Info    struct {
+		Text string `xml:",chardata"`
+		URL  string `xml:"url,attr"`
+	} `xml:"info"`
+	ResultStatus struct {
+		Status struct {
+			Text string `xml:",chardata"`
+			Type string `xml:"type,attr"`
+		} `xml:"status"`
+		PollingURL struct {
+			Text       string `xml:",chardata"`
+			IntervalMs string `xml:"interval_ms,attr"`
+		} `xml:"polling_url"`
+		Conditions struct {
+			Condition []struct {
+				Text         string `xml:",chardata"`
+				Type         string `xml:"type,attr"`
+				CodingSystem string `xml:"coding_system,attr"`
+			} `xml:"condition"`
+		} `xml:"conditions"`
+	} `xml:"result_status"`
+}
+
+// MessageBody is an i2b2 XML generic body
+type MessageBody interface{}
+

i2b2/common_query.go

@@ -0,0 +1,50 @@
+package i2b2
+
+import (
+	"bytes"
+	"encoding/xml"
+	"github.com/sirupsen/logrus"
+	"io/ioutil"
+	"net/http"
+)
+
+// todo doc
+func i2b2XMLRequest(url string, xmlRequest interface{}, xmlResponse *Response) error {
+	logrus.Info("i2b2 XML request to " + url)
+
+	// marshal request
+	marshaledRequest, err := xml.MarshalIndent(xmlRequest, "  ", "    ")
+	if err != nil {
+		logrus.Error("error in i2b2 request marshalling:", err)
+		return err
+	}
+	marshaledRequest = append([]byte(xml.Header), marshaledRequest...)
+	logrus.Debug("i2b2 request:\n", string(marshaledRequest))
+
+	// execute HTTP request
+	httpResponse, err := http.Post(url, "application/xml", bytes.NewBuffer(marshaledRequest))
+	if err != nil {
+		logrus.Error("error in i2b2 request HTTP POST:", err)
+		return err
+	}
+	defer httpResponse.Body.Close()
+
+	// unmarshal response
+	httpBody, err := ioutil.ReadAll(httpResponse.Body)
+	logrus.Debug("i2b2 response:\n", string(httpBody))
+
+	err = xml.Unmarshal(httpBody, xmlResponse)
+	if err != nil {
+		logrus.Error("error in i2b2 response unmarshalling:", err)
+		return err
+	}
+
+	// check i2b2 request status
+	err = xmlResponse.checkStatus()
+	if err != nil {
+		logrus.Error("i2b2 error:", err)
+		return err
+	}
+
+	return nil
+}