merge commit

.ebextensions/.config

@@ -1,5 +1,5 @@
 option_settings:
   - option_name: WB_DB_URI
-    value: datomic:ddb://us-east-1/WS269/wormbase
+    value: datomic:ddb://us-east-1/WS270/wormbase
   - option_name: _JAVA_OPTIONS
     value: "-Xmx14g"

.ebextensions/aws-autoscaling.config

@@ -15,7 +15,7 @@ option_settings:
     UpperThreshold: 70
   aws:autoscaling:launchconfiguration:
     BlockDeviceMappings: /dev/xvdcz=:12:true:gp2
-    EC2KeyName: eb-d2c
+    EC2KeyName: eb_wormbase_rest
     IamInstanceProfile: aws-elasticbeanstalk-ec2-role
     InstanceType: m4.xlarge
     MonitoringInterval: 5 minute

.ebextensions/elasticbeanstalk-environment.config

@@ -45,5 +45,5 @@ option_settings:
   aws:elasticbeanstalk:sns:topics:
     Notification Endpoint: [email protected]
     Notification Protocol: email
-    Notification Topic ARN: arn:aws:sns:us-east-1:357210185381:ElasticBeanstalkNotifications-Environment-datomic-to-catalyst
+    Notification Topic ARN: arn:aws:sns:us-east-1:357210185381:ElasticBeanstalkNotifications-Environment-rest
     Notification Topic Name: null

Dockerrun.aws.json

@@ -1,7 +1,7 @@
 {
   "AWSEBDockerrunVersion": 1,
   "Image": {
-    "Name": "357210185381.dkr.ecr.us-east-1.amazonaws.com/wormbase/datomic-to-catalyst:0.8.4",
+    "Name": "357210185381.dkr.ecr.us-east-1.amazonaws.com/wormbase/rest:0.8.3",
     "Update": "true"
   },
   "Ports": [

Makefile

@@ -1,6 +1,5 @@
-NAME := wormbase/datomic-to-catalyst
-VERSION ?= $(shell git describe --abbrev=0 --tags)
-#VERSION = "latest"
+NAME := wormbase/rest
+VERSION ?= "0.8.3"
 EBX_CONFIG := .ebextensions/.config
 WB_DB_URI ?= $(shell sed -rn 's|value:(.*)|\1|p' \
                   ${EBX_CONFIG} | tr -d " " | head -n 1)
@@ -10,6 +9,7 @@ DEPLOY_JAR := app.jar
 PORT := 3000
 WB_ACC_NUM := 357210185381
 FQ_TAG := ${WB_ACC_NUM}.dkr.ecr.us-east-1.amazonaws.com/${NAME}:${VERSION}
+FQ_TAG_LATEST := ${WB_ACC_NUM}.dkr.ecr.us-east-1.amazonaws.com/${NAME}:latest
 WB_FTP_URL := ftp://ftp.wormbase.org/pub/wormbase/releases/${WS_VERSION}
 
 define print-help
@@ -43,30 +43,52 @@ docker-tag: $(call print-help,docker-tag,\
 	@docker tag ${NAME}:${VERSION} \
 		    ${WB_ACC_NUM}.dkr.ecr.us-east-1.amazonaws.com/${NAME}
 
+
+.PHONY: docker-tag-latest
+docker-tag-latest: $(call print-help,docker-tag,\
+	     "Tag the image with current git revision \
+	      and ':latest' alias")
+	@docker tag ${NAME}:latest ${FQ_TAG_LATEST}
+
 .PHONY: docker-push-ecr
 docker-push-ecr: docker-ecr-login $(call print-help,docker-push-ecr,\
 	                           "Push the image tagged with the \
                                     current git revision to ECR")
 	@docker push ${FQ_TAG}
 
+.PHONY: docker-push-ecr-latest
+docker-push-ecr-latest: docker-ecr-login $(call print-help,docker-push-ecr,\
+	                           "Push the image tagged with the \
+                                    current git revision to ECR")
+	@docker push ${FQ_TAG_LATEST}
+
 .PHONY: eb-create
 eb-create: $(call print-help,eb-create,\
 	    "Create an ElasticBeanStalk environment using \
 	     the Docker platofrm.")
-	@eb create datomic-to-catalyst-${WS_VERSION} \
+	@eb create rest-${WS_VERSION} \
+		--region=us-east-1 \
+		--tags="CreatedBy=${AWS_EB_PROFILE},Role=RestAPI" \
+		--cname="wormbase-rest-${LOWER_WS_VERSION}"
+
+.PHONY: eb-create-staging
+eb-create-staging: $(call print-help,eb-create,\
+	    "Create an ElasticBeanStalk environment using \
+	     the Docker platofrm.")
+	@eb create rest-staging \
 		--region=us-east-1 \
 		--tags="CreatedBy=${AWS_EB_PROFILE},Role=RestAPI" \
-		--cname="datomic-to-catalyst-${LOWER_WS_VERSION}"
+		--cname="wormbase-rest-staging"
 
-.PHONY: eb-env
-eb-setenv: $(call print-help,eb-env,\
+.PHONY: eb-setenv
+eb-setenv: $(call print-help,eb-setenv,\
 	     "Set enviroment variables for the \
 	      ElasticBeanStalk environment")
 	eb setenv WB_DB_URI="${WB_DB_URI}" \
 		  _JAVA_OPTIONS="-Xmx14g" \
 		  AWS_SECRET_ACCESS_KEY="${AWS_SECRET_ACCESS_KEY}" \
 		  AWS_ACCESS_KEY_ID="${AWS_ACCESS_KEY_ID}" \
-		  -e "datomic-to-catalyst"
+		  -e "rest"
 
 .PHONY: eb-local
 eb-local: docker-ecr-login $(call print-help,eb-local,\
@@ -86,11 +108,24 @@ build: docker/${DEPLOY_JAR} \
 			aws_access_key_id=${AWS_ACCESS_KEY_ID} \
 		--rm ./docker/
 
+.PHONY: build-staging
+build-staging: docker/${DEPLOY_JAR} \
+       $(call print-help,build,\
+	"Build the docker images from using the current git revision.")
+	@docker build -t ${NAME}:latest \
+		--build-arg uberjar_path=${DEPLOY_JAR} \
+		--build-arg \
+			aws_secret_access_key=${AWS_SECRET_ACCESS_KEY} \
+		--build-arg \
+			aws_access_key_id=${AWS_ACCESS_KEY_ID} \
+		--rm ./docker/
+
 .PHONY: run
 run: $(call print-help,run,"Run the application in docker (locally).")
 	docker run \
-		--name datomic-to-catalyst \
+		--name wormbase-rest \
 		--publish-all=true \
+		--restart=always \
 		--publish ${PORT}:${PORT} \
 		--detach \
 		-e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \
@@ -99,14 +134,37 @@ run: $(call print-help,run,"Run the application in docker (locally).")
 		-e PORT=${PORT} \
 		${NAME}:${VERSION}
 
+.PHONY: run-latest
+run-latest: $(call print-help,run,"Run the application in docker (locally).")
+	docker run \
+		--name wormbase-rest \
+		--publish-all=true \
+		--restart=always \
+		--publish ${PORT}:${PORT} \
+		--detach \
+		-e AWS_SECRET_ACCESS_KEY=${AWS_SECRET_ACCESS_KEY} \
+		-e AWS_ACCESS_KEY_ID=${AWS_ACCESS_KEY_ID} \
+		-e WB_DB_URI=${WB_DB_URI} \
+		-e PORT=${PORT} \
+		${NAME}:latest
+
 .PHONY: docker-build
 docker-build: clean build \
-              $(call print-help,docker-build, "Create docker container")
+	$(call print-help,docker-build, "Create docker container")
 
 docker-clean: $(call print-help,docker-clean,\
                "Stop and remove the docker container (if running).")
-	@docker stop datomic-to-catalyst
-	@docker rm datomic-to-catalyst
+	@docker stop wormbase-rest
+	@docker rm wormbase-rest
+
+.PHONY: dockerrun-latest
+dockerrun-latest: $(call print-help,dockerrun-latest, "Change docker run file to point to latest")
+	@sed -i -r 's/rest:[^"]+/rest:'"latest"'/g' Dockerrun.aws.json
+
+.PHONY: staging-deploy
+staging-deploy:
+	eb use rest-staging
+	eb deploy --region us-east-1 --timeout 10
 
 .PHONY: clean
 clean: $(call print-help,clean,"Remove the locally built JAR file.")

README.md

@@ -1,4 +1,4 @@
-# datomic-to-catalyst
+# wormbase-rest
 
 - Provide interface to datomic database to WormBase website.
 
@@ -14,7 +14,7 @@
 Run following commands and test each step happens correctly.
 
 ```bash
-export WB_DB_URI="datomic:ddb://us-east-1/WS269/wormbase"
+export WB_DB_URI="datomic:ddb://us-east-1/WS270/wormbase"
 lein ring server-headless 8130
 lein do eastwood, test
 make docker-build
@@ -33,7 +33,7 @@ eb deploy
 ## Setting environment variables
 
 ```bash
-export WB_DB_URI="datomic:ddb://us-east-1/WS269/wormbase"
+export WB_DB_URI="datomic:ddb://us-east-1/WS270/wormbase"
 ```
 
 ## Starting server in development

jenkins-ci-deploy.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+set -e
+
+# Output of unit tests; path cannot contain spaces:
+export REST_TEST_LOG=/tmp/jenkins_rest_test_log_`date '+%s'`.log
+
+export PATH="${HOME}/.local/bin:$PATH";
+
+echo $PATH
+env
+
+# make the jar
+make clean && make docker/app.jar
+
+# build container
+make build-staging
+
+# Unit tests: WormBase API and REST API
+#make build-run-test | tee $TEST_LOG
+
+# tag container
+make docker-tag-latest
+
+# push containers to AWS ECR
+make docker-push-ecr-latest
+
+# deploy container
+make dockerrun-latest
+cat Dockerrun.aws.json
+git add Dockerrun.aws.json
+git commit -m "use latest wormbase/rest container"  # only needed locally and subsequent build will discard this commit
+make staging-deploy

project.clj

@@ -1,7 +1,7 @@
 (defproject wormbase/rest-api "0.8.4"
   :description
   "REST API for retrieving data from datomic on a per widget basis"
-  :url "https://github.com/WormBase/datomic-to-catalyst"
+  :url "https://github.com/WormBase/wormbase-rest"
   :min-lein-version "2.7.0"
   :sign-releases false
   :dependencies
@@ -62,7 +62,7 @@
           :source-paths ["dev"]
           :jvm-opts ["-Xmx1G"]
           :env
-          {:wb-db-uri "datomic:ddb://us-east-1/WS269/wormbase"
+          {:wb-db-uri "datomic:ddb://us-east-1/WS270/wormbase"
            :swagger-validator-url "http://localhost:8002"}
           :plugins
           [[jonase/eastwood "0.2.3"

src/rest_api/classes/expr_pattern/widgets/overview.clj

@@ -3,6 +3,7 @@
    [clojure.string :as str]
    [pseudoace.utils :as pace-utils]
    [rest-api.classes.generic-fields :as generic]
+   [rest-api.classes.picture.core :as picture-fns]
    [rest-api.formatters.object :as obj :refer [pack-obj]]))
 
 (defn- index-of
@@ -43,29 +44,7 @@
 			 {:format extension
 			  :name (str/join "/" [id basename])
 			  :class "/img-static/pictures"}))
-               :external_source (not-empty
-                                  (pace-utils/vmap
-                                    :template
-                                    (:picture/acknowledgement-template picture)
-
-                                    :template-items
-                                    (not-empty
-                                      (pace-utils/vmap
-                                        :Article_URL
-                                        (when-let [ah (:picture/article-url picture)]
-                                          (let [d (:picture.article-url/database ah)]
-                                            {:db (:database/id d)
-                                             :text (:database/name d)}))
-
-                                        :Journal_URL
-                                        (when-let [d (:picture/journal-url picture)]
-                                          {:db (:database/id d)
-                                           :text (:database/name d)})
-
-                                        :Publisher_URL
-                                        (when-let [d (:picture/publisher-url picture)]
-                                          {:db (:database/id d)
-                                           :text (:database/name d)})))))
+               :external_source (picture-fns/external-sources picture)
               :group_id id
               :id (:picture/id picture)})))
    :description "Curated images of the expression pattern"})

src/rest_api/classes/feature.clj

@@ -14,6 +14,6 @@
    {:overview overview/widget
     :history history/widget
     :associations associations/widget
-    ;:molecular_details molecular-details/widget
+    :molecular_details molecular-details/widget
     :evidence evidence/widget
     :location location/widget}})

src/rest_api/classes/feature/widgets/molecular_details.clj

@@ -6,22 +6,24 @@
     [rest-api.classes.generic-functions :as generic-functions]
     [rest-api.classes.generic-fields :as generic]))
 
+; This was being displayed instead of the sequence if the sequence was not in the database
+;{:flanks flanks  ; section tested with WBsf000519
+; :seq seq-obj
+; :method method
+; :sequences [{:sequence five-prime-flank
+;              :comment "flanking sequence (upstream)"}
+;             {:sequence three-prime-flank
+;              :comment "flanking sequence (downstream)"}]}
+
 (defn sequence-context [f]
   {:data (when-let [s (:locatable/parent f)]
            (let [five-prime-flank (:feature.flanking-sequences/five-prime (:feature/flanking-sequences f))
                  three-prime-flank (:feature.flanking-sequences/three-prime (:feature/flanking-sequences f))
                  flanks [five-prime-flank three-prime-flank]
                  seq-obj (pack-obj s)
                  method (-> f :locatable/method :method/id)]
-             (if (or (some #(= method %) ["SL1" "SL2" "polyA_site" "history feature"])
-                     (not (contains? f :locatable/min)))
-               {:flanks flanks  ; section tested with WBsf000519
-                :seq seq-obj
-                :method method
-                :sequences [{:sequence five-prime-flank
-                             :comment "flanking sequence (upstream)"}
-                            {:sequence three-prime-flank
-                             :comment "flanking sequence (downstream)"}]}
+             (when (not (or (some #(= method %) ["SL1" "SL2" "polyA_site" "history feature"])
+                     (not (contains? f :locatable/min))))
                (let [refseqobj (sequence-fns/genomic-obj f) ;tested with WBsf019129
                      positive-strand-wide (sequence-fns/get-sequence
                                  (conj
@@ -30,7 +32,7 @@
                                     :stop (+ (max (count five-prime-flank) (count three-prime-flank)) (:stop refseqobj))}))
                      strand (if (and (str/includes? positive-strand-wide five-prime-flank)
                                      (str/includes? positive-strand-wide three-prime-flank))
-                              "positive" "negative")
+                              "+" "-")
                      padding 30
                      positive-sequence-raw (sequence-fns/get-sequence
                                          (conj
@@ -52,13 +54,13 @@
                   :sequences {:positive_strand
                               {:features
                                [{:type "feature"
-                                 :start padding
-                                 :stop (+ padding (count feature-seq))}]
+                                 :start (+ 1 padding)
+                                 :stop  (+ padding (count feature-seq))}]
                                :sequence positive-sequence}
                               :negative_strand
                               {:features
                                [{:type "feature"
-                                 :start padding
+                                 :start (+ 1 padding)
                                  :stop (+ padding feature-length)}]
                                 :sequence negative-sequence}}}))))
    :description "sequences flanking the feature"})