Merge pull request #435 from plantinformatics/develop

Update Germinate connection
plantinformatics · Nov 27, 2024 · 8d5d099 · 8d5d099
2 parents 8b56df9 + a462b9f
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diff --git a/doc/adminGuides/docker-compose.prod.yaml b/doc/adminGuides/docker-compose.prod.yaml
@@ -0,0 +1,86 @@
+# NOTE refer to the accompanying '.env' file in this folder to access
+# environment variables which are passed through to docker-compose.yaml
+# at run time
+
+# NOTE this has been updated to the docker compose V2 format, this will not work with docker-compose
+
+name: pretzel-prod
+
+networks:
+  pretzel-prod:
+    driver: bridge
+
+services:
+  database: # mongo database
+    # MongoDb up to v5 has been tested OK
+    image: 9b5c4a4fdcb5 # 4.2.24.  library/mongo-4.2.24 # base image off dockerhub
+#    environment:
+#      - "MONGO_INITDB_ROOT_USERNAME=${DB_USER}"
+#      - "MONGO_INITDB_ROOT_PASSWORD=${DB_PASS}"
+    volumes:
+      - ${DATA_DIR}:/data/db
+    expose:
+      - "${MONGO_DEFAULT_PORT}"
+    networks:
+      - pretzel-prod
+
+  api: # node environment
+    depends_on:
+      - database
+      # Could have depends_on: blastserver, but it is not a critical dependency
+    build:
+      context: .
+      dockerfile: ./scripts/Dockerfile
+    image: plantinformaticscollaboration/pretzel:v3.1.0
+    command: node /app/lb3app/server/server.js
+    environment:
+      - "API_HOST=${API_HOST}"
+      - "API_PORT_EXT=${API_PORT_EXT}"
+      - "API_PORT_PROXY=${API_PORT_PROXY}"
+      - "hostIp=${hostIp}"
+      # Flask port is now internal to the compose network, so use fixed (default) 4000; 
+      # no need to configure via FLASK_PORT / BLASTSERVER_PORT.
+      - "FLASK_PORT=4000"       # ${BLASTSERVER_PORT}"
+      - "DB_HOST=database"
+      - "DB_PORT=${MONGO_DEFAULT_PORT}"
+      - "DB_NAME=${DB_NAME}"
+      - "DB_USER=${DB_USER}"
+      - "DB_PASS=${DB_PASS}"
+      - "EMAIL_HOST=${EMAIL_HOST}"
+      - "EMAIL_PORT=${EMAIL_PORT}"
+      - "EMAIL_USER=${EMAIL_USER}"
+      - "EMAIL_PASS=${EMAIL_PASS}"
+      - "EMAIL_FROM=${EMAIL_FROM}"
+      - "EMAIL_VERIFY=${EMAIL_VERIFY}"
+      - "EMAIL_ADMIN=${EMAIL_ADMIN}"
+      - "mntData=${mntData}"
+      - "handsOnTableLicenseKey=${handsOnTableLicenseKey}"
+    volumes:
+      # landingPage
+      - $landingPage:/app/client/landingPageContent
+      # blastVolume
+      - $mntData/blast:$mntData/blast
+      # vcfVolume
+      - $mntData/vcf:$mntData/vcf
+      - ${resultsCacheDir}:/app/node_modules/flat-cache/.cache
+
+    ports:
+      # match ext / int ports for loopback
+      - "${API_PORT_EXT}:${API_PORT_EXT}"
+    networks:
+      - pretzel-prod
+
+  blastserver: # Python Flask blastn server, based on a python image, used for DNA Sequence Search
+    image: plantinformaticscollaboration/blastserver:latest
+    environment:
+      - "FLASK_PORT=${BLASTSERVER_PORT}"
+    volumes:
+      # mntData=/mnt/data_blast
+      - $mntData/blast:/mnt/data/blast
+      # Enables scripts/blastn_cont.bash to run blastn via docker
+      - /usr/bin/docker:/usr/bin/docker
+      - /var/run/docker.sock:/var/run/docker.sock
+    expose:
+      - "4000"
+    networks:
+      - pretzel-prod
diff --git a/doc/adminGuides/install_and_configure.md b/doc/adminGuides/install_and_configure.md
@@ -0,0 +1,142 @@
+### Audience
+
+This guide is for system administrators tasked with installation and configuration of Pretzel, and administration of software systems and data.
+
+This documentation will guide them through configuration of docker compose yaml files and related environment files, and provide templates of these as a starting point.
+
+There are separate documentation resources for other audiences :
+- User Documentation : https://docs.plantinformatics.io	
+- Development team : pretzel/doc/notes/
+
+---
+
+### Background
+
+The method of installation of Pretzel has evolved along with the application.
+Our early recommendations were to use individual docker containers for the mongoDb database and Pretzel API server, but with the addition of the blastserver (Python Flask micro-service), and access to additional external databases (Blast and VCF), we have moved to docker compose to package the configuration and connection of these components.
+
+### Docker Compose elements
+
+In the same directory as this document there is a sample docker compose yaml file, and sample environment files.
+
+The following section discusses configurations the system administrator may make to these files.
+
+### Configuration of docker compose .yaml
+
+The most important configuration is the version of the Pretzel API server :
+```
+  api: # node environment
+    ...
+    image: plantinformaticscollaboration/pretzel:v3.1.0
+```
+
+These configurations support optional features :
+
+```
+  api: # node environment
+    ...
+    volumes:
+      # landingPage
+      - $landingPage:/app/client/landingPageContent
+      # blastVolume
+      - $mntData/blast:$mntData/blast
+      # vcfVolume
+      - $mntData/vcf:$mntData/vcf
+      - ${resultsCacheDir}:/app/node_modules/flat-cache/.cache
+```
+####	landingPage 
+A directory which contains index.html and other html and image files referenced by index.html.  If provided, this content is displayed in the Pretzel home page before the user logs in.
+
+#### blastVolume
+A directory containing blastn databases.
+If mntData is provided, then the default value of blastDir is $mntData/blast.
+
+#### vcfVolume
+A directory containing VCF genotype data.
+If mntData is provided, then the default value of vcfDir is $mntData/vcf.
+
+#### resultsCacheDir
+The Pretzel API server will cache results for common requests, enabling them to be served more quickly and efficiently.  This directory will be created within the Pretzel API server container, or if it is configured as a shared volume, then the resultsCache will be stored in the directory passed in.  The benefit of this is that when the container is re-created, the resultsCache will be preserved.  This is not essential, but will improve performance in particular for histograms where the chromosomes (Blocks) contain 1e5 - 1e7 features.
+
+---
+
+### Configuration of pretzel.compose.prod.env
+
+The template .env file has these variables commented out;  you will need to provide values for them :
+- DATA_DIR
+- mntData
+- API_HOST
+- EMAIL_*
+
+
+---
+
+Configuration for compose down & up :
+```
+logDate=$(date +%Y%b%d)
+echo $logDate
+# Location of docker compose templates
+export Dc=~/pretzel/doc/adminGuides
+# Use other values if you are running multiple Pretzel servers,  e.g. stage=dev
+# You can simplify the naming by omitting $stage if only running a single server.
+stage=prod
+L=~/log/compose/$stage/$logDate
+```
+
+Docker compose down and up :
+```
+docker compose --progress=plain   --file $Dc/docker-compose.$stage.yaml  --env-file $Dc/pretzel.compose.$stage.env down
+nohup docker compose --progress=plain   --file $Dc/docker-compose.$stage.yaml  --env-file $Dc/pretzel.compose.$stage.env  up > $L &
+```
+
+The above log file `$L` will contain the output from the 3 containers, api database and blastserver.  To record the logs into separate log files the following can be used.  This would be done before replacing them;  i.e. before compose down.
+```
+for i in api database blastserver; do \
+docker logs pretzel-$stage-$i-1 >& ~/log/compose/$stage/$i.$logDate; done
+```
+
+---
+
+### Preparing a custom Pretzel API server container image
+
+This section describes how to build a Pretzel API server image from a particular version or branch, e.g. if a hot-fix branch has been provided.
+
+Image build
+```
+# cd '<build_directory>'
+git clone https://github.com/plantinformatics/pretzel.git
+cd pretzel
+
+export GIT_PAGER=cat
+# replace 'master' here with the name of the branch or version to build
+git checkout master
+
+logDate=$(date +%Y%b%d)
+echo $logDate
+export DOCKER_BUILDKIT=1
+
+app=pretzel
+# you can use some other label name; this example uses the build date.
+export PRETZEL_VERSION=v$logDate
+# e.g. export PRETZEL_VERSION=v3.1.0
+image=$app:$PRETZEL_VERSION
+
+mkdir -p ~/log/build/docker
+time nohup sudo docker build -t $image . > ~/log/build/docker/$logDate    &
+```
+
+Observe the image tag name; this will be used in docker compose .yaml : api : image.
+```
+docker image inspect $image | jq '.[] | .RepoTags'
+```
+
+Tag the built image for push to dockerhub
+```
+# If pushing the result to dockerhub :
+# baseName='<dockerhub_organisation_name>'/$app
+docker tag $image $baseName:$PRETZEL_VERSION
+docker tag $image $baseName:latest
+docker image inspect $image | jq '.[] | .RepoTags'
+```
+
+---
diff --git a/doc/adminGuides/pretzel.compose.prod.env b/doc/adminGuides/pretzel.compose.prod.env
@@ -0,0 +1,32 @@
+# Prod
+
+# DATA_DIR= # directory for mongoDb database
+# mntData= # directory for Blast and VCF databases
+# landingPage= # directory containing index.html and web page content to display on the home page before the user logs in.
+# This dir maps to /app/node_modules/flat-cache/.cache and contains 1 file : resultsCache
+resultsCacheDir=/home/ec2-user/home/resultsCache/prod
+#PORT=3010
+
+# Not used ?
+# INSTANCE=agg
+DB_NAME=pretzel
+# API_HOST=agg.plantinformatics.io
+API_PORT_PROXY=80
+API_PORT_EXT=3010
+hostIp=blastserver
+# Flask port is now internal to the compose network, so use fixed (default) 4000; 
+# no need to configure via FLASK_PORT / BLASTSERVER_PORT.
+BLASTSERVER_PORT=4000
+# The value of API_PORT_PROXY is not (currently) a port, it is just defined or undefined.
+MONGO_DEFAULT_PORT=27017
+EMAIL_VERIFY=ADMIN
+# [email protected]
+# EMAIL_HOST=email-smtp.<region>.amazonaws.com
+EMAIL_PORT=25
+# EMAIL_PASS=...
+# EMAIL_USER=...
+# [email protected]
+# This enables using Feature.value_0 as an index field; all datbases now contain this field and this option can be made to default to true (1).
+use_value_0=1
+# If a handsOnTableLicenseKey is not provided, a prompt message will be displayed in the GUI. Insert your license here; Hands On Table allows non-commercial and evaluation use.
+# handsOnTableLicenseKey=non-commercial-and-evaluation
diff --git a/frontend/app/components/draw/axis-1d.js b/frontend/app/components/draw/axis-1d.js
@@ -1441,7 +1441,7 @@ export default Component.extend(Evented, AxisEvents, AxisPosition, {
     as.classed("extended", this.get('extended'));
   },
   buttonStateEffect : computed('brushed', 'zoomed', function () {
-    later(() => this.isDestroying && this.showZoomResetButtonState(), 200);
+    later(() => ! this.isDestroying && this.showZoomResetButtonState(), 200);
   }),
   showZoomResetButtonState() {
     let

diff --git a/frontend/app/components/form/dataset-graph.hbs b/frontend/app/components/form/dataset-graph.hbs
@@ -22,7 +22,7 @@
 
     <BsButton @type="info" class="margin-top" @onClick={{@close}}>Close</BsButton>
 
-    {{input type="search" value=naturalQuery
+    {{input type="search" value=this.naturalQuery
       enter=(action this.naturalQueryChanged)
       placeholder="Natural language search" }}
 

diff --git a/frontend/app/components/panel/manage-genotype.hbs b/frontend/app/components/panel/manage-genotype.hbs
@@ -838,12 +838,8 @@
     {{!-- ----------------------------------------------------------------- --}}
 
     {{#if this.vcfGenotypeLookupDomain}}
-      {{!-- disabled if ! All && no samples selected, or All && Common && no samples to select --}}
       <button type="button" onclick={{action this.vcfGenotypeLookup}}
-        disabled={{or
-          (and (not @userSettings.requestSamplesAll) (not this.vcfGenotypeSamplesSelected.length))
-          (and @userSettings.requestSamplesAll @userSettings.samplesIntersection (not this.samples.length))
-        }}
+        disabled={{this.vcfGenotypeLookupButtonDisabled}}
         class="btn btn-info">VCF Lookup</button>
     {{else}}
       {{#if this.urlOptions.gtIntervalLimit}}