Merge pull request #414 from plantinformatics/develop

Release 3.0.0
plantinformatics · Oct 22, 2024 · 265f76d · 265f76d
2 parents ddb7490 + 65ed247
commit 265f76d
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diff --git a/.dockerignore b/.dockerignore
@@ -0,0 +1,3 @@
+.git
+doc
+tmp
diff --git a/.gitignore b/.gitignore
@@ -5,6 +5,7 @@
 # was /backend/
 /lb4app/lb3app/client
 /lb4app/lb3app/tmp
+/lb4app/tmp
 /tmp
 /log
 *.log
@@ -27,3 +28,4 @@ bower_components
 # etags file
 TAGS
 .vscodeignore
+.aider*
diff --git a/Dockerfile b/Dockerfile
@@ -4,12 +4,12 @@
 
 # samtools build layer is based on https://hub.docker.com/r/bschiffthaler/samtools/dockerfile
 
-ARG NODE_ALPINE_VERSION 12
+ARG NODE_ALPINE_VERSION=18
 
 # ${NODE_ALPINE_VERSION}
-FROM node:12-alpine as node-alpine-build-samtools
+FROM node:18-alpine as node-alpine-build-samtools
 
-ARG NODE_ALPINE_VERSION 12
+ARG NODE_ALPINE_VERSION=18
 ARG SAMTOOLS_VERSION=1.15.1
 ARG BUILD_NCPU=1
 
@@ -74,10 +74,10 @@ WORKDIR /
 #-------------------------------------------------------------------------------
 
 # ${NODE_ALPINE_VERSION}
-FROM node:12-alpine as node-alpine-pretzel
+FROM node:18-alpine as node-alpine-pretzel
 
-ARG PRETZEL_VERSION 2.15.0
-ARG NODE_ALPINE_VERSION 12
+ARG PRETZEL_VERSION 2.17.8
+ARG NODE_ALPINE_VERSION 18
 
 # node-sass version is selected so that the binary can be downloaded;
 # otherwise, node-gyp will be built, and hence the following dependencies on python, make, c++.
@@ -105,8 +105,7 @@ RUN apk add --no-cache git \
      terminus-font	\
      curl	\
      jq	\
-openssh \
-  && npm install bower -g
+openssh
 
 
 # ------------------------------------------------------------------------------
@@ -155,29 +154,35 @@ RUN mkdir $NODE_BE $NODE_BE/bin $NODE_BE/lib
 COPY --from=node:16-alpine /usr/local/bin  $NODE_BE/bin
 COPY --from=node:16-alpine /usr/local/lib  $NODE_BE/lib
 
-
+# may be required later, for upgradeFrontend2 : -g rollup && npm install [email protected]
 RUN date \
   && ls -sF $NODE_BE/lib \
   && export PATH=$NODE_BE/bin:$PATH \
   && export NODE_PATH=$NODE_BE/lib/node_modules \
   && cd $NODE_BE/lib && npm -v && node -v \
   && npm config set scripts-prepend-node-path true \
-  && cd /app && npm install [email protected] && npm ci \
+  && cd /app && npm install -g rollup && npm install [email protected] [email protected] && npm ci \
   && date
 
 
 RUN node --version
-RUN cd /frontend && (npm ci || npm install)  && bower install --allow-root
+RUN cd /frontend && (npm ci || npm install)
 
 # RUN cd /app && npm install [email protected] && npm ci
 
-RUN cd /frontend && node_modules/ember-cli/bin/ember build --environment production
+ARG ROOT_URL
+ENV ROOT_URL=${ROOT_URL}
+LABEL ROOT_URL=${ROOT_URL}
+# if sass binary binding not available may need : npm rebuild node-sass &&
+#
+# ROOT_URL should be configurable via e.g. --build-arg ROOT_URL=/app
+# or can hard-wired here via :  && ROOT_URL=/pretzelUpdate 
+RUN cd /frontend && npm rebuild node-sass && echo ROOT_URL=${ROOT_URL} && node_modules/ember-cli/bin/ember build --environment production
 
 RUN ( [ ! -L /app/client ] || rm /app/client ) && \
   mv /frontend/dist /app/client \
   && cd / \
   && rm -rf /frontend \
-  && npm uninstall -g bower \
   && npm cache clean --force
 
 ENV EMAIL_VERIFY=NONE AUTH=ALL
@@ -187,10 +192,10 @@ ENTRYPOINT ["/usr/local/node16/bin/node", "/app/lb3app/server/server.js"]
 
 # ------------------------------------------------------------------------------
 
-ARG NODE_ALPINE_VERSION 12
+ARG NODE_ALPINE_VERSION=18
 ARG SAMTOOLS_VERSION=1.15.1
 ARG bcftoolsVer=1.15.1
-ARG PRETZEL_VERSION 2.15.0
+ARG PRETZEL_VERSION=2.17.8
 
 
 LABEL maintainer='github.com/plantinformatics'

diff --git a/doc/notes/design_diagram_genotype_web_API.html b/doc/notes/design_diagram_genotype_web_API.html
@@ -0,0 +1,116 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+
+  <!-- using jsdelivr for css because unpkg gets :
+Refused to apply style from 'https://unpkg.com/[email protected]/dist/mermaid.css' because its MIME type ('text/plain') is not a supported stylesheet MIME type, and strict MIME checking is enabled.
+ -->
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/mermaid/dist/mermaid.css">
+</head>
+
+  <body>
+
+    <script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
+
+    <script>
+mermaid.initialize({startOnLoad:true});
+    </script>
+
+<!-- based on copy of ./design_diagram_dnaSequenceSearch.html, via design_diagram_vcfFeature.html
+
+ -->
+
+<h1>
+<a id="user-content-design" class="anchor" href="#design" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>
+Design
+</h1>
+<h2>
+<a id="user-content-explorer-CF-data-flow-diagrams" class="anchor" href="#explorer-CF-data-flow-diagrams" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>
+Design diagram showing the Genotype web API requests
+</h2>
+
+<!-- seems like recent versions of mermaid css make this additional formatting unnecessary, and possibly not used. -->
+<!-- for local editing, change href to mermaid_classDiagram.css -->
+<link type="text/css" rel="Stylesheet" href="https://cdn.jsdelivr.net/gh/plantinformatics/pretzel/doc/notes/mermaid_classDiagram.css" />
+
+<!-- Note below about clearfix. -->
+<div  class="clearfix">
+
+<h2>Custom API</h2>
+
+<div class="mermaid classDiagram" style="width: 100%;" >
+sequenceDiagram
+  participant C as Pretzel Frontend GUI
+  participant S as Pretzel Server
+
+  C->>S: Blocks/vcfGenotypeLookup
+  create participant B as bcftools
+  S->>B: bcftools query or view
+  destroy B
+  B->>S: VCF result
+  S->>C: VCF result
+</div>
+<!--     destroy B -->
+
+<h2>BrAPI</h2>
+<div class="mermaid classDiagram" style="width: 100%;" >
+sequenceDiagram
+
+  participant C as Pretzel Frontend GUI
+  participant S as Pretzel Server
+
+  C->>S: brapi/v2/search/allelematrix
+  create participant B as bcftools
+  S->>B: bcftools query or view 
+  destroy B
+  B->>S: VCF result
+  S->>C: allelematrix result
+
+</div>
+
+<!--
+
+/** not used */
+
+: ! 
+
+ -->
+
+<div  class="clearfix">
+</div>
+
+<p>
+Notes :
+<ul>
+<li></li>
+</ul>
+</p>
+
+
+
+<p>Code links</p>
+<ul>
+  <li><a href="https://github.com/plantinformatics/vcf-genotype-brapi/blob/develop/src/utils/data/vcf-feature.js">vcf-genotype-brapi/blob/develop/src/utils/data/vcf-feature.js</a></li>
+  <li><a href="https://github.com/plantinformatics/pretzel/blob/feature/ongoingGenotype/frontend/app/services/auth.js">frontend/app/services/auth.js</a></li>
+</ul>
+
+<div  class="clearfix">
+</div>
+
+
+<p> Diagram drawn by :
+<a href="https://mermaidjs.github.io/">Mermaid</a>, 
+github <a href="https://github.com/knsv/mermaid">readme</a>
+</p>
+
+<hr>
+<!-- Use either this, or class="clearfix" on the previous div. -->
+<div style="clear:both">
+</div>
+
+
+
+</body>
+</html>
diff --git a/doc/notes/design_diagram_vcfFeature.html b/doc/notes/design_diagram_vcfFeature.html
@@ -0,0 +1,123 @@
+<!DOCTYPE html>
+<html>
+<head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+
+  <!-- using jsdelivr for css because unpkg gets :
+Refused to apply style from 'https://unpkg.com/[email protected]/dist/mermaid.css' because its MIME type ('text/plain') is not a supported stylesheet MIME type, and strict MIME checking is enabled.
+ -->
+  <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/mermaid/dist/mermaid.css">
+</head>
+
+  <body>
+
+    <script src="https://unpkg.com/mermaid/dist/mermaid.min.js"></script>
+
+    <script>
+mermaid.initialize({startOnLoad:true});
+    </script>
+
+<!-- based on copy of ./design_diagram_dnaSequenceSearch.html, with call graph extracted by aider
+ -->
+
+<h1>
+<a id="user-content-design" class="anchor" href="#design" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>
+Design
+</h1>
+<h2>
+<a id="user-content-explorer-CF-data-flow-diagrams" class="anchor" href="#explorer-CF-data-flow-diagrams" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a>
+Design diagram showing the calls between function defined within vcf-feature.js
+</h2>
+
+<!-- seems like recent versions of mermaid css make this additional formatting unnecessary, and possibly not used. -->
+<!-- for local editing, change href to mermaid_classDiagram.css -->
+<link type="text/css" rel="Stylesheet" href="https://cdn.jsdelivr.net/gh/plantinformatics/pretzel/doc/notes/mermaid_classDiagram.css" />
+
+<!-- Note below about clearfix. -->
+<div  class="clearfix">
+
+
+<div class="mermaid classDiagram" style="width: 100%;" >
+graph TD
+
+A(vcf-feature.js functions) --> |calls| B(featureMafFilter)
+A --> |calls| C(featureCallRateFilter)		
+A --> |calls| D(featuresFilterNalleles)
+A --> |calls| E(genotypeSNPFiltersApply)
+A --> |calls| F(featuresSampleMAF)
+A --> |calls| G(featureSampleMAF)
+A --> |calls| H(vcfFeatures2MatrixView)
+A --> |calls| I(vcfFeatures2MatrixViewRows)
+A --> |calls| J(rowsAddFeature)
+A --> |calls| K(annotateRowsFromFeatures)
+A --> |calls| L(featuresValuesFields)
+A --> |calls| M(featureSampleNames)
+A --> |calls| N(objectSymbolNameArray)
+A --> |calls| O(genotypeSNPFiltersDefined)
+</div>
+
+<div class="mermaid classDiagram" style="width: 100%;" >
+graph TD
+
+B(featureMafFilter)		--> |used by| P(vcfFeatures2MatrixView)
+C(featureCallRateFilter)	--> |used by| Q(vcfFeatures2MatrixViewRows)
+D(featuresFilterNalleles)	--> |used by| R(vcfFeatures2MatrixViewRows)
+E(genotypeSNPFiltersApply)	--> |used by| S(vcfFeatures2MatrixView)
+F(featuresSampleMAF)		--> |used by| T(vcfFeatures2MatrixViewRows)
+G(featureSampleMAF)		--> |used by| U(vcfFeatures2MatrixViewRows)
+H(vcfFeatures2MatrixView)	--> |used by| V(vcfFeatures2MatrixViewRowsResult)
+I(vcfFeatures2MatrixViewRows)	--> |used by| W(vcfFeatures2MatrixViewRows)
+J(rowsAddFeature)		--> |used by| X(vcfFeatures2MatrixViewRowsResult)
+K(annotateRowsFromFeatures)	--> |used by| Y(vcfFeatures2MatrixViewRowsResult)
+L(featuresValuesFields)		--> |used by| Z(vcfFeatures2MatrixViewRowsResult)
+M(featureSampleNames)		--> |used by| AA(vcfFeatures2MatrixViewRows)
+N(objectSymbolNameArray)	--> |used by| AB(vcfFeatures2MatrixViewRowsResult)
+O(genotypeSNPFiltersDefined)	--> |used by| AC(vcfFeatures2MatrixView)
+
+
+</div>
+
+<!--
+
+/** not used */
+
+: ! 
+
+ -->
+
+<div  class="clearfix">
+</div>
+
+<p>
+Notes :
+<ul>
+<li></li>
+</ul>
+</p>
+
+
+
+<p>Code links</p>
+<ul>
+  <li><a href="https://github.com/plantinformatics/pretzel/blob/feature/ongoingGenotype/frontend/app/utils/data/vcf-feature.js">frontend/app/utils/data/vcf-feature.js</a></li>
+</ul>
+
+<div  class="clearfix">
+</div>
+
+
+<p> Diagram drawn by :
+<a href="https://mermaidjs.github.io/">Mermaid</a>, 
+github <a href="https://github.com/knsv/mermaid">readme</a>
+</p>
+
+<hr>
+<!-- Use either this, or class="clearfix" on the previous div. -->
+<div style="clear:both">
+</div>
+
+
+
+</body>
+</html>
diff --git a/frontend/.bowerrc b/frontend/.bowerrc
diff --git a/frontend/.ember-cli b/frontend/.ember-cli
@@ -7,5 +7,11 @@
   */
   "liveReload": true,
   "watcher": "polling",
-  "disableAnalytics": true
+  "disableAnalytics": true,
+
+  /**
+    Setting `isTypeScriptProject` to true will force the blueprint generators to generate TypeScript
+    rather than JavaScript by default, when a TypeScript version of a given blueprint is available.
+  */
+  "isTypeScriptProject": false
 }
diff --git a/frontend/.eslintignore b/frontend/.eslintignore
@@ -13,8 +13,13 @@
 # misc
 /coverage/
 !.*
+.*/
+.eslintcache
 
 # ember-try
 /.node_modules.ember-try/
 /bower.json.ember-try
+/npm-shrinkwrap.json.ember-try
 /package.json.ember-try
+/package-lock.json.ember-try
+/yarn.lock.ember-try
-Original file line number
+Diff line change
@@ -0,0 +1,3 @@
+    .git
+    doc
+    tmp