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Merge branch 'master' into dependabot/npm_and_yarn/multi-0acb442647
2 parents 1ff6fcd + 88609e9 commit e4b4792

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‎config.json‎

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@@ -33,6 +33,10 @@
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"requireComplete": false,
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"requireBestPractice": false,
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"removePublicEnabled": false,
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"suppressInfoLogs": false,
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"suppressDebugLogs": false,
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"suppressWarningLogs": false,
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"suppressErrorLogs": false,
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"namespaces" : {
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"xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#",
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"xmlns:dcterms": "http://purl.org/dc/terms/",

‎docker/Dockerfile‎

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@@ -5,29 +5,16 @@ RUN apk add nss git openjdk8-jre openjdk8 maven python alpine-sdk libxml2-dev ya
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WORKDIR /synbiohub
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COPY . .
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RUN rm -rf .git
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# RUN rm -rf .git
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RUN cd java && mvn package
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RUN git config --global url."https://".insteadOf git://
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RUN yarn install
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RUN mkdir /mnt/data && \
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mkdir /mnt/data/backup && \
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mkdir /mnt/data/uploads && \
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mkdir /mnt/data/logs && \
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mkdir /mnt/data/icons && \
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mkdir /mnt/config
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COPY docker/config.local.json /mnt/config/config.local.json
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COPY docker/config.local.json config.initial.local.json
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COPY docker/healthcheck.js healthcheck.js
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COPY docker/entry.sh entry.sh
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RUN ln -s /mnt/config/config.local.json ./config.local.json && \
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touch /mnt/data/synbiohub.sqlite && ln -s /mnt/data/synbiohub.sqlite ./synbiohub.sqlite && \
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ln -s /mnt/data/backup . && \
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ln -s /mnt/data/uploads . && \
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ln -s /mnt/data/logs . && \
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ln -s /mnt/data/icons public/.
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COPY docker/first_run.sh first_run.sh
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EXPOSE 7777
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‎docker/entry.sh‎

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@@ -1,3 +1,4 @@
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#!/bin/bash
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./first_run.sh
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node synbiohub.js | tee synbiohub.log

‎docker/first_run.sh‎

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#!/bin/bash
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# make directories if needed:
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mkdir -p /mnt/data
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mkdir -p /mnt/data/backup
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mkdir -p /mnt/data/uploads
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mkdir -p /mnt/data/logs
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mkdir -p /mnt/data/icons
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mkdir -p /mnt/config
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SBH_DIR="/synbiohub"
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MNT_CONFIG="/mnt/config/config.local.json"
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if [ ! -e "$MNT_CONFIG" ]; then
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echo "config missing. Copying initial config"
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cp "$SBH_DIR/config.initial.local.json" "$MNT_CONFIG"
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fi
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MNT_SQL="/mnt/data/synbiohub.sqlite"
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if [ ! -e "$MNT_SQL" ]; then
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echo "sqlite file missing. Creating."
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touch "$MNT_SQL"
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fi
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# check for links:
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if [ ! -e "$SBH_DIR/config.local.json" ]; then
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ln -s "$MNT_CONFIG" "$SBH_DIR/config.local.json"
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fi
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if [ ! -e "$SBH_DIR/synbiohub.sqlite" ]; then
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ln -s "$MNT_SQL" "$SBH_DIR/synbiohub.sqlite"
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fi
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if [ ! -e "$SBH_DIR/data/backup" ]; then
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ln -s "/mnt/data/backup" "$SBH_DIR/."
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fi
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if [ ! -e "$SBH_DIR/data/uploads" ]; then
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ln -s "/mnt/data/uploads" "$SBH_DIR/."
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fi
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if [ ! -e "$SBH_DIR/data/logs" ]; then
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ln -s "/mnt/data/logs" "$SBH_DIR/."
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fi
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if [ ! -e "$SBH_DIR/data/icons" ]; then
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ln -s "/mnt/data/icons" "$SBH_DIR/public/."
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fi

‎java/pom.xml‎

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@@ -42,15 +42,15 @@
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</plugins>
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</build>
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<repositories>
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<repository>
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<id>ossrh</id>
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<url>https://oss.sonatype.org/content/repositories/snapshots</url>
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</repository>
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<repository>
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<id>biojava-legacy-repo</id>
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<name>BioJava's Git based legacy maven repo</name>
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<url>https://github.com/biojava/maven-repo/raw/master/</url>
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</repository>
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</repository>
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<repository>
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<id>local-repo</id>
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<url>file://${project.basedir}/repo</url>
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</repository>
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</repositories>
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<dependencies>
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<dependency>

‎java/repo/org/sbolstandard/libSBOLj/2.4.1-SNAPSHOT/libSBOLj-2.4.1-SNAPSHOT.jar‎

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‎java/repo/org/sbolstandard/libSBOLj/2.4.1-SNAPSHOT/libSBOLj-2.4.1-SNAPSHOT.pom‎

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<?xml version="1.0" encoding="UTF-8"?>
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<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
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xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
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<modelVersion>4.0.0</modelVersion>
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<groupId>org.sbolstandard</groupId>
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<artifactId>libSBOLj</artifactId>
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<version>2.4.1-SNAPSHOT</version>
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<description>POM was created from install:install-file</description>
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</project>

‎java/repo/org/sbolstandard/libSBOLj/2.4.1-SNAPSHOT/maven-metadata-local.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<metadata modelVersion="1.1.0">
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<groupId>org.sbolstandard</groupId>
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<artifactId>libSBOLj</artifactId>
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<version>2.4.1-SNAPSHOT</version>
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<versioning>
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<snapshot>
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<localCopy>true</localCopy>
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</snapshot>
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<lastUpdated>20251018220309</lastUpdated>
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<snapshotVersions>
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<snapshotVersion>
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<extension>jar</extension>
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<value>2.4.1-SNAPSHOT</value>
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<updated>20251018220309</updated>
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</snapshotVersion>
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<snapshotVersion>
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<extension>pom</extension>
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<value>2.4.1-SNAPSHOT</value>
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<updated>20251018215724</updated>
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</snapshotVersion>
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</snapshotVersions>
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</versioning>
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</metadata>

‎java/repo/org/sbolstandard/libSBOLj/maven-metadata-local.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<metadata>
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<groupId>org.sbolstandard</groupId>
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<artifactId>libSBOLj</artifactId>
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<versioning>
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<versions>
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<version>2.4.1-SNAPSHOT</version>
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</versions>
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<lastUpdated>20251018220309</lastUpdated>
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</versioning>
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</metadata>

‎lib/actions/updateCollectionIcon.js‎

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const fs = require('fs')
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const config = require('../config')
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const extend = require('xtend')
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const path = require('path')
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const getOwnedBy = require('../query/ownedBy')
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@@ -13,41 +14,52 @@ const mkdirp = require('mkdirp')
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1415
module.exports = function (req, res) {
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const { graphUri, uri, url } = getUrisFromReq(req, res)
16-
return getOwnedBy(uri, graphUri).then((ownedBy) => {
17-
if (ownedBy.indexOf(config.get('databasePrefix') + 'user/' + req.user.username) === -1) {
18-
if (!req.accepts('text/html')) {
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res.status(403).type('text/plain').send('Not authorized to update this collection icon')
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} else {
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const locals = {
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config: config.get(),
23-
section: 'errors',
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user: req.user,
25-
errors: [ 'Not authorized to update this collection icon' ]
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if (req.method === 'GET') {
18+
const collectionIcons = config.get('collectionIcons')
19+
const iconFile = collectionIcons[uri]
20+
if (iconFile) {
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const dir = path.resolve(__dirname, '../../public')
22+
res.sendFile(iconFile, { root: dir })
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} else {
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res.status(403).type('text/plain').send('No icon for this collection')
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}
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} else {
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return getOwnedBy(uri, graphUri).then((ownedBy) => {
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if (ownedBy.indexOf(config.get('databasePrefix') + 'user/' + req.user.username) === -1) {
29+
if (!req.accepts('text/html')) {
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res.status(403).type('text/plain').send('Not authorized to update this collection icon')
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} else {
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const locals = {
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config: config.get(),
34+
section: 'errors',
35+
user: req.user,
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errors: [ 'Not authorized to update this collection icon' ]
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}
38+
res.status(403).send(pug.renderFile('templates/views/errors/errors.jade', locals))
2639
}
27-
res.status(403).send(pug.renderFile('templates/views/errors/errors.jade', locals))
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}
29-
}
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31-
if (req.file) {
32-
var iconFile = req.file
42+
if (req.file) {
43+
var iconFile = req.file
3344

34-
var collectionIcons = config.get('collectionIcons')
35-
const iconFilename = 'public/icons/' + iconFile.originalname
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var collectionIcons = config.get('collectionIcons')
46+
const iconFilename = 'public/icons/' + iconFile.originalname
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mkdirp('public/icons').then(() => {
38-
fs.writeFileSync(iconFilename, iconFile.buffer)
39-
})
48+
mkdirp('public/icons').then(() => {
49+
fs.writeFileSync(iconFilename, iconFile.buffer)
50+
})
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41-
collectionIcons = extend(collectionIcons, {
42-
[uri]: '/icons/' + iconFile.originalname
43-
})
52+
collectionIcons = extend(collectionIcons, {
53+
[uri]: '/icons/' + iconFile.originalname
54+
})
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45-
config.set('collectionIcons', collectionIcons)
46-
}
47-
if (!req.accepts('text/html')) {
48-
res.status(200).type('text/plain').send('Success')
49-
} else {
50-
res.redirect(url)
51-
}
52-
})
56+
config.set('collectionIcons', collectionIcons)
57+
}
58+
if (!req.accepts('text/html')) {
59+
res.status(200).type('text/plain').send('Success')
60+
} else {
61+
res.redirect(url)
62+
}
63+
})
64+
}
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}

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