From 0515a0b8e357991f1f3b2762d7044fe9c0d0eceb Mon Sep 17 00:00:00 2001
From: Piotr Gawron <p.gawron@atcomp.pl>
Date: Thu, 9 Nov 2023 15:43:45 +0100
Subject: [PATCH] check removal with future date
---
.project | 1 -
annotation/.project | 16 +-
checkstyle.xml | 2 +-
commons/.project | 2 -
converter-CellDesigner/.project | 2 -
converter-SBGNML/.project | 2 -
converter-graphics/.project | 2 -
converter-sbml/.project | 2 -
converter/.project | 2 -
frontend-js/.project | 2 -
frontend-js/package-lock.json | 14949 +++++++++-------
model-command/.project | 2 -
model/.project | 2 -
pathvisio/.project | 2 -
persist/.project | 2 -
.../persist/dao/StacktraceDaoTest.java | 4 +-
pom.xml | 2 +-
rest-api/.project | 2 -
service/.project | 2 -
web/.project | 2 -
20 files changed, 8243 insertions(+), 6759 deletions(-)
diff --git a/.project b/.project
index 1ec56e4e53..aae2a771a7 100644
--- a/.project
+++ b/.project
@@ -29,6 +29,5 @@
<natures>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/annotation/.project b/annotation/.project
index cc8da93dfb..94bc32f295 100644
--- a/annotation/.project
+++ b/annotation/.project
@@ -6,8 +6,13 @@
</projects>
<buildSpec>
<buildCommand>
- <name>org.eclipse.wst.common.project.facet.core.builder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/org.eclipse.wst.common.project.facet.core.builder.launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
@@ -26,8 +31,13 @@
</arguments>
</buildCommand>
<buildCommand>
- <name>org.eclipse.wst.validation.validationbuilder</name>
+ <name>org.eclipse.ui.externaltools.ExternalToolBuilder</name>
+ <triggers>full,incremental,</triggers>
<arguments>
+ <dictionary>
+ <key>LaunchConfigHandle</key>
+ <value><project>/.externalToolBuilders/org.eclipse.wst.validation.validationbuilder.launch</value>
+ </dictionary>
</arguments>
</buildCommand>
<buildCommand>
@@ -37,9 +47,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/checkstyle.xml b/checkstyle.xml
index 3c2bb57bf4..067f3ce464 100644
--- a/checkstyle.xml
+++ b/checkstyle.xml
@@ -21,7 +21,7 @@
</module>
<!-- https://checkstyle.org/config_filters.html#SuppressionFilter -->
<module name="SuppressionFilter">
- <property name="file" value="${org.checkstyle.google.suppressionfilter.config}"
+ <property name="file" value="checkstyle-suppressions.xml"
default="checkstyle-suppressions.xml" />
<property name="optional" value="true"/>
</module>
diff --git a/commons/.project b/commons/.project
index a26883597d..d78ffdd751 100644
--- a/commons/.project
+++ b/commons/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/converter-CellDesigner/.project b/converter-CellDesigner/.project
index bf1a13a878..c14b323769 100644
--- a/converter-CellDesigner/.project
+++ b/converter-CellDesigner/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/converter-SBGNML/.project b/converter-SBGNML/.project
index 339d4b3234..c433691b2c 100644
--- a/converter-SBGNML/.project
+++ b/converter-SBGNML/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/converter-graphics/.project b/converter-graphics/.project
index 98b2440a4a..d568b9a4c0 100644
--- a/converter-graphics/.project
+++ b/converter-graphics/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/converter-sbml/.project b/converter-sbml/.project
index 93cbc4b2f7..59bac4c6df 100644
--- a/converter-sbml/.project
+++ b/converter-sbml/.project
@@ -27,9 +27,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/converter/.project b/converter/.project
index 3057141270..92d0bb0a3f 100644
--- a/converter/.project
+++ b/converter/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/frontend-js/.project b/frontend-js/.project
index 4994d966f2..de65cd97e7 100644
--- a/frontend-js/.project
+++ b/frontend-js/.project
@@ -12,9 +12,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/frontend-js/package-lock.json b/frontend-js/package-lock.json
index d28fc2559f..90527a548b 100644
--- a/frontend-js/package-lock.json
+++ b/frontend-js/package-lock.json
@@ -1,6758 +1,8286 @@
{
"name": "minerva-frontend",
"version": "1.0.0",
- "lockfileVersion": 2,
+ "lockfileVersion": 1,
"requires": true,
- "packages": {
- "": {
- "name": "minerva-frontend",
- "version": "1.0.0",
- "license": "AGPL-3.0",
- "dependencies": {
- "@fortawesome/fontawesome-free": "^5.11.2",
- "autocomplete.js": "^0.36.0",
- "bootstrap": "^4.3.1",
- "csv-stringify": "^5.3.1",
- "datatables.net": "^1.10.19",
- "datatables.net-dt": "^1.10.19",
- "datatables.net-rowreorder": "^1.2.5",
- "datatables.net-rowreorder-dt": "^1.2.5",
- "dual-listbox": "^1.1.0",
- "file-saver": "^1.3.8",
- "http-status-codes": "^1.3.2",
- "is-url": "^1.2.4",
- "jquery": "2.2.4",
- "jquery-ui": "1.10.5",
- "jstree": "^3.3.8",
- "jszip": "^3.2.2",
- "log4js": "^4.5.1",
- "md5": "^2.2.1",
- "molart": "1.15.0",
- "multi-checkbox-list": "^0.3.1",
- "openlayers": "^4.6.5",
- "pileup": "^0.6.12",
- "popper.js": "^1.15.0",
- "request": "^2.88.0",
- "semver": "^6.3.0",
- "spectrum-colorpicker": "^1.8.0",
- "text-encoding": "^0.7.0",
- "vanilla-cookieconsent": "^2.7.2",
- "xss": "^1.0.6"
- },
- "devDependencies": {
- "bluebird": "^3.5.5",
- "browserify": "^16.5.0",
- "chai": "^4.2.0",
- "clean-css": "^4.2.1",
- "del": "^5.0.0",
- "exorcist": "^1.0.1",
- "istanbul": "0.4.5",
- "jsdom": "11.7.0",
- "jshint": "^2.10.2",
- "log4js-in-memory-appender": "^0.1.2",
- "mkdirp": "^0.5.1",
- "mocha": "^3.5.3",
- "mock-local-storage": "^1.1.8",
- "node-fetch": "^2.6.0",
- "stream-to-blob": "^1.0.1",
- "uglifyjs": "^2.4.10"
- }
- },
- "node_modules/@fortawesome/fontawesome-free": {
+ "dependencies": {
+ "@fortawesome/fontawesome-free": {
"version": "5.11.2",
"resolved": "https://registry.npmjs.org/@fortawesome/fontawesome-free/-/fontawesome-free-5.11.2.tgz",
- "integrity": "sha512-XiUPoS79r1G7PcpnNtq85TJ7inJWe0v+b5oZJZKb0pGHNIV6+UiNeQWiFGmuQ0aj7GEhnD/v9iqxIsjuRKtEnQ==",
- "engines": {
- "node": ">=6"
- }
+ "integrity": "sha512-XiUPoS79r1G7PcpnNtq85TJ7inJWe0v+b5oZJZKb0pGHNIV6+UiNeQWiFGmuQ0aj7GEhnD/v9iqxIsjuRKtEnQ=="
},
- "node_modules/@nodelib/fs.scandir": {
+ "@nodelib/fs.scandir": {
"version": "2.1.1",
"resolved": "https://registry.npmjs.org/@nodelib/fs.scandir/-/fs.scandir-2.1.1.tgz",
"integrity": "sha512-NT/skIZjgotDSiXs0WqYhgcuBKhUMgfekCmCGtkUAiLqZdOnrdjmZr9wRl3ll64J9NF79uZ4fk16Dx0yMc/Xbg==",
"dev": true,
- "dependencies": {
+ "requires": {
"@nodelib/fs.stat": "2.0.1",
"run-parallel": "^1.1.9"
- },
- "engines": {
- "node": ">= 8"
}
},
- "node_modules/@nodelib/fs.stat": {
+ "@nodelib/fs.stat": {
"version": "2.0.1",
"resolved": "https://registry.npmjs.org/@nodelib/fs.stat/-/fs.stat-2.0.1.tgz",
"integrity": "sha512-+RqhBlLn6YRBGOIoVYthsG0J9dfpO79eJyN7BYBkZJtfqrBwf2KK+rD/M/yjZR6WBmIhAgOV7S60eCgaSWtbFw==",
- "dev": true,
- "engines": {
- "node": ">= 8"
- }
+ "dev": true
},
- "node_modules/@nodelib/fs.walk": {
+ "@nodelib/fs.walk": {
"version": "1.2.2",
"resolved": "https://registry.npmjs.org/@nodelib/fs.walk/-/fs.walk-1.2.2.tgz",
"integrity": "sha512-J/DR3+W12uCzAJkw7niXDcqcKBg6+5G5Q/ZpThpGNzAUz70eOR6RV4XnnSN01qHZiVl0eavoxJsBypQoKsV2QQ==",
"dev": true,
- "dependencies": {
+ "requires": {
"@nodelib/fs.scandir": "2.1.1",
"fastq": "^1.6.0"
- },
- "engines": {
- "node": ">= 8"
}
},
- "node_modules/@types/downloadjs": {
+ "@types/downloadjs": {
"version": "1.4.3",
"resolved": "https://registry.npmjs.org/@types/downloadjs/-/downloadjs-1.4.3.tgz",
"integrity": "sha512-MjJepFle/tLtT2/jmDNth6ZnwWzEhm40L+olE5HKR70ISUCfgT55eqreeHldAzFLY2HDUGsn8zgyto8KygN0CA=="
},
- "node_modules/@types/events": {
+ "@types/events": {
"version": "3.0.0",
"resolved": "https://registry.npmjs.org/@types/events/-/events-3.0.0.tgz",
"integrity": "sha512-EaObqwIvayI5a8dCzhFrjKzVwKLxjoG9T6Ppd5CEo07LRKfQ8Yokw54r5+Wq7FaBQ+yXRvQAYPrHwya1/UFt9g==",
"dev": true
},
- "node_modules/@types/glob": {
+ "@types/glob": {
"version": "7.1.1",
"resolved": "https://registry.npmjs.org/@types/glob/-/glob-7.1.1.tgz",
"integrity": "sha512-1Bh06cbWJUHMC97acuD6UMG29nMt0Aqz1vF3guLfG+kHHJhy3AyohZFFxYk2f7Q1SQIrNwvncxAE0N/9s70F2w==",
"dev": true,
- "dependencies": {
+ "requires": {
"@types/events": "*",
"@types/minimatch": "*",
"@types/node": "*"
}
},
- "node_modules/@types/minimatch": {
+ "@types/minimatch": {
"version": "3.0.3",
"resolved": "https://registry.npmjs.org/@types/minimatch/-/minimatch-3.0.3.tgz",
"integrity": "sha512-tHq6qdbT9U1IRSGf14CL0pUlULksvY9OZ+5eEgl1N7t+OA3tGvNpxJCzuKQlsNgCVwbAs670L1vcVQi8j9HjnA==",
"dev": true
},
- "node_modules/@types/node": {
+ "@types/node": {
"version": "12.7.1",
"resolved": "https://registry.npmjs.org/@types/node/-/node-12.7.1.tgz",
"integrity": "sha512-aK9jxMypeSrhiYofWWBf/T7O+KwaiAHzM4sveCdWPn71lzUSMimRnKzhXDKfKwV1kWoBo2P1aGgaIYGLf9/ljw==",
"dev": true
},
- "node_modules/@types/react": {
+ "@types/react": {
"version": "15.7.12",
"resolved": "https://registry.npmjs.org/@types/react/-/react-15.7.12.tgz",
"integrity": "sha512-FbIDKxGEzmf0jM+1ArXAJwJzg7GkUq5nLVBIz/PSBwVUzATuAjbPrN+UUEAW6zpt/A2WF8XMfSKsNfGX95xCsQ=="
},
- "node_modules/@types/react-dom": {
+ "@types/react-dom": {
"version": "15.5.15",
"resolved": "https://registry.npmjs.org/@types/react-dom/-/react-dom-15.5.15.tgz",
"integrity": "sha512-o8gV2O5yS4BEIPFu0u6JJEzi0k62+tSpyOy11fzAS3Hlei+Pa/s2L6hnHRDIJkEKDY2UTKGl7iQpL5yoJt5/zA==",
- "dependencies": {
+ "requires": {
"@types/react": "^15"
}
},
- "node_modules/abab": {
- "version": "1.0.4",
- "resolved": "https://registry.npmjs.org/abab/-/abab-1.0.4.tgz",
- "integrity": "sha1-X6rZwsB/YN12dw9xzwJbYqY8/U4=",
- "dev": true
- },
- "node_modules/abbrev": {
- "version": "1.0.9",
- "resolved": "https://registry.npmjs.org/abbrev/-/abbrev-1.0.9.tgz",
- "integrity": "sha1-kbR5JYinc4wl813W9jdSovh3YTU="
- },
- "node_modules/accepts": {
+ "JSONStream": {
"version": "1.3.5",
- "resolved": "https://registry.npmjs.org/accepts/-/accepts-1.3.5.tgz",
- "integrity": "sha1-63d99gEXI6OxTopywIBcjoZ0a9I=",
- "dependencies": {
- "mime-types": "~2.1.18",
- "negotiator": "0.6.1"
- },
- "engines": {
- "node": ">= 0.6"
- }
- },
- "node_modules/accepts/node_modules/mime-db": {
- "version": "1.33.0",
- "resolved": "https://registry.npmjs.org/mime-db/-/mime-db-1.33.0.tgz",
- "integrity": "sha512-BHJ/EKruNIqJf/QahvxwQZXKygOQ256myeN/Ew+THcAa5q+PjyTTMMeNQC4DZw5AwfvelsUrA6B67NKMqXDbzQ==",
- "engines": {
- "node": ">= 0.6"
- }
- },
- "node_modules/accepts/node_modules/mime-types": {
- "version": "2.1.18",
- "resolved": "https://registry.npmjs.org/mime-types/-/mime-types-2.1.18.tgz",
- "integrity": "sha512-lc/aahn+t4/SWV/qcmumYjymLsWfN3ELhpmVuUFjgsORruuZPVSwAQryq+HHGvO/SI2KVX26bx+En+zhM8g8hQ==",
- "dependencies": {
- "mime-db": "~1.33.0"
- },
- "engines": {
- "node": ">= 0.6"
- }
- },
- "node_modules/acorn": {
- "version": "6.4.2",
- "resolved": "https://registry.npmjs.org/acorn/-/acorn-6.4.2.tgz",
- "integrity": "sha512-XtGIhXwF8YM8bJhGxG5kXgjkEuNGLTkoYqVE+KMR+aspr4KGYmKYg7yUe3KghyQ9yheNwLnjmzh/7+gfDBmHCQ==",
- "dev": true,
- "bin": {
- "acorn": "bin/acorn"
- },
- "engines": {
- "node": ">=0.4.0"
- }
- },
- "node_modules/acorn-dynamic-import": {
- "version": "4.0.0",
- "resolved": "https://registry.npmjs.org/acorn-dynamic-import/-/acorn-dynamic-import-4.0.0.tgz",
- "integrity": "sha512-d3OEjQV4ROpoflsnUA8HozoIR504TFxNivYEUi6uwz0IYhBkTDXGuWlNdMtybRt3nqVx/L6XqMt0FxkXuWKZhw==",
- "dev": true,
- "peerDependencies": {
- "acorn": "^6.0.0"
- }
- },
- "node_modules/acorn-globals": {
- "version": "4.3.3",
- "resolved": "https://registry.npmjs.org/acorn-globals/-/acorn-globals-4.3.3.tgz",
- "integrity": "sha512-vkR40VwS2SYO98AIeFvzWWh+xyc2qi9s7OoXSFEGIP/rOJKzjnhykaZJNnHdoq4BL2gGxI5EZOU16z896EYnOQ==",
- "dev": true,
- "dependencies": {
- "acorn": "^6.0.1",
- "acorn-walk": "^6.0.1"
- }
- },
- "node_modules/acorn-node": {
- "version": "1.7.0",
- "resolved": "https://registry.npmjs.org/acorn-node/-/acorn-node-1.7.0.tgz",
- "integrity": "sha512-XhahLSsCB6X6CJbe+uNu3Mn9sJBNFxtBN9NLgAOQovfS6Kh0lDUtmlclhjn9CvEK7A7YyRU13PXlNcpSiLI9Yw==",
- "dev": true,
- "dependencies": {
- "acorn": "^6.1.1",
- "acorn-dynamic-import": "^4.0.0",
- "acorn-walk": "^6.1.1",
- "xtend": "^4.0.1"
- }
- },
- "node_modules/acorn-walk": {
- "version": "6.2.0",
- "resolved": "https://registry.npmjs.org/acorn-walk/-/acorn-walk-6.2.0.tgz",
- "integrity": "sha512-7evsyfH1cLOCdAzZAd43Cic04yKydNx0cF+7tiA19p1XnLLPU4dpCQOqpjqwokFe//vS0QqfqqjCS2JkiIs0cA==",
- "dev": true,
- "engines": {
- "node": ">=0.4.0"
- }
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- "node_modules/after": {
- "version": "0.8.2",
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- "integrity": "sha1-/ts5T58OAqqXaOcCvaI7UF+ufh8="
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- "node_modules/align-text": {
- "version": "0.1.4",
- "resolved": "https://registry.npmjs.org/align-text/-/align-text-0.1.4.tgz",
- "integrity": "sha1-DNkKVhCT810KmSVsIrcGlDP60Rc=",
- "optional": true,
- "dependencies": {
- "kind-of": "^3.0.2",
- "longest": "^1.0.1",
- "repeat-string": "^1.5.2"
- },
- "engines": {
- "node": ">=0.10.0"
- }
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- "node_modules/amdefine": {
- "version": "1.0.1",
- "resolved": "https://registry.npmjs.org/amdefine/-/amdefine-1.0.1.tgz",
- "integrity": "sha1-SlKCrBZHKek2Gbz9OtFR+BfOkfU=",
- "engines": {
- "node": ">=0.4.2"
- }
- },
- "node_modules/ansi-regex": {
- "version": "2.1.1",
- "resolved": "https://registry.npmjs.org/ansi-regex/-/ansi-regex-2.1.1.tgz",
- "integrity": "sha1-w7M6te42DYbg5ijwRorn7yfWVN8=",
- "engines": {
- "node": ">=0.10.0"
- }
- },
- "node_modules/ansi-styles": {
- "version": "1.0.0",
- "resolved": "https://registry.npmjs.org/ansi-styles/-/ansi-styles-1.0.0.tgz",
- "integrity": "sha1-yxAt8cVvUSPquLZ817mAJ6AnkXg=",
- "engines": {
- "node": ">=0.8.0"
- }
- },
- "node_modules/aproba": {
- "version": "1.2.0",
- "resolved": "https://registry.npmjs.org/aproba/-/aproba-1.2.0.tgz",
- "integrity": "sha512-Y9J6ZjXtoYh8RnXVCMOU/ttDmk1aBjunq9vO0ta5x85WDQiQfUF9sIPBITdbiiIVcBo03Hi3jMxigBtsddlXRw=="
- },
- "node_modules/are-we-there-yet": {
- "version": "1.1.4",
- "resolved": "https://registry.npmjs.org/are-we-there-yet/-/are-we-there-yet-1.1.4.tgz",
- "integrity": "sha1-u13KOCu5TwXhUZQ3PRb9O6HKEQ0=",
- "dependencies": {
- "delegates": "^1.0.0",
- "readable-stream": "^2.0.6"
- }
- },
- "node_modules/are-we-there-yet/node_modules/isarray": {
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+ "cached-path-relative": "^1.0.2",
+ "concat-stream": "~1.6.0",
+ "defined": "^1.0.0",
+ "detective": "^5.2.0",
+ "duplexer2": "^0.1.2",
+ "inherits": "^2.0.1",
+ "parents": "^1.0.0",
+ "readable-stream": "^2.0.2",
+ "resolve": "^1.4.0",
+ "stream-combiner2": "^1.1.1",
+ "subarg": "^1.0.0",
+ "through2": "^2.0.0",
+ "xtend": "^4.0.0"
+ }
+ },
+ "object-assign": {
+ "version": "4.1.1",
+ "resolved": "https://registry.npmjs.org/object-assign/-/object-assign-4.1.1.tgz",
+ "integrity": "sha1-IQmtx5ZYh8/AXLvUQsrIv7s2CGM="
+ },
+ "os-browserify": {
+ "version": "0.3.0",
+ "resolved": "https://registry.npmjs.org/os-browserify/-/os-browserify-0.3.0.tgz",
+ "integrity": "sha1-hUNzx/XCMVkU/Jv8a9gjj92h7Cc="
+ },
+ "read-only-stream": {
+ "version": "2.0.0",
+ "resolved": "https://registry.npmjs.org/read-only-stream/-/read-only-stream-2.0.0.tgz",
+ "integrity": "sha1-JyT9aoET1zdkrCiNQ4YnDB2/F/A=",
+ "requires": {
+ "readable-stream": "^2.0.2"
+ }
+ },
+ "shell-quote": {
+ "version": "1.7.3",
+ "resolved": "https://registry.npmjs.org/shell-quote/-/shell-quote-1.7.3.tgz",
+ "integrity": "sha512-Vpfqwm4EnqGdlsBFNmHhxhElJYrdfcxPThu+ryKS5J8L/fhAwLazFZtq+S+TWZ9ANj2piSQLGj6NQg+lKPmxrw=="
+ },
+ "source-map": {
+ "version": "0.5.7",
+ "resolved": "https://registry.npmjs.org/source-map/-/source-map-0.5.7.tgz",
+ "integrity": "sha1-igOdLRAh0i0eoUyA2OpGi6LvP8w="
+ },
+ "stream-browserify": {
+ "version": "2.0.2",
+ "resolved": "https://registry.npmjs.org/stream-browserify/-/stream-browserify-2.0.2.tgz",
+ "integrity": "sha512-nX6hmklHs/gr2FuxYDltq8fJA1GDlxKQCz8O/IM4atRqBH8OORmBNgfvW5gG10GT/qQ9u0CzIvr2X5Pkt6ntqg==",
+ "requires": {
+ "inherits": "~2.0.1",
+ "readable-stream": "^2.0.2"
+ }
+ },
+ "stream-combiner2": {
+ "version": "1.1.1",
+ "resolved": "https://registry.npmjs.org/stream-combiner2/-/stream-combiner2-1.1.1.tgz",
+ "integrity": "sha1-+02KFCDqNidk4hrUeAOXvry0HL4=",
+ "requires": {
+ "duplexer2": "~0.1.0",
+ "readable-stream": "^2.0.2"
+ }
+ },
+ "stream-splicer": {
+ "version": "2.0.1",
+ "resolved": "https://registry.npmjs.org/stream-splicer/-/stream-splicer-2.0.1.tgz",
+ "integrity": "sha512-Xizh4/NPuYSyAXyT7g8IvdJ9HJpxIGL9PjyhtywCZvvP0OPIdqyrr4dMikeuvY8xahpdKEBlBTySe583totajg==",
+ "requires": {
+ "inherits": "^2.0.1",
+ "readable-stream": "^2.0.2"
+ }
+ },
+ "through2": {
+ "version": "2.0.5",
+ "resolved": "https://registry.npmjs.org/through2/-/through2-2.0.5.tgz",
+ "integrity": "sha512-/mrRod8xqpA+IHSLyGCQ2s8SPHiCDEeQJSep1jqLYeEUClOFG2Qsh+4FU6G9VeqpZnGW/Su8LQGc4YKni5rYSQ==",
+ "requires": {
+ "readable-stream": "~2.3.6",
+ "xtend": "~4.0.1"
+ }
+ },
+ "url": {
+ "version": "0.11.0",
+ "resolved": "https://registry.npmjs.org/url/-/url-0.11.0.tgz",
+ "integrity": "sha1-ODjpfPxgUh63PFJajlW/3Z4uKPE=",
+ "requires": {
+ "punycode": "1.3.2",
+ "querystring": "0.2.0"
+ },
+ "dependencies": {
+ "punycode": {
+ "version": "1.3.2",
+ "resolved": "https://registry.npmjs.org/punycode/-/punycode-1.3.2.tgz",
+ "integrity": "sha1-llOgNvt8HuQjQvIyXM7v6jkmxI0="
+ }
+ }
+ },
+ "vm-browserify": {
+ "version": "1.1.2",
+ "resolved": "https://registry.npmjs.org/vm-browserify/-/vm-browserify-1.1.2.tgz",
+ "integrity": "sha512-2ham8XPWTONajOR0ohOKOHXkm3+gaBmGut3SRuu75xLd/RRaY6vqgh8NBYYk7+RW3u5AtzPQZG8F10LHkl0lAQ=="
+ }
+ }
+ },
+ "which": {
+ "version": "1.3.1",
+ "resolved": "https://registry.npmjs.org/which/-/which-1.3.1.tgz",
+ "integrity": "sha512-HxJdYWq1MTIQbJ3nw0cqssHoTNU267KlrDuGZ1WYlxDStUtKUhOaJmh112/TZmHxxUfuJqPXSOm7tDyas0OSIQ==",
+ "requires": {
+ "isexe": "^2.0.0"
+ }
+ },
+ "window-size": {
+ "version": "0.1.0",
+ "resolved": "https://registry.npmjs.org/window-size/-/window-size-0.1.0.tgz",
+ "integrity": "sha1-VDjNLqk7IC76Ohn+iIeu58lPnJ0="
+ },
+ "word-wrap": {
+ "version": "1.2.3",
+ "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.3.tgz",
+ "integrity": "sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ=="
+ },
+ "wordwrap": {
+ "version": "1.0.0",
+ "resolved": "https://registry.npmjs.org/wordwrap/-/wordwrap-1.0.0.tgz",
+ "integrity": "sha1-J1hIEIkUVqQXHI0CJkQa3pDLyus="
+ },
+ "wrappy": {
+ "version": "1.0.2",
+ "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz",
+ "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8="
+ },
+ "xtend": {
+ "version": "4.0.2",
+ "resolved": "https://registry.npmjs.org/xtend/-/xtend-4.0.2.tgz",
+ "integrity": "sha512-LKYU1iAXJXUgAXn9URjiu+MWhyUXHsvfp7mcuYm9dSUKK0/CjtrUwFAxD82/mCWbtLsGjFIad0wIsod4zrTAEQ=="
+ },
+ "xunit-file": {
+ "version": "0.0.6",
+ "resolved": "https://registry.npmjs.org/xunit-file/-/xunit-file-0.0.6.tgz",
+ "integrity": "sha1-+pAfF+J0bGjoC0GWLAqqsos4VaM="
+ },
+ "yargs": {
+ "version": "3.10.0",
+ "resolved": "https://registry.npmjs.org/yargs/-/yargs-3.10.0.tgz",
+ "integrity": "sha1-9+572FfdfB0tOMDnTvvWgdFDH9E=",
+ "requires": {
+ "camelcase": "^1.0.2",
+ "cliui": "^2.1.0",
+ "decamelize": "^1.0.0",
+ "window-size": "0.1.0"
+ },
+ "dependencies": {
+ "camelcase": {
+ "version": "1.2.1",
+ "resolved": "https://registry.npmjs.org/camelcase/-/camelcase-1.2.1.tgz",
+ "integrity": "sha1-m7UwTS4LVmmLLHWLCKPqqdqlijk="
+ }
+ }
+ },
+ "yauzl": {
+ "version": "2.4.1",
+ "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.4.1.tgz",
+ "integrity": "sha1-lSj0QtqxsihOWLQ3m7GU4i4MQAU=",
+ "requires": {
+ "fd-slicer": "~1.0.1"
+ }
+ }
}
},
"abab": {
@@ -6800,8 +8328,7 @@
"version": "4.0.0",
"resolved": "https://registry.npmjs.org/acorn-dynamic-import/-/acorn-dynamic-import-4.0.0.tgz",
"integrity": "sha512-d3OEjQV4ROpoflsnUA8HozoIR504TFxNivYEUi6uwz0IYhBkTDXGuWlNdMtybRt3nqVx/L6XqMt0FxkXuWKZhw==",
- "dev": true,
- "requires": {}
+ "dev": true
},
"acorn-globals": {
"version": "4.3.3",
@@ -7166,8 +8693,7 @@
"bootstrap": {
"version": "4.3.1",
"resolved": "https://registry.npmjs.org/bootstrap/-/bootstrap-4.3.1.tgz",
- "integrity": "sha512-rXqOmH1VilAt2DyPzluTi2blhk17bO7ef+zLLPlWvG494pDxcM234pJ8wTc/6R40UWizAIIMgxjvxZg5kmsbag==",
- "requires": {}
+ "integrity": "sha512-rXqOmH1VilAt2DyPzluTi2blhk17bO7ef+zLLPlWvG494pDxcM234pJ8wTc/6R40UWizAIIMgxjvxZg5kmsbag=="
},
"brace-expansion": {
"version": "1.1.8",
@@ -7200,9 +8726,9 @@
"integrity": "sha512-erYug8XoqzU3IfcU8fUgyHqyOXqIE4tUTTQ+7mqUjQlvnXkOO6OlT9c/ZoJVHYoAaqGxr09CN53G7XIsO4KtWA==",
"dev": true,
"requires": {
+ "JSONStream": "^1.0.3",
"combine-source-map": "~0.8.0",
"defined": "^1.0.0",
- "JSONStream": "^1.0.3",
"safe-buffer": "^5.1.1",
"through2": "^2.0.0",
"umd": "^3.0.0"
@@ -7243,6 +8769,7 @@
"integrity": "sha512-6bfI3cl76YLAnCZ75AGu/XPOsqUhRyc0F/olGIJeCxtfxF2HvPKEcmjU9M8oAPxl4uBY1U7Nry33Q6koV3f2iw==",
"dev": true,
"requires": {
+ "JSONStream": "^1.0.3",
"assert": "^1.4.0",
"browser-pack": "^6.0.1",
"browser-resolve": "^1.11.0",
@@ -7264,7 +8791,6 @@
"https-browserify": "^1.0.0",
"inherits": "~2.0.1",
"insert-module-globals": "^7.0.0",
- "JSONStream": "^1.0.3",
"labeled-stream-splicer": "^2.0.0",
"mkdirp": "^0.5.0",
"module-deps": "^6.0.0",
@@ -9240,11 +10766,11 @@
"integrity": "sha512-VE6NlW+WGn2/AeOMd496AHFYmE7eLKkUY6Ty31k4og5vmA3Fjuwe9v6ifH6Xx/Hz27QvdoMoviw1/pqWRB09Sw==",
"dev": true,
"requires": {
+ "JSONStream": "^1.0.3",
"acorn-node": "^1.5.2",
"combine-source-map": "^0.8.0",
"concat-stream": "^1.6.1",
"is-buffer": "^1.1.0",
- "JSONStream": "^1.0.3",
"path-is-absolute": "^1.0.1",
"process": "~0.11.0",
"through2": "^2.0.0",
@@ -9699,16 +11225,6 @@
"integrity": "sha1-P02uSpH6wxX3EGL4UhzCOfE2YoA=",
"dev": true
},
- "JSONStream": {
- "version": "1.3.5",
- "resolved": "https://registry.npmjs.org/JSONStream/-/JSONStream-1.3.5.tgz",
- "integrity": "sha512-E+iruNOY8VV9s4JEbe1aNEm6MiszPRr/UfcHMz0TQh1BXSxHK+ASV1R6W4HpjBhSeS+54PIsAMCBmwD06LLsqQ==",
- "dev": true,
- "requires": {
- "jsonparse": "^1.2.0",
- "through": ">=2.2.7 <3"
- }
- },
"jsprim": {
"version": "1.4.1",
"resolved": "https://registry.npmjs.org/jsprim/-/jsprim-1.4.1.tgz",
@@ -10265,6 +11781,7 @@
"integrity": "sha512-UnEn6Ah36Tu4jFiBbJVUtt0h+iXqxpLqDvPS8nllbw5RZFmNJ1+Mz5BjYnM9ieH80zyxHkARGLnMIHlPK5bu6A==",
"dev": true,
"requires": {
+ "JSONStream": "^1.0.3",
"browser-resolve": "^1.7.0",
"cached-path-relative": "^1.0.2",
"concat-stream": "~1.6.0",
@@ -10272,7 +11789,6 @@
"detective": "^5.0.2",
"duplexer2": "^0.1.2",
"inherits": "^2.0.1",
- "JSONStream": "^1.0.3",
"parents": "^1.0.0",
"readable-stream": "^2.0.2",
"resolve": "^1.4.0",
@@ -10307,13 +11823,13 @@
"integrity": "sha512-9Mq880f/wEh0uQz/pvwNJPA3Fe+ZQZH19/K0yfU9ruNFLoouxzfza6Bc6NU9o7IIv8PULQbXyNToO6HPeaUxTw==",
"requires": {
"@types/downloadjs": "^1.4.2",
+ "ProtVista": "ProtVista@git+https://github.com/davidhoksza/protvista.git#scaling",
"color-blend": "^1.0.0",
"downloadjs": "^1.4.7",
"events": "^1.1.1",
"jquery": "^3.6.0",
- "litemol": "github:dsehnal/LiteMol",
+ "litemol": "litemol@github:dsehnal/LiteMol",
"lodash": "^4.17.21",
- "ProtVista": "git+https://github.com/davidhoksza/protvista.git#scaling",
"semantic-ui-button": "^2.3.2",
"semantic-ui-dropdown": "^2.2.12",
"semantic-ui-label": "^2.2.12",
@@ -10765,17 +12281,6 @@
"resolved": "https://registry.npmjs.org/protocol-buffers-schema/-/protocol-buffers-schema-2.2.0.tgz",
"integrity": "sha1-0pxs1z+2VZePtpiWkRgNuEQRn2E="
},
- "ProtVista": {
- "version": "git+ssh://git@github.com/davidhoksza/protvista.git#d5e8390c7a58a902d1d815524acf7e118729360a",
- "from": "ProtVista@git+https://github.com/davidhoksza/protvista.git#scaling",
- "requires": {
- "d3": "^3.4.13",
- "file-saver": "^1.3.2",
- "jquery": "^2.1.4",
- "jszip": "^3.1.2",
- "underscore": "^1.7.0"
- }
- },
"psl": {
"version": "1.1.29",
"resolved": "https://registry.npmjs.org/psl/-/psl-1.1.29.tgz",
@@ -10911,8 +12416,7 @@
"react-dom": {
"version": "0.14.9",
"resolved": "https://registry.npmjs.org/react-dom/-/react-dom-0.14.9.tgz",
- "integrity": "sha1-BQZKPc8PsYgKOyv8nVjFXY2fYpM=",
- "requires": {}
+ "integrity": "sha1-BQZKPc8PsYgKOyv8nVjFXY2fYpM="
},
"read-only-stream": {
"version": "2.0.0",
@@ -11743,11 +13247,6 @@
}
}
},
- "string_decoder": {
- "version": "0.10.31",
- "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-0.10.31.tgz",
- "integrity": "sha1-YuIDvEF2bGwoyfyEMB2rHFMQ+pQ="
- },
"string-width": {
"version": "1.0.2",
"resolved": "https://registry.npmjs.org/string-width/-/string-width-1.0.2.tgz",
@@ -11768,6 +13267,11 @@
}
}
},
+ "string_decoder": {
+ "version": "0.10.31",
+ "resolved": "https://registry.npmjs.org/string_decoder/-/string_decoder-0.10.31.tgz",
+ "integrity": "sha1-YuIDvEF2bGwoyfyEMB2rHFMQ+pQ="
+ },
"stringstream": {
"version": "0.0.5",
"resolved": "https://registry.npmjs.org/stringstream/-/stringstream-0.0.5.tgz",
@@ -12038,7 +13542,6 @@
"version": "1.0.2",
"resolved": "https://registry.npmjs.org/uglify-to-browserify/-/uglify-to-browserify-1.0.2.tgz",
"integrity": "sha1-bgkk1r2mta/jSeOabWMoUKD4grc=",
- "dev": true,
"optional": true
},
"uglifyjs": {
diff --git a/model-command/.project b/model-command/.project
index 76db27f2b5..148ac25e3d 100644
--- a/model-command/.project
+++ b/model-command/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/model/.project b/model/.project
index 44a99170d5..b09fe38b6b 100644
--- a/model/.project
+++ b/model/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/pathvisio/.project b/pathvisio/.project
index d68188f8af..43c04e8dd4 100644
--- a/pathvisio/.project
+++ b/pathvisio/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/persist/.project b/persist/.project
index 6988b02d15..ea9c8d5df0 100644
--- a/persist/.project
+++ b/persist/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/persist/src/test/java/lcsb/mapviewer/persist/dao/StacktraceDaoTest.java b/persist/src/test/java/lcsb/mapviewer/persist/dao/StacktraceDaoTest.java
index dc984d44df..94c006fe31 100644
--- a/persist/src/test/java/lcsb/mapviewer/persist/dao/StacktraceDaoTest.java
+++ b/persist/src/test/java/lcsb/mapviewer/persist/dao/StacktraceDaoTest.java
@@ -44,7 +44,9 @@ public class StacktraceDaoTest extends PersistTestFunctions {
stacktraceDao.add(st);
assertEquals(1, stacktraceDao.getCount());
- stacktraceDao.removeBeforeDate(Calendar.getInstance());
+ Calendar calendar = Calendar.getInstance();
+ calendar.add(Calendar.DATE, 1);
+ stacktraceDao.removeBeforeDate(calendar);
assertEquals(0, stacktraceDao.getCount());
}
diff --git a/pom.xml b/pom.xml
index e4916359e3..83b66a813c 100644
--- a/pom.xml
+++ b/pom.xml
@@ -117,7 +117,7 @@
<git-commit-id-plugin.version>4.0.4</git-commit-id-plugin.version>
<surefire.rerunFailingTestsCount>4</surefire.rerunFailingTestsCount>
- <checkstyle.version>3.1.1</checkstyle.version>
+ <checkstyle.version>3.1.2</checkstyle.version>
<surefireArgLine></surefireArgLine>
</properties>
diff --git a/rest-api/.project b/rest-api/.project
index fc78f7be58..106f29a0c9 100644
--- a/rest-api/.project
+++ b/rest-api/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/service/.project b/service/.project
index ba2b83aa61..0bd1df9664 100644
--- a/service/.project
+++ b/service/.project
@@ -37,9 +37,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
diff --git a/web/.project b/web/.project
index fc438eb8ab..2699034dae 100644
--- a/web/.project
+++ b/web/.project
@@ -42,9 +42,7 @@
</buildCommand>
</buildSpec>
<natures>
- <nature>org.eclipse.wst.common.modulecore.ModuleCoreNature</nature>
<nature>org.eclipse.jdt.core.javanature</nature>
<nature>org.eclipse.m2e.core.maven2Nature</nature>
- <nature>org.eclipse.wst.common.project.facet.core.nature</nature>
</natures>
</projectDescription>
--
GitLab