ORT scan command error Exception in thread "main" java.io.FileNotFoundException: /project (Is a directory)

[roshvin]

we are doing scan with docker image from https://github.com/alliander-opensource/ort-container/pkgs/container/ort-container
we have used ``download command ` and got all the module from package.json under /project/out/NPM

[root@devops-foss Node-Training]# tree out/NPM/unknown/
out/NPM/unknown/
├── accepts
│   └── 1.3.8
│       ├── HISTORY.md
│       ├── index.js
│       ├── LICENSE
│       ├── package.json
│       ├── README.md
│       └── test
│           ├── charset.js
│           ├── encoding.js
│           ├── language.js
│           └── type.js
├── array-flatten
│   └── 1.1.1
│       ├── array-flatten.js
│       ├── bower.json
│       ├── LICENSE
│       ├── package.json
│       ├── README.md
│       └── test.js
├── balanced-match
│   └── 1.0.2
│       ├── example.js
│       ├── index.js
│       ├── LICENSE.md
│       ├── package.json
│       ├── README.md
│       └── test
│           ├── bench.js
│           ├── looping.js
│           └── test.js

getting below error during scan.

[root@devops-foss Node-Training]# docker run  -v /ort/ORTTESTRESULTS/Node-Training:/project  ghcr.io/alliander-opensource/ort-container:ort-sha-9edefa7 --debug  scan --input-path  /project/  -o /project/out

07:11:06,383 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
07:11:06,394 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:/opt/ort/lib/cli-DOCKER-SNAPSHOT.jar!/logback.xml]
07:11:06,395 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@53ac845a - Resource [logback.xml] occurs multiple times on the classpath.
07:11:06,395 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@53ac845a - Resource [logback.xml] occurs at [jar:file:/opt/ort/lib/helper-cli-DOCKER-SNAPSHOT.jar!/logback.xml]
07:11:06,395 |-WARN in ch.qos.logback.classic.util.DefaultJoranConfigurator@53ac845a - Resource [logback.xml] occurs at [jar:file:/opt/ort/lib/cli-DOCKER-SNAPSHOT.jar!/logback.xml]
07:11:06,407 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@5136207f - URL [jar:file:/opt/ort/lib/cli-DOCKER-SNAPSHOT.jar!/logback.xml] is not of type file
07:11:06,556 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - Processing appender named [STDOUT]
07:11:06,557 |-INFO in ch.qos.logback.core.model.processor.AppenderModelHandler - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
07:11:06,578 |-INFO in ch.qos.logback.core.model.processor.ImplicitModelHandler - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
07:11:06,614 |-INFO in ch.qos.logback.classic.model.processor.RootLoggerModelHandler - Setting level of ROOT logger to WARN
07:11:06,621 |-INFO in ch.qos.logback.core.model.processor.AppenderRefModelHandler - Attaching appender named [STDOUT] to Logger[ROOT]
07:11:06,623 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org.apache.http.headers] to ERROR
07:11:06,623 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org.apache.http.wire] to ERROR
07:11:06,623 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org.eclipse.jgit.internal.storage.file.FileSnapshot] to ERROR
07:11:06,623 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org.ossreviewtoolkit.analyzer.managers.Yarn2] to INFO
07:11:06,623 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org.ossreviewtoolkit.clients.fossid.FossIdRestService] to INFO
07:11:06,624 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org.ossreviewtoolkit.reporter.reporters.fossid.FossIdReporter] to INFO
07:11:06,624 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org.ossreviewtoolkit.scanner.scanners.fossid.FossId] to INFO
07:11:06,624 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org.ossreviewtoolkit.scanner.scanners.fossid.FossIdConfig] to INFO
07:11:06,624 |-INFO in ch.qos.logback.classic.model.processor.LoggerModelHandler - Setting level of logger [org.ossreviewtoolkit.scanner.scanners.fossid.FossIdUrlProvider] to INFO
07:11:06,624 |-INFO in ch.qos.logback.core.model.processor.DefaultProcessor@26a4551a - End of configuration.
07:11:06,625 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@3fdecce - Registering current configuration as safe fallback point

07:11:06.768 [main] DEBUG org.ossreviewtoolkit.cli.OrtMain - Used command line arguments: [--debug, -c, /project/config.yaml, scan, --input-path, /project/out/NPM/unknown/accepts/1.3.8/, -o, /project/out]
07:11:06.904 [main] INFO  org.ossreviewtoolkit.model.config.OrtConfiguration - Using ORT configuration file '/project/config.yaml'.
________ _____________________
\_____  \\______   \__    ___/ the OSS Review Toolkit, version DOCKER-SNAPSHOT.
 /   |   \|       _/ |    |
/    |    \    |   \ |    |    Running 'scan' under Java 11.0.17 on Linux with
\_______  /____|_  / |____|    8 CPUs and a maximum of 5006 MiB of memory.
        \/       \/
Environment variables:
ORT_CONFIG_DIR = /home/ort/.ort/config
ORT_DATA_DIR = /home/ort/.ort
JAVA_HOME = /opt/java/openjdk
ANDROID_HOME = /opt/android-sdk

Scanning projects with:
07:11:07.557 [main] INFO  org.ossreviewtoolkit.utils.common.ProcessCapture - Running '/opt/python/shims/scancode --version' in '/opt/python/shims'...
07:11:09.458 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - ScanCode version 30.1.0
07:11:09.458 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - ScanCode Output Format version 1.0.0
07:11:09.458 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - SPDX License list version 3.14
07:11:09.458 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -
07:11:09.459 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - /opt/python/versions/3.10.6/lib/python3.10/site-packages/cluecode/copyrights.py:3382: FutureWarning: Possible set difference at position 3
07:11:09.459 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -   remove_tags = re.compile(
07:11:09.459 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -
07:11:09.462 [main] INFO  org.ossreviewtoolkit.utils.common.ProcessCapture - Running '/opt/python/shims/scancode --version' in '/opt/python/shims'...
07:11:11.305 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - ScanCode version 30.1.0
07:11:11.305 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - ScanCode Output Format version 1.0.0
07:11:11.305 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - SPDX License list version 3.14
07:11:11.305 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -
07:11:11.306 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - /opt/python/versions/3.10.6/lib/python3.10/site-packages/cluecode/copyrights.py:3382: FutureWarning: Possible set difference at position 3
07:11:11.306 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -   remove_tags = re.compile(
07:11:11.306 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -
        ScanCode (30.1.0)
Scanning packages with:
07:11:11.315 [main] INFO  org.ossreviewtoolkit.utils.common.ProcessCapture - Running '/opt/python/shims/scancode --version' in '/opt/python/shims'...
07:11:13.045 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - ScanCode version 30.1.0
07:11:13.046 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - ScanCode Output Format version 1.0.0
07:11:13.046 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - SPDX License list version 3.14
07:11:13.046 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -
07:11:13.046 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - /opt/python/versions/3.10.6/lib/python3.10/site-packages/cluecode/copyrights.py:3382: FutureWarning: Possible set difference at position 3
07:11:13.046 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -   remove_tags = re.compile(
07:11:13.047 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -
07:11:13.049 [main] INFO  org.ossreviewtoolkit.utils.common.ProcessCapture - Running '/opt/python/shims/scancode --version' in '/opt/python/shims'...
07:11:14.763 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - ScanCode version 30.1.0
07:11:14.763 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - ScanCode Output Format version 1.0.0
07:11:14.763 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - SPDX License list version 3.14
07:11:14.763 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -
07:11:14.764 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture - /opt/python/versions/3.10.6/lib/python3.10/site-packages/cluecode/copyrights.py:3382: FutureWarning: Possible set difference at position 3
07:11:14.764 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -   remove_tags = re.compile(
07:11:14.764 [main] DEBUG org.ossreviewtoolkit.utils.common.ProcessCapture -
        ScanCode (30.1.0)
07:11:14.791 [main] DEBUG org.ossreviewtoolkit.utils.ort.storage.LocalFileStorage - Creating directory '/home/ort/.ort/scanner/results' for local file storage.
07:11:14.799 [main] DEBUG org.ossreviewtoolkit.utils.ort.storage.LocalFileStorage - Creating directory '/home/ort/.ort/scanner/package_provenance' for local file storage.
07:11:14.802 [main] DEBUG org.ossreviewtoolkit.utils.ort.storage.LocalFileStorage - Creating directory '/home/ort/.ort/scanner/nested_provenance' for local file storage.
07:11:14.820 [main] DEBUG org.ossreviewtoolkit.utils.ort.storage.LocalFileStorage - Creating directory '/home/ort/.ort/scanner/archive' for local file storage.
Exception in thread "main" java.io.FileNotFoundException: /project/out/NPM/unknown/accepts/1.3.8 (Is a directory)
        at java.base/java.io.FileInputStream.open0(Native Method)
        at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
        at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
        at org.ossreviewtoolkit.model.HashAlgorithm.calculate(HashAlgorithm.kt:127)
        at org.ossreviewtoolkit.cli.utils.ExtensionsKt$readOrtResult$1.invoke(Extensions.kt:56)
        at org.apache.logging.log4j.kotlin.SuppliersKt$asLog4jSupplier$1.get(Suppliers.kt:21)
        at org.apache.logging.log4j.util.LambdaUtil.getMessage(LambdaUtil.java:91)
        at org.apache.logging.log4j.spi.AbstractLogger.logMessage(AbstractLogger.java:2008)
        at org.apache.logging.log4j.spi.AbstractLogger.logIfEnabled(AbstractLogger.java:1868)
        at org.apache.logging.log4j.kotlin.KotlinLogger.debug(KotlinLogger.kt:292)
        at org.ossreviewtoolkit.cli.utils.ExtensionsKt.readOrtResult(Extensions.kt:56)
        at org.ossreviewtoolkit.cli.commands.ScannerCommand.runScanners(ScannerCommand.kt:227)
        at org.ossreviewtoolkit.cli.commands.ScannerCommand.run(ScannerCommand.kt:155)
        at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:198)
        at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:211)
        at com.github.ajalt.clikt.parsers.Parser.parse(Parser.kt:18)
        at com.github.ajalt.clikt.core.CliktCommand.parse(CliktCommand.kt:400)
        at com.github.ajalt.clikt.core.CliktCommand.parse$default(CliktCommand.kt:397)
        at com.github.ajalt.clikt.core.CliktCommand.main(CliktCommand.kt:415)
        at com.github.ajalt.clikt.core.CliktCommand.main(CliktCommand.kt:440)
        at org.ossreviewtoolkit.cli.OrtMainKt.main(OrtMain.kt:82)
[root@devops-foss Node-Training]#

[nicorikken]

Thanks for reporting, could be that the ort user has no access to the /project directory? I'm not sure, I'd have to check.