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Workflow management system for the automated and distributed analysis of large-scale experimental data.

License: GNU General Public License v3.0

Shell 4.53% Perl 4.67% XS 2.44% Java 73.48% CSS 0.26% JavaScript 0.06% Python 0.06% HTML 14.49%
bioinformatics-pipeline workflow-management-system bioinformatics rna-seq-analysis cluster-computing big-data-analytics

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watchdog's Issues

FastClasspathScanner is outdated -- consider porting to ClassGraph

Your project, klugem/watchdog, depends on the outdated library FastClasspathScanner in the following source files:

FastClasspathScanner has been significantly reworked since the version your code depends upon:

  • a significant number of bugs have been fixed
  • some nontrivial API changes have been made to simplify and unify the API
  • FastClasspathScanner has been renamed to ClassGraph: https://github.com/classgraph/classgraph

ClassGraph is a significantly more robust library than FastClasspathScanner, and is more future-proof. All future development work will be focused on ClassGraph, and FastClasspathScanner will see no future development.

Please consider porting your code over to the new ClassGraph API, particularly if your project is in production or has downstream dependencies:

Feel free to close this bug report if this code is no longer in use. (You were sent this bug report because your project depends upon FastClasspathScanner, and has been starred by 5 users. Apologies if this bug report is not helpful.)

Missing license/attribution for java_external_lib JARs

Several of the files in java_external_lib have licenses that require them to be provided to the user, but they are missing or not easy to find in watchdog.

For instance commons-codec-1.10.jar is licensed under https://www.apache.org/licenses/LICENSE-2.0 and can be used and redistributed by GPL 3, but only according to clause 4 in the license:

  1. Redistribution. You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions (my emphasis):

4. Redistribution You may reproduce and distribute copies of the Work or Derivative Works thereof in any medium, with or without modifications, and in Source or Object form, provided that You meet the following conditions:
a) You must give any other recipients of the Work or Derivative Works a copy of this License; and
b) You must cause any modified files to carry prominent notices stating that You changed the files; and
c) You must retain, in the Source form of any Derivative Works that You distribute, all copyright, patent, trademark, and attribution notices from the Source form of the Work, excluding those notices that do not pertain to any part of the Derivative Works; and
d) If the Work includes a "NOTICE" text file as part of its distribution, then any Derivative Works that You distribute must include a readable copy of the attribution notices contained within such NOTICE file, excluding those notices that do not pertain to any part of the Derivative Works, in at least one of the following places: within a NOTICE text file distributed as part of the Derivative Works; within the Source form or documentation, if provided along with the Derivative Works; or, within a display generated by the Derivative Works, if and wherever such third-party notices normally appear. The contents of the NOTICE file are for informational purposes only and do not modify the License. You may add Your own attribution notices within Derivative Works that You distribute, alongside or as an addendum to the NOTICE text from the Work, provided that such additional attribution notices cannot be construed as modifying the License.
You may add Your own copyright statement to Your modifications and may provide additional or different license terms and conditions for use, reproduction, or distribution of Your modifications, or for any such Derivative Works as a whole, provided Your use, reproduction, and distribution of the Work otherwise complies with the conditions stated in this License.

I do find that LICENSE.txt and NOTICE.txt is contained inside some of the JAR files, e.g.:

(base) stain@biggie:~/src/watchdog/java_external_lib$ cat ./commons-io-2.4/META-INF/NOTICE.txt
Apache Commons IO
Copyright 2002-2012 The Apache Software Foundation

This product includes software developed by
The Apache Software Foundation (http://www.apache.org/).

..but not all of them. These are missing any kind of license at all: nanoHTTPD, jsch-0.1.54, jcommander-1.30, SGE_61_drmaa (and others?)

As some of these are a bit more obscure dependencies I don't know where they come from or their license.

Some only contain license hidden as part of their META-INF/maven pom files: slf4j-api-1.7.21 gson-2.8.5 etc.

The clause d) on NOTICE means you have to lift these to the root project, either add your own NOTICE, add their content to the documentation. The good news if the upstream JARs don't have any NOTICE.txt you probably just have to propagate their license text or leave it in place where it is.

It is probably still good to also lift their LICENSE.txt etc to licenses/ (which you may download) so users and devs know what is the license of the whole of watchdog, specially considering GPL 3 means you have committed to providing the source code for each of the JARs you are redistributing.

Missing build script

While the source code is included under java_source it is a bit odd that the git repository have loads of binaries, including the result of compiling.

There seems to be no build script (e.g. Maven) or IDE configuration (e.g. Eclipse) so there is no easy way to recompile and recreate the various files under jars. In particular it is hard to know what goes in which jar.

Could you create build scripts? If you use Maven dependencies you can avoid filling up java_external_lib in the source repository.

HTTP ui: "The link you used was only valid one time!" when using back button

When trying to use the HTTP status UI I go into a task from under "List failed tasks", and select "Display parameters". Then I go Back in the browser (Firefox) and click "Modify parameters" - but I get an error:

The link you used was only valid one time!"

I have to then go back to the front page and again select "List failed tasks".

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