cellprofiler / prokaryote Goto Github PK

CellProfiler’s Java dependencies

License: GNU General Public License v3.0

Java 99.56% Python 0.44%

prokaryote's Introduction

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. More information can be found in the CellProfiler Wiki.

What version of CellProfiler should I use?

We recommend the stable release of CellProfiler.

You can download a stable release for macOS and Windows from the CellProfiler website.

If you’re contributing or planning to contribute to CellProfiler, you should compile CellProfiler from source. Instructions for compiling CellProfiler on Linux, macOS and Windows are available from CellProfiler’s GitHub wiki.

If you’re the maintainer of a third-party CellProfiler module, you should use the nightly release of CellProfiler. You can download a nightly release for macOS and Windows from the CellProfiler website. Let us know if we’ve inadvertently broken your module by submitting a GitHub issue.

If you’re an enthusiastic CellProfiler user, you should try the beta release of CellProfiler. You can download a beta release for macOS and Windows from the CellProfiler website. Let us know if you encounter a bug by submitting a GitHub issue.

prokaryote's People

Contributors

Stargazers

Watchers

Forkers

annecarpenter hajaalin chris-allan bramalingam emilroz philloidin hinerm muhanadz

prokaryote's Issues

Update dependencies

Ensure the project uses the latest versions of its dependencies.

ImageJ

r

java.util.zip.ZipException: invalid CEN header (bad signature)

I'm unable to load any classes from the prokaryote-1.0.2.jar when I access it using the javabridge on the cluster, e.g. javabridge.JClassWrapper("loci.common.Location") gives me a classpath error. The jar does work on my machine with Java 8 installed.

Running javap on the jar produced by Maven results in the following error which makes me think that the zip structure of the jar is bad:

javap" -classpath target/prokaryote-1.0.2.jar loci.common.Location
java.util.zip.ZipException: invalid CEN header (bad signature)
    at java.util.zip.ZipFile.open(Native Method)
    at java.util.zip.ZipFile.<init>(ZipFile.java:127)
    at java.util.jar.JarFile.<init>(JarFile.java:136)
    at java.util.jar.JarFile.<init>(JarFile.java:100)
    at sun.tools.javap.JavapEnvironment.resolveclasspathhelper(JavapEnvironment.java:312)
    at sun.tools.javap.JavapEnvironment.resolveclasspath(JavapEnvironment.java:242)
    at sun.tools.javap.JavapEnvironment.resolvefilename(JavapEnvironment.java:197)
    at sun.tools.javap.JavapEnvironment.getFileInputStream(JavapEnvironment.java:133)
    at sun.tools.javap.Main.displayResults(Main.java:198)
    at sun.tools.javap.Main.perform(Main.java:61)
    at sun.tools.javap.Main.entry(Main.java:49)
    at sun.tools.javap.Main.main(Main.java:34)
ERROR:fatal exception
java.util.zip.ZipException: invalid CEN header (bad signature)
    at java.util.zip.ZipFile.open(Native Method)
    at java.util.zip.ZipFile.<init>(ZipFile.java:127)
    at java.util.jar.JarFile.<init>(JarFile.java:136)
    at java.util.jar.JarFile.<init>(JarFile.java:100)
    at sun.tools.javap.JavapEnvironment.resolveclasspathhelper(JavapEnvironment.java:312)
    at sun.tools.javap.JavapEnvironment.resolveclasspath(JavapEnvironment.java:242)
    at sun.tools.javap.JavapEnvironment.resolvefilename(JavapEnvironment.java:197)
    at sun.tools.javap.JavapEnvironment.getFileInputStream(JavapEnvironment.java:133)
    at sun.tools.javap.Main.displayResults(Main.java:198)
    at sun.tools.javap.Main.perform(Main.java:61)
    at sun.tools.javap.Main.entry(Main.java:49)
    at sun.tools.javap.Main.main(Main.java:34)
ERROR:fatal exception
java.util.zip.ZipException: invalid CEN header (bad signature)
    at java.util.zip.ZipFile.open(Native Method)
    at java.util.zip.ZipFile.<init>(ZipFile.java:127)
    at java.util.jar.JarFile.<init>(JarFile.java:136)
    at java.util.jar.JarFile.<init>(JarFile.java:100)
    at sun.tools.javap.JavapEnvironment.resolveclasspathhelper(JavapEnvironment.java:312)
    at sun.tools.javap.JavapEnvironment.resolveclasspath(JavapEnvironment.java:242)
    at sun.tools.javap.JavapEnvironment.resolvefilename(JavapEnvironment.java:197)
    at sun.tools.javap.JavapEnvironment.getFileInputStream(JavapEnvironment.java:133)
    at sun.tools.javap.Main.displayResults(Main.java:198)
    at sun.tools.javap.Main.perform(Main.java:61)
    at sun.tools.javap.Main.entry(Main.java:49)
    at sun.tools.javap.Main.main(Main.java:34)
ERROR:fatal exception
ERROR:Could not find loci.common.Location

LoadData fails with OMERO 5.4

Hi,

I am with the PhenomicAI group and we are trying to get Cell Profiler work with OMERO.server 5.4.8. This issue is the same nature with issue #33. The current prokaryote library only supports Blitz up to 5.3.4.

Running cell profiler with these decencies create a "Ice.UnmarshalOutOfBoundsException"

Thanks,
Frank

Support Java 9

From CellProfiler/CellProfiler#3465:

I have no idea how big or complex an issue this is, and I'm not pushing for it to have a particular timeline, but it's popping up time-to-time in the forum so I thought if nothing else we should have a ticket for it. I didn't see one already open but feel free to close if a duplicate.

POM errors while building Prokaryote with Maven 3.5.0

On a machine with Oracle Java 1.8 installed, and using Miniconda python installation, I create an environment to build prokaryote:

conda create -n _b_prokaryote python setuptools maven --yes
source _b_prokaryote

Then, I clone CellProfiler/prokaryote repo, and while using revision cfeb877 execute mvn clean package. I get the following error:

(_b_prokaryote) [11:51:46 fxsatlin04 prokaryote]$ mvn clean package
[INFO] Scanning for projects...
Downloading: https://oss.sonatype.org/content/repositories/releases/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://maven.imagej.net/content/groups/public/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://artifacts.openmicroscopy.org/artifactory/ome.releases/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://artifacts.openmicroscopy.org/artifactory/ome.snapshots/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://artifacts.openmicroscopy.org/artifactory/springsource-release/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://repository.springsource.com/maven/bundles/release/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://repository.springsource.com/maven/bundles/external/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://repository.springsource.com/maven/libraries/release/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: http://repository.springsource.com/maven/libraries/external/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
Downloading: https://repo.maven.apache.org/maven2/org/scijava/pom-scijava/10.4.1/pom-scijava-10.4.1.pom
[ERROR] [ERROR] Some problems were encountered while processing the POMs:
[FATAL] Non-resolvable parent POM for org.cellprofiler:prokaryote:2.3.0: Could not transfer artifact org.scijava:pom-scijava:pom:10.4.1 from/to sonatype-nexus-releases (https://oss.sonatype.org/content/repositories/releases): Connect to oss.sonatype.org:443 [oss.sonatype.org/107.23.166.173, oss.sonatype.org/34.199.111.237] failed: Connection timed out (Connection timed out) and 'parent.relativePath' points at wrong local POM @ line 245, column 13
 @ 
[ERROR] The build could not read 1 project -> [Help 1]
[ERROR]   
[ERROR]   The project org.cellprofiler:prokaryote:2.3.0 (/localdisk/work/opavlyk/projects/cellprofiler/sources/prokaryote/pom.xml) has 1 error
[ERROR]     Non-resolvable parent POM for org.cellprofiler:prokaryote:2.3.0: Could not transfer artifact org.scijava:pom-scijava:pom:10.4.1 from/to sonatype-nexus-releases (https://oss.sonatype.org/content/repositories/releases): Connect to oss.sonatype.org:443 [oss.sonatype.org/107.23.166.173, oss.sonatype.org/34.199.111.237] failed: Connection timed out (Connection timed out) and 'parent.relativePath' points at wrong local POM @ line 245, column 13 -> [Help 2]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/ProjectBuildingException
[ERROR] [Help 2] http://cwiki.apache.org/confluence/display/MAVEN/UnresolvableModelException

The conda environment I used:

(_b_prokaryote) [12:20:44 fxsatlin04 prokaryote]$ conda list --explicit
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
@EXPLICIT
https://repo.continuum.io/pkgs/free/linux-64/certifi-2016.2.28-py36_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/maven-3.5.0-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/openjdk-8.0.121-1.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/openssl-1.0.2l-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/pip-9.0.1-py36_1.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/python-3.6.2-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/readline-6.2-2.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/setuptools-36.4.0-py36_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/sqlite-3.13.0-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/tk-8.5.18-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/wheel-0.29.0-py36_0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/xz-5.2.3-0.tar.bz2
https://repo.continuum.io/pkgs/free/linux-64/zlib-1.2.11-0.tar.bz2

I noticed that Travis is using an older version of Maven, specifically 3.3.9, but I am not sure if it the version of Maven that is the problem.

Please advise.

Use AppendingTransformer to fix ImageJ magic

The Maven shaded plugin has an AppendingTransformer that solves a problem we have with multiple copies of META-INF/json/org.scijava.plugin.Plugin. All of these need to be concatenated.

Combination of bdist_wheel + pip install does not install prokaryote.jar

I did the following:

python setup.py bdist_wheel
pip install dist/prokaryote-1.0.6-py2-none-any.whl

The prokaryote directory does not contain prokaryote.jar

pip likes to use its cache, building the wheel and then installing the wheel, so I have seen this on Travis and on the Mac Jenkins.

.travis.yml shouldn’t use a hardcoded version

LoadData error with OMERO 5.3

Hi,
Since our upgrade to OMERO 5.3 we can't connect to it via the LoadData module in CellProfiler. After discussing with people from OME and reading some issues about it, it seems that it's because prokaryote is only working for 5.2.

Do you guys have any working version for 5.3 available ? Or any version working for all the future versions as well ? I read somewhere about using python readers ?

Thanks for your help.

2.3.2 release

The current version (2.3.1) available on PyPI is broken in a series of ways. A release needs to be made and pushed to PyPI. OMERO compatibility, at a minimum, is out of the box broken at present.

This would not be such a problem except CellProfiler 2.2.x will NOT start up when this version of the dependency is installed. Installation of 2.3.1 is the current behaviour when installing 2.2.x from source. #38 should be merged to restore this compatibility before releasing the current master.

/cc @lguerard, @ehrenfeu

pip uninstall leaves prokaryote.jar behind

To reproduce:

pip install prokaryote
pip uninstall prokaryote

site-packages/prokaryote still has prokaryote.jar. Perhaps this is cosmetic - a subsequent pip install prokaryote successfully overwrote the old version.

Perhaps downloading should happen as part of the "build" command, targeting perhaps "build/lib/prokaryote" as the directory and the build step might add the files it creates to package data?

Upgrade OME dependencies to 5.5.3

OME dependencies must be consistent with the version of loci_tools.jar packaged in python-bioformats. Both should be upgraded to the latest stable version, which is 5.5.3.

See: CellProfiler/python-bioformats#82

Cellprofiler generates a lot of java warnings on startup due to ImageJ

Hi,

I installed CellProfiler 2.2.0 using Prokaryote 1.0.10. When I start cellprofiler, then I receive a lot of java warnings and exceptions:

[sfux@euler01 ~]$ cellprofiler -L 20
Picked up _JAVA_OPTIONS: -XX:ParallelGCThreads=1
java.lang.IllegalArgumentException: Cannot handle replace call to list in ij.Menus's public static synchronized java.lang.String[] getPlugins()
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:725)
at net.imagej.patcher.CodeHacker.replaceCallInMethod(CodeHacker.java:650)
at net.imagej.patcher.LegacyExtensions.addExtraPlugins(LegacyExtensions.java:477)
at net.imagej.patcher.LegacyExtensions.injectHooks(LegacyExtensions.java:175)
at net.imagej.patcher.LegacyInjector.inject(LegacyInjector.java:308)
at net.imagej.patcher.LegacyInjector.injectHooks(LegacyInjector.java:109)
at net.imagej.patcher.LegacyEnvironment.initialize(LegacyEnvironment.java:101)
at net.imagej.patcher.LegacyEnvironment.applyPatches(LegacyEnvironment.java:495)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:397)
at net.imagej.patcher.LegacyInjector.preinit(LegacyInjector.java:376)
at net.imagej.patcher.JavaAgent.preinit(JavaAgent.java:147)
at net.imagej.patcher.JavaAgent.premain(JavaAgent.java:95)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at sun.instrument.InstrumentationImpl.loadClassAndStartAgent(InstrumentationImpl.java:386)
at sun.instrument.InstrumentationImpl.loadClassAndCallPremain(InstrumentationImpl.java:401)

According to imagej/tutorials#24 this problem can be solved by updating ImageJ. Would it be possible to bundle a newer version of ImageJ with prokaryote ?

Thank you.

Best regards

Sam

Need to add a pre-main entry point for the ij1-patcher in the manifest

See https://github.com/imagej/ij1-patcher/blob/master/pom.xml#L48
See CellProfiler/CellProfiler#1683