From: Egon W. <ego...@gm...> - 2012-05-21 10:17:08
|
Hi all, after a slip on my side this morning where I accidentally deleted my local cdk-jchempaint/ development repository, I recovered it from other repositories and patches on SourceForge, I just uploaded release 26 of the CDK-JChemPaint patch: https://sourceforge.net/projects/cdk/files/CDK-JChemPaint/26/ And the source code can also be found in my GitHub repository: https://github.com/egonw/cdk/commits/cdk-jchempaint-26 This CDK-JChemPaint patch is against CDK 1.4.10 and has additional rendering and controller functionality. To make it clear, this patch is not the JChemPaint applet, application code. The major difference with release 25 is that the renderextra module is now part of the CDK library itself. What remains for this patch now, is to clean up the remaining modules, that for the controller API basic implementation, and the rendering extension for controller feedback, but also the modules to SWT and SVG. Other than that, there are also a few core problems with the renderer, the most prominent one being to misuse of the scaling factor, which was needed to get the fonts to size properly. It would be great if that gets fixed. But otherwise, we could really use help with writing JavaDoc, unit tests, and doing general code cleanup. I also like to see more SWT code from Bioclips integrated into the renderswt module, and finally, if someone like to get a CDK-JChemPaint based rendering working on Android, please join in! On the JChemPaint applet/application side, it would be great if someone can help out with backporting patches from the fork of CDK-JChemPaint made for the applet/application back into the CDK and/or CDK-JChemPaint patch. Oh, and if you are not a experienced programmer, but still love this project, we can also use help with documentation for both users and developers... like which repository to use when... Greetings, Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: Nina J. <jel...@gm...> - 2012-05-21 15:48:53
|
Hi All, CDK 1.4.10, CDK-JChemPaint and JChemPaint compiled with CDK 1.4.10 is now deployed at the maven repository CDK 1.4.10 http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~~1.4.10~~ CDK-JChemPaint 26 http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~cdk-jchempaint~26~~ JChemPaint http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~jchempaint-nodeps-cdk-1.4.10~~~ Best regards, Nina On 21 May 2012 13:16, Egon Willighagen <ego...@gm...> wrote: > Hi all, > > after a slip on my side this morning where I accidentally deleted my > local cdk-jchempaint/ development repository, I recovered it from > other repositories and patches on SourceForge, I just uploaded release > 26 of the CDK-JChemPaint patch: > > https://sourceforge.net/projects/cdk/files/CDK-JChemPaint/26/ > > And the source code can also be found in my GitHub repository: > > https://github.com/egonw/cdk/commits/cdk-jchempaint-26 > > This CDK-JChemPaint patch is against CDK 1.4.10 and has additional > rendering and controller functionality. To make it clear, this patch > is not the JChemPaint applet, application code. > > The major difference with release 25 is that the renderextra module is > now part of the CDK library itself. What remains for this patch now, > is to clean up the remaining modules, that for the controller API > basic implementation, and the rendering extension for controller > feedback, but also the modules to SWT and SVG. > > Other than that, there are also a few core problems with the renderer, > the most prominent one being to misuse of the scaling factor, which > was needed to get the fonts to size properly. It would be great if > that gets fixed. But otherwise, we could really use help with writing > JavaDoc, unit tests, and doing general code cleanup. > > I also like to see more SWT code from Bioclips integrated into the > renderswt module, and finally, if someone like to get a CDK-JChemPaint > based rendering working on Android, please join in! > > On the JChemPaint applet/application side, it would be great if > someone can help out with backporting patches from the fork of > CDK-JChemPaint made for the applet/application back into the CDK > and/or CDK-JChemPaint patch. > > Currently JChemPaint compiles with CDK 1.4.10 with a single deprecation warning, which is expected (this is an improvement over CDK 1.4.9). compile-jcp: [echo] Compiling JChemPaint classes. [mkdir] Created dir: /home/me/jcp/20120521/jchempaint/trunk/dist/classes [javac] /home/me/jcp/20120521/jchempaint/trunk/build.xml:233: warning: 'includeantruntime' was not set, defaulting to build.sysclasspath=last; set to false for repeatable builds [javac] Compiling 262 source files to /home/me/jcp/20120521/jchempaint/trunk/dist/classes [javac] /home/me/jcp/20120521/jchempaint/trunk/src/main/org/openscience/jchempaint/controller/ControllerHub.java:67: warning: [deprecation] org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder in org.openscience.cdk.nonotify has been deprecated [javac] import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder; [javac] ^ [javac] /home/me/jcp/20120521/jchempaint/trunk/src/main/org/openscience/jchempaint/controller/ControllerHub.java:1234: warning: [deprecation] org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder in org.openscience.cdk.nonotify has been deprecated [javac] IChemObjectBuilder builder = NoNotificationChemObjectBuilder [javac] ^ [javac] Note: Some input files use unchecked or unsafe operations. [javac] Note: Recompile with -Xlint:unchecked for details. [javac] 2 warnings [copy] Copying 1 file to /home/me/jcp/20120521/jchempaint/trunk/src/main/org/openscience/jchempaint/resources/userhelp_jcp [copy] Copying 1 file to /home/me/jcp/20120521/jchempaint/trunk/src/main/org/openscience/jchempaint/resources/u > Oh, and if you are not a experienced programmer, but still love this > project, we can also use help with documentation for both users and > developers... like which repository to use when... > > Greetings, > > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-jchempaint mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-jchempaint > |
From: Tomas P. <pl...@oi...> - 2012-05-22 00:49:15
|
Hi Nina, Thanks for the update! I got this error after adding cdk-all-1.4.10 as a dependency to our project: [ERROR] Failed to execute goal on project MZmine: Could not resolve dependencies for project net.sf.mzmine:MZmine:jar:2.9: Could not find artifact org.openscience.cdk:cdk-all:jar:1.4.10 in ambit-plovdiv (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases) -> [Help 1] It seems the pom.xml files are in the repository, but no jar files for the CDK, only for jchempaint (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases/org/openscience/cdk/) Are you going to add the CDK jar files later, or is this on purpose? Best, Tomas On May 22, 2012, at 12:48 AM, Nina Jeliazkova wrote: Hi All, CDK 1.4.10, CDK-JChemPaint and JChemPaint compiled with CDK 1.4.10 is now deployed at the maven repository CDK 1.4.10 http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~~1.4.10~~ CDK-JChemPaint 26 http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~cdk-jchempaint~26~~ JChemPaint http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~jchempaint-nodeps-cdk-1.4.10~~~ Best regards, Nina =============================================== Tomáš Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan TEL: +81-98-966-8684 Fax: +81-98-966-2890 |
From: Tomas P. <pl...@oi...> - 2012-05-22 02:26:48
|
Ah, nevermind, I found the cause of the problem. The CDK artifacts are published to the "thirdparty" repository, while the jchempaint artifacts are published to the "releases" repository. If you want to use both, you need to specify both repositories in your pom.xml: <repository> <!-- CDK repository --> <id>ambit-plovdiv-thirdparty</id> <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty</url> </repository> <repository> <!-- JChemPaint repository --> <id>ambit-plovdiv-releases</id> <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases</url> </repository> Best regards, Tomas On May 22, 2012, at 9:49 AM, Tomas Pluskal wrote: > Hi Nina, > > Thanks for the update! > > I got this error after adding cdk-all-1.4.10 as a dependency to our project: > [ERROR] Failed to execute goal on project MZmine: Could not resolve dependencies for project net.sf.mzmine:MZmine:jar:2.9: Could not find artifact org.openscience.cdk:cdk-all:jar:1.4.10 in ambit-plovdiv (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases) -> [Help 1] > > It seems the pom.xml files are in the repository, but no jar files for the CDK, only for jchempaint (http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases/org/openscience/cdk/) > > Are you going to add the CDK jar files later, or is this on purpose? > > Best, > > Tomas > > > On May 22, 2012, at 12:48 AM, Nina Jeliazkova wrote: > >> Hi All, >> >> CDK 1.4.10, CDK-JChemPaint and JChemPaint compiled with CDK 1.4.10 is now deployed at the maven repository >> >> CDK 1.4.10 >> http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~~1.4.10~~ >> >> CDK-JChemPaint 26 >> http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~cdk-jchempaint~26~~ >> >> JChemPaint >> http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~jchempaint-nodeps-cdk-1.4.10~~~ >> >> Best regards, >> Nina >> > > > =============================================== > Tomáš Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel =============================================== Tomáš Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan TEL: +81-98-966-8684 Fax: +81-98-966-2890 |
From: Egon W. <ego...@gm...> - 2012-05-26 08:12:14
|
Hi all, On Tue, May 22, 2012 at 10:37 AM, Nina Jeliazkova <jel...@gm...> wrote: > On 22 May 2012 11:31, Tomas Pluskal <pl...@oi...> wrote: Did your maven work result in patches for the CDK? Please make sure to file them in the tracker then, otherwise they might get lost... Egon -- Dr E.L. Willighagen Postdoctoral Researcher Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Homepage: http://egonw.github.com/ LinkedIn: http://se.linkedin.com/in/egonw Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers |
From: <ra...@ar...> - 2012-06-10 08:14:13
|
As I'm now looking into cdk testing, I see I have need of a pom.xml or other automatized or scripted means of batch-testing cdk. Can someone with a solution please publish it? Regards, ralf On Sat, May 26, 2012 at 10:11:46AM +0200, Egon Willighagen wrote: > On Tue, May 22, 2012 at 10:37 AM, Nina Jeliazkova > <jel...@gm...> wrote: > > On 22 May 2012 11:31, Tomas Pluskal <pl...@oi...> wrote: > > Did your maven work result in patches for the CDK? Please make sure to > file them in the tracker then, otherwise they might get lost... |
From: Nina J. <jel...@gm...> - 2012-05-22 06:11:39
|
Hi Tomas, On 22 May 2012 05:26, Tomas Pluskal <pl...@oi...> wrote: > Ah, nevermind, I found the cause of the problem. > > The CDK artifacts are published to the "thirdparty" repository, while the > jchempaint artifacts are published to the "releases" repository. > If you want to use both, you need to specify both repositories in your > pom.xml: > Yes, my fault, JCP was meant to be in the third party as well. I'll add it there as well. Regarding cdk-all jar not found, this is normal, cdk-all is not a jar, it is a pom dependency - basically a placeholder for the multimodule cdk project. Neither it was a jar dependency in the previous versions. If you are using the single jar, it should be org.openscience.cdk:cdk-pure:1.4.10; otherwise add org.openscience.cdk: cdk-*:1.4.10 for the individual jars , e.g. org.openscience.cdk: cdk-core:1.4.10 org.openscience.cdk: cdk-smiles:1.4.10 ... Regards, Nina > <repository> > <!-- CDK repository --> > <id>ambit-plovdiv-thirdparty</id> > <url> > http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty > </url> > </repository> > <repository> > <!-- JChemPaint repository --> > <id>ambit-plovdiv-releases</id> > <url> > http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases</url> > </repository> > > Best regards, > > Tomas > > > On May 22, 2012, at 9:49 AM, Tomas Pluskal wrote: > > > Hi Nina, > > > > Thanks for the update! > > > > I got this error after adding cdk-all-1.4.10 as a dependency to our > project: > > [ERROR] Failed to execute goal on project MZmine: Could not resolve > dependencies for project net.sf.mzmine:MZmine:jar:2.9: Could not find > artifact org.openscience.cdk:cdk-all:jar:1.4.10 in ambit-plovdiv ( > http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases) -> > [Help 1] > > > > It seems the pom.xml files are in the repository, but no jar files for > the CDK, only for jchempaint ( > http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/releases/org/openscience/cdk/ > ) > > > > Are you going to add the CDK jar files later, or is this on purpose? > > > > Best, > > > > Tomas > > > > > > On May 22, 2012, at 12:48 AM, Nina Jeliazkova wrote: > > > >> Hi All, > >> > >> CDK 1.4.10, CDK-JChemPaint and JChemPaint compiled with CDK 1.4.10 is > now deployed at the maven repository > >> > >> CDK 1.4.10 > >> > http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~~1.4.10~~ > >> > >> CDK-JChemPaint 26 > >> > http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~cdk-jchempaint~26~~ > >> > >> JChemPaint > >> > http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;gav~org.openscience.cdk~jchempaint-nodeps-cdk-1.4.10~~~ > >> > >> Best regards, > >> Nina > >> > > > > > > =============================================== > > Tomáš Pluskal > > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate > University > > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > > TEL: +81-98-966-8684 > > Fax: +81-98-966-2890 > > > > > ------------------------------------------------------------------------------ > > Live Security Virtual Conference > > Exclusive live event will cover all the ways today's security and > > threat landscape has changed and how IT managers can respond. Discussions > > will include endpoint security, mobile security and the latest in malware > > threats. > http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ > > Cdk-devel mailing list > > Cdk...@li... > > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > =============================================== > Tomáš Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate > University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > |
From: Nina J. <jel...@gm...> - 2012-05-22 06:45:13
|
On 22 May 2012 09:11, Nina Jeliazkova <jel...@gm...> wrote: > Hi Tomas, > > > On 22 May 2012 05:26, Tomas Pluskal <pl...@oi...> wrote: > >> Ah, nevermind, I found the cause of the problem. >> >> The CDK artifacts are published to the "thirdparty" repository, while the >> jchempaint artifacts are published to the "releases" repository. >> If you want to use both, you need to specify both repositories in your >> pom.xml: >> > > Yes, my fault, JCP was meant to be in the third party as well. I'll add it > there as well. > > You should be able to use http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty only for both CDK and JChempaint now. <repository> <id>ambit-plovdiv-thirdparty</id> <url> http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty</url> </repository> Best regards, Nina |
From: Nina J. <jel...@gm...> - 2012-06-11 16:36:47
|
On 10 June 2012 11:10, <ra...@ar...> wrote: > As I'm now looking into cdk testing, I see I have need of a pom.xml > or other automatized or scripted means of batch-testing cdk. > > Can someone with a solution please publish it? > The CDK ant based build does run tests - or do you need to build and test from maven ? The maven project [1] is only used for deployment into a repository, not for build / test (yet). Regards, Nina [1] https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/cdk-maven > Regards, > ralf > > On Sat, May 26, 2012 at 10:11:46AM +0200, Egon Willighagen wrote: >> On Tue, May 22, 2012 at 10:37 AM, Nina Jeliazkova >> <jel...@gm...> wrote: >> > On 22 May 2012 11:31, Tomas Pluskal <pl...@oi...> wrote: >> >> Did your maven work result in patches for the CDK? Please make sure to >> file them in the tracker then, otherwise they might get lost... > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: <ra...@ar...> - 2012-06-11 17:51:03
|
On Mon, Jun 11, 2012 at 07:36:36PM +0300, Nina Jeliazkova wrote: > The CDK ant based build does run tests - or do you need to build and > test from maven ? The maven project [1] is only used for deployment > into a repository, not for build / test (yet). I first thought maven could be of use with eclipse development, then I tried sonar which would give metrics but somehow not test. I completely forgot ant for testing. Thanks. |
From: Tomas P. <pl...@oi...> - 2012-05-22 06:59:11
|
Thanks Nina! I noticed that some parts of CDK have dependencies (e.g. jgrapht, jama, log4j, xerces etc.), but these are currently not listed in the pom.xml of cdk-pure. Have you thought about that? Tomas On May 22, 2012, at 3:45 PM, Nina Jeliazkova wrote: You should be able to use http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty only for both CDK and JChempaint now. <repository> <id>ambit-plovdiv-thirdparty</id> <url>http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty</url> </repository> Best regards, Nina =============================================== Tomáš Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan TEL: +81-98-966-8684 Fax: +81-98-966-2890 |
From: Nina J. <jel...@gm...> - 2012-05-22 07:23:34
|
Hi Tomas, On 22 May 2012 09:58, Tomas Pluskal <pl...@oi...> wrote: > Thanks Nina! > > I noticed that some parts of CDK have dependencies (e.g. jgrapht, jama, > log4j, xerces etc.), but these are currently not listed in the pom.xml > of cdk-pure. > Have you thought about that? > > They are listed in cdk-* etc. artifacts. We are not using cdk-pure (imho it defeats the purpose of maven dependencies to use the entire blob at once) , so it gets less attention :) You could help here, if you wish. The CDK has own mechanism of defining dependencies in *.cdkdepends files and *.libdepends. The maven poms I am using had been created manually some time ago from *.cdkdepends files and *.libdepends. The real solution would be to have a script (shell, ant, doesn't matter) to read *.cdkdepends files and *.libdepends and update the pom.xml files. I think there was a parallel effort from somebody else on the list , but these had not been synced. Regards, Nina > Tomas > > On May 22, 2012, at 3:45 PM, Nina Jeliazkova wrote: > > > You should be able to use > http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty only > for both CDK and JChempaint now. > > <repository> > <id>ambit-plovdiv-thirdparty</id> > <url> > http://ambit.uni-plovdiv.bg:8083/nexus/content/repositories/thirdparty > </url> > </repository> > > Best regards, > Nina > > > > =============================================== > Tomáš Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate > University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > |
From: Tomas P. <pl...@oi...> - 2012-05-22 07:52:26
|
> They are listed in cdk-* etc. artifacts. We are not using cdk-pure (imho it defeats the purpose of maven dependencies to use the entire blob at once) , so it gets less attention :) > > You could help here, if you wish. Thanks, I will take a look at it. In the meantime, is there any way how to add all cdk modules including their dependencies to my maven project? I was hoping that adding <dependency> <groupId>org.openscience.cdk</groupId> <artifactId>cdk-all</artifactId> <version>1.4.10</version> <type>pom</type> </dependency> to my pom.xml would download all the jar files of all CDK modules, but it did not happen. Do I need to list the individual modules one by one? Best, Tomas =============================================== Tomáš Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan TEL: +81-98-966-8684 Fax: +81-98-966-2890 |
From: Nina J. <jel...@gm...> - 2012-05-22 08:08:21
|
On 22 May 2012 10:52, Tomas Pluskal <pl...@oi...> wrote: > > They are listed in cdk-* etc. artifacts. We are not using cdk-pure > (imho it defeats the purpose of maven dependencies to use the entire blob > at once) , so it gets less attention :) > > > > You could help here, if you wish. > > Thanks, I will take a look at it. > > In the meantime, is there any way how to add all cdk modules including > their dependencies to my maven project? > <dependency> <groupId>org.openscience.cdk</groupId> <artifactId>cdk-pure</artifactId> <version>1.4.10</version> <type>jar</type> </dependency> (but it doesn't have the transitive dependencies defined, sorry - this should be corrected) > I was hoping that adding > > <dependency> > <groupId>org.openscience.cdk</groupId> > <artifactId>cdk-all</artifactId> > <version>1.4.10</version> > <type>pom</type> > </dependency> > > to my pom.xml would download all the jar files of all CDK modules, but it > did not happen. > > Do I need to list the individual modules one by one? > That's what we do, and you probably don't need all the modules. You could start adding cdk-core, cdk-smiles, etc. , they all have their dependencies defined. Your IDE / compiler will for sure say which modules /classes are missing. Nexus has classname search, so it is possible to figure out which module is missing, without even looking up the source. http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-search;classname~IAtomContainer For example if you are not using RDF serialisation, it doesn't make sense to add cdk-iordf ; if not generating 3D structures, it's not necessary to add cdk-builder3d, etc. Besides, some of the modules are actually different implementations of the same interfaces (e.g. cdk-data & cdk-silent & cdk-nonotify) and one normally needs only one of each. I should probably be explaining all this at some online resource, and I will, but no earlier than the end of this week. Best regards, Nina > > Best, > > Tomas > > > > =============================================== > Tomáš Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate > University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > |
From: John M. <joh...@gm...> - 2012-05-22 08:04:46
|
Hi Tomas, Yep you have to add them one by one. They are quite tightly coupled though so you'll find you'll inherit most of them very quickly (but should declare the ones you're using). As a start you'll probably always need core, standard, data, io and extra. > <dependency> > <groupId>org.openscience.cdk</groupId> > <artifactId>cdk-core</artifactId> > <version>${cdk.version}</version> > </dependency> > <dependency> > <groupId>org.openscience.cdk</groupId> > <artifactId>cdk-io</artifactId> > <version>${cdk.version}</version> > </dependency> > <dependency> > <groupId>org.openscience.cdk</groupId> > <artifactId>cdk-standard</artifactId> > <version>${cdk.version}</version> > </dependency> > <dependency> > <groupId>org.openscience.cdk</groupId> > <artifactId>cdk-extra</artifactId> > <version>${cdk.version}</version> > </dependency> > <dependency> > <groupId>org.openscience.cdk</groupId> > <artifactId>cdk-data</artifactId> > <version>${cdk.version}</version> > </dependency> you can put a property in your parent pom to centralise the version also (otherwise there is a "versions" plugin) > <properties> > <cdk.version>1.4.9</cdk.version> > </properties> Hope that helps, On 22 May 2012, at 08:52, Tomas Pluskal wrote: >> They are listed in cdk-* etc. artifacts. We are not using cdk-pure (imho it defeats the purpose of maven dependencies to use the entire blob at once) , so it gets less attention :) >> >> You could help here, if you wish. > > Thanks, I will take a look at it. > > In the meantime, is there any way how to add all cdk modules including their dependencies to my maven project? > I was hoping that adding > > <dependency> > <groupId>org.openscience.cdk</groupId> > <artifactId>cdk-all</artifactId> > <version>1.4.10</version> > <type>pom</type> > </dependency> > > to my pom.xml would download all the jar files of all CDK modules, but it did not happen. > > Do I need to list the individual modules one by one? > > Best, > > Tomas > > > > =============================================== > Tomáš Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Tomas P. <pl...@oi...> - 2012-05-22 08:32:01
|
Thanks a lot, this is indeed very neat and works nicely. Does anybody have a complete list of CDK modules that JChemPaint currently depends on? Best, Tomas On May 22, 2012, at 5:04 PM, John May wrote: > Hi Tomas, > > Yep you have to add them one by one. > They are quite tightly coupled though so you'll find you'll inherit most of them very quickly (but should declare the ones you're using). > > As a start you'll probably always need core, standard, data, io and extra. > > >> <dependency> >> <groupId>org.openscience.cdk</groupId> >> <artifactId>cdk-core</artifactId> >> <version>${cdk.version}</version> >> </dependency> >> <dependency> >> <groupId>org.openscience.cdk</groupId> >> <artifactId>cdk-io</artifactId> >> <version>${cdk.version}</version> >> </dependency> >> <dependency> >> <groupId>org.openscience.cdk</groupId> >> <artifactId>cdk-standard</artifactId> >> <version>${cdk.version}</version> >> </dependency> >> <dependency> >> <groupId>org.openscience.cdk</groupId> >> <artifactId>cdk-extra</artifactId> >> <version>${cdk.version}</version> >> </dependency> >> <dependency> >> <groupId>org.openscience.cdk</groupId> >> <artifactId>cdk-data</artifactId> >> <version>${cdk.version}</version> >> </dependency> > > you can put a property in your parent pom to centralise the version also (otherwise there is a "versions" plugin) > >> <properties> >> <cdk.version>1.4.9</cdk.version> >> </properties> > > > > Hope that helps, > > > On 22 May 2012, at 08:52, Tomas Pluskal wrote: > >>> They are listed in cdk-* etc. artifacts. We are not using cdk-pure (imho it defeats the purpose of maven dependencies to use the entire blob at once) , so it gets less attention :) >>> >>> You could help here, if you wish. >> >> Thanks, I will take a look at it. >> >> In the meantime, is there any way how to add all cdk modules including their dependencies to my maven project? >> I was hoping that adding >> >> <dependency> >> <groupId>org.openscience.cdk</groupId> >> <artifactId>cdk-all</artifactId> >> <version>1.4.10</version> >> <type>pom</type> >> </dependency> >> >> to my pom.xml would download all the jar files of all CDK modules, but it did not happen. >> >> Do I need to list the individual modules one by one? >> >> Best, >> >> Tomas >> >> >> >> =============================================== >> Tomáš Pluskal >> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University >> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan >> TEL: +81-98-966-8684 >> Fax: +81-98-966-2890 >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel =============================================== Tomáš Pluskal G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan TEL: +81-98-966-8684 Fax: +81-98-966-2890 |
From: John M. <joh...@gm...> - 2012-05-22 08:37:05
|
I've just sent a mail with this but it's awaiting approval. I'll forward to you separately. J On 22 May 2012, at 09:31, Tomas Pluskal wrote: > Thanks a lot, this is indeed very neat and works nicely. > > Does anybody have a complete list of CDK modules that JChemPaint currently depends on? > > Best, > > Tomas > > > On May 22, 2012, at 5:04 PM, John May wrote: > >> Hi Tomas, >> >> Yep you have to add them one by one. >> They are quite tightly coupled though so you'll find you'll inherit most of them very quickly (but should declare the ones you're using). >> >> As a start you'll probably always need core, standard, data, io and extra. >> >> >>> <dependency> >>> <groupId>org.openscience.cdk</groupId> >>> <artifactId>cdk-core</artifactId> >>> <version>${cdk.version}</version> >>> </dependency> >>> <dependency> >>> <groupId>org.openscience.cdk</groupId> >>> <artifactId>cdk-io</artifactId> >>> <version>${cdk.version}</version> >>> </dependency> >>> <dependency> >>> <groupId>org.openscience.cdk</groupId> >>> <artifactId>cdk-standard</artifactId> >>> <version>${cdk.version}</version> >>> </dependency> >>> <dependency> >>> <groupId>org.openscience.cdk</groupId> >>> <artifactId>cdk-extra</artifactId> >>> <version>${cdk.version}</version> >>> </dependency> >>> <dependency> >>> <groupId>org.openscience.cdk</groupId> >>> <artifactId>cdk-data</artifactId> >>> <version>${cdk.version}</version> >>> </dependency> >> >> you can put a property in your parent pom to centralise the version also (otherwise there is a "versions" plugin) >> >>> <properties> >>> <cdk.version>1.4.9</cdk.version> >>> </properties> >> >> >> >> Hope that helps, >> >> >> On 22 May 2012, at 08:52, Tomas Pluskal wrote: >> >>>> They are listed in cdk-* etc. artifacts. We are not using cdk-pure (imho it defeats the purpose of maven dependencies to use the entire blob at once) , so it gets less attention :) >>>> >>>> You could help here, if you wish. >>> >>> Thanks, I will take a look at it. >>> >>> In the meantime, is there any way how to add all cdk modules including their dependencies to my maven project? >>> I was hoping that adding >>> >>> <dependency> >>> <groupId>org.openscience.cdk</groupId> >>> <artifactId>cdk-all</artifactId> >>> <version>1.4.10</version> >>> <type>pom</type> >>> </dependency> >>> >>> to my pom.xml would download all the jar files of all CDK modules, but it did not happen. >>> >>> Do I need to list the individual modules one by one? >>> >>> Best, >>> >>> Tomas >>> >>> >>> >>> =============================================== >>> Tomáš Pluskal >>> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University >>> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan >>> TEL: +81-98-966-8684 >>> Fax: +81-98-966-2890 >>> >>> >>> ------------------------------------------------------------------------------ >>> Live Security Virtual Conference >>> Exclusive live event will cover all the ways today's security and >>> threat landscape has changed and how IT managers can respond. Discussions >>> will include endpoint security, mobile security and the latest in malware >>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >>> _______________________________________________ >>> Cdk-devel mailing list >>> Cdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >> >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel > > =============================================== > Tomáš Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Nina J. <jel...@gm...> - 2012-05-22 08:37:23
|
On 22 May 2012 11:31, Tomas Pluskal <pl...@oi...> wrote: > Thanks a lot, this is indeed very neat and works nicely. > > Does anybody have a complete list of CDK modules that JChemPaint currently > depends on? > (only guessing) cdk-data, cdk-smiles, cdk-renderbasic, cdk-sdg, cdk-inchi , cdk-valency-check If you find a working list, let me know, I'll update the maven artifact. Best regards, Nina > > Best, > > Tomas > > > On May 22, 2012, at 5:04 PM, John May wrote: > > > Hi Tomas, > > > > Yep you have to add them one by one. > > They are quite tightly coupled though so you'll find you'll inherit most > of them very quickly (but should declare the ones you're using). > > > > As a start you'll probably always need core, standard, data, io and > extra. > > > > > >> <dependency> > >> <groupId>org.openscience.cdk</groupId> > >> <artifactId>cdk-core</artifactId> > >> <version>${cdk.version}</version> > >> </dependency> > >> <dependency> > >> <groupId>org.openscience.cdk</groupId> > >> <artifactId>cdk-io</artifactId> > >> <version>${cdk.version}</version> > >> </dependency> > >> <dependency> > >> <groupId>org.openscience.cdk</groupId> > >> <artifactId>cdk-standard</artifactId> > >> <version>${cdk.version}</version> > >> </dependency> > >> <dependency> > >> <groupId>org.openscience.cdk</groupId> > >> <artifactId>cdk-extra</artifactId> > >> <version>${cdk.version}</version> > >> </dependency> > >> <dependency> > >> <groupId>org.openscience.cdk</groupId> > >> <artifactId>cdk-data</artifactId> > >> <version>${cdk.version}</version> > >> </dependency> > > > > you can put a property in your parent pom to centralise the version also > (otherwise there is a "versions" plugin) > > > >> <properties> > >> <cdk.version>1.4.9</cdk.version> > >> </properties> > > > > > > > > Hope that helps, > > > > > > On 22 May 2012, at 08:52, Tomas Pluskal wrote: > > > >>> They are listed in cdk-* etc. artifacts. We are not using cdk-pure > (imho it defeats the purpose of maven dependencies to use the entire blob > at once) , so it gets less attention :) > >>> > >>> You could help here, if you wish. > >> > >> Thanks, I will take a look at it. > >> > >> In the meantime, is there any way how to add all cdk modules including > their dependencies to my maven project? > >> I was hoping that adding > >> > >> <dependency> > >> <groupId>org.openscience.cdk</groupId> > >> <artifactId>cdk-all</artifactId> > >> <version>1.4.10</version> > >> <type>pom</type> > >> </dependency> > >> > >> to my pom.xml would download all the jar files of all CDK modules, but > it did not happen. > >> > >> Do I need to list the individual modules one by one? > >> > >> Best, > >> > >> Tomas > >> > >> > >> > >> =============================================== > >> Tomáš Pluskal > >> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate > University > >> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > >> TEL: +81-98-966-8684 > >> Fax: +81-98-966-2890 > >> > >> > >> > ------------------------------------------------------------------------------ > >> Live Security Virtual Conference > >> Exclusive live event will cover all the ways today's security and > >> threat landscape has changed and how IT managers can respond. > Discussions > >> will include endpoint security, mobile security and the latest in > malware > >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > >> _______________________________________________ > >> Cdk-devel mailing list > >> Cdk...@li... > >> https://lists.sourceforge.net/lists/listinfo/cdk-devel > > > > > > > ------------------------------------------------------------------------------ > > Live Security Virtual Conference > > Exclusive live event will cover all the ways today's security and > > threat landscape has changed and how IT managers can respond. Discussions > > will include endpoint security, mobile security and the latest in malware > > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > _______________________________________________ > > Cdk-devel mailing list > > Cdk...@li... > > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > =============================================== > Tomáš Pluskal > G0 Cell Unit, Okinawa Institute of Science and Technology Graduate > University > 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan > TEL: +81-98-966-8684 > Fax: +81-98-966-2890 > > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > |