PaxTools release

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IgorRodchenkov

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Mar 17, 2011, 12:48:53 PM3/17/11
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It used to be "released" regularly and quietly before, over last couple of years.., but worth now (and in the future) mentioning here in this group.

PaxTools library 2.0.110316 has been released!

Details:

IgorRodchenkov

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Apr 16, 2011, 7:46:01 PM4/16/11
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PaxTools library 3.0.0beta1 has been released!
    Summary of important changes (that's why we're changing from v2 to v3):
    • BioPAXFactory and Model (and the core implementations) were re-factored - one cannot easily create a BioPAX element without ID or change the ID anymore; model has got new export and repair methods; etc.
    • removed 'hashCode', 'equals' methods override from BioPAXElementImpl (should generate less "funny" bugs when used in such frameworks as Hibernate, Spring)
    • SimpleMerger and SimpleExporter (and entire module paxtools-simple-io) were removed; - replaced by org.biopax.paxtools.io.SimpleIOHandler (from paxtools-core)
    • more Javadoc
    • new utility classes in org.biopax.paxtools.controller that are both very useful and also - good as example of using the API (e.g., ModelUtils and its JUnit tests)
    • SBGN converter module

    IgorRodchenkov

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    May 4, 2011, 8:20:49 PM5/4/11
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    PaxTools 3.0.0 has been released!

    Note: auto-generated documentation for this release 
    and the latest (development) one are still at http://biopax.sourceforge.net/paxtools/.

    We continue with v4.0.0-SNAPSHOT from now 
    (next version jump from 3.x.x to 4.x.x was due to some, although minor, 
    API incompatibilities, mainly in SimpleEditorMap; 
    see also semver.org for why/how we change versions these days).

    IgorRodchenkov

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    Jul 27, 2011, 4:49:55 PM7/27/11
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    PaxTools 4.0.0b released.

    As usual, binary jars were deployed to the BioPAX maven repository,
    (the latest snapshots API docs were also relocated from http://biopax.sourceforge.net/paxtools to http://biopax.sourceforge.net/paxtools-4.0.0-SNAPSHOT).

    This (intermediate) release includes:
    • re-factoring, mainly in the org.biopax.paxtools.controller package (property editors, property path accessors, model utils) and other core classes (BioPAX factory, io), affecting the public API, which led to this jump in the major version number (from 3 to 4)
    • ORM optimized (particularly, cascades were disabled); dependency upgrades
    • several bugs fixed in the BioPAX to a text format converters and in PSI-MI to BioPAX converter
    • bugs fixed and new features added in paxtools-query module
    (for all changes, see http://biopax.hg.sourceforge.net/hgweb/biopax/paxtools/graph/tip)

    IgorRodchenkov

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    Oct 4, 2011, 1:29:23 PM10/4/11
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    PaxTools 4.0.0b3 released 

    Pradeep Kumar Sreenivasaiah

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    Oct 5, 2011, 2:18:31 AM10/5/11
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    Thank you Igor! 

    IgorRodchenkov

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    Nov 15, 2011, 6:05:44 PM11/15/11
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    PaxTools 4.0.1 released!

    JARs were deployed to the BioPAX public maven repository, http://biopax.sf.net/m2repo/releases; auto-generated documentation - http://biopax.sourceforge.net/paxtools-4.0.1/project-summary.html; and Javadoc - http://biopax.sourceforge.net/paxtools-4.0.1/paxtools-query/apidocs/.

    This release includes changes fixes since v4.0.0b3 (and v4.0.0 was quietly skipped ;) : 
    • important bugs in the SimpleIOHandler and SIF converter were fixed;
    • pathwaycommons-client module is not released this time (and will be released separately in the future), and paxtools-console (console app, tutorial, and examples) still depends on pathwaycommons-client-4.0.0b3 (current demo cPath2 api)
    • graph queries (in paxtools-query module, QueryExecuter) can now optionally use a blacklist, i.e., URIs of "ubiquitous" physical entities or entity references (e.g., see this javadoc)
    See also: all changes

    Here is a Paxtools User Guide (draft; this is to be updated and posted/published separately soon; please use 4.0.1 instead 4.0.0; see also other Paxtools documents and wiki pages, or www.biopax.org/paxtools)

    IgorRodchenkov

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    Feb 28, 2012, 1:17:14 PM2/28/12
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    PaxTools 4.1.0 released!

    JARs were deployed to the BioPAX public maven repository, http://biopax.sf.net/m2repo/releases; auto-generated documentation - http://biopax.sourceforge.net/paxtools-4.1.0/project-summary.html; and complete Javadoc - http://biopax.sourceforge.net/paxtools-4.1.0/apidocs/ or per module, e.g., paxtools-core or sif-converter javadoc. Fat (with all dependencies) release JARs are as usual available to download from http://sourceforge.net/projects/biopax/files/paxtools/.

    Summary of changes since v4.0.1: 
    • very important performance fix in the SimpleIOHandler (which make it work as fast as it used to be before v4)
    • pathwaycommons-client module is removed from Paxtools sources (use previous releases or try new pathway-commons cpath-client instead)
    • graph queries and SIF exporter fixes
    See also: all changes

    IgorRodchenkov

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    Feb 28, 2012, 7:06:12 PM2/28/12
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    PaxTools 4.1.1 released!

    Please ignore the previous release v4.1.0.
    One important fix since v4.1.0: Fixed the scope of Hibernate dependencies back to "provided", which results in much smaller (~12M) assembly ("fat") JAR size, and that projects that use Paxtools do not necessarily need Hibernate to compile, etc. This is how things were in v4.0.1 and before.

    Igor Rodchenkov

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    Oct 24, 2012, 10:28:26 AM10/24/12
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     PaxTools 4.1.5b2 (beta)

    Fixed the BioPAX L1, L2 to L3 converter (biopax-converter module) and GSEA (.gmt) exporter (gsea-converter). Updates to the SBGN converter and advanced graph query and analysis modules (work in progress).


    Downloads, documents:

      Igor Rodchenkov

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      Jan 17, 2013, 8:34:42 PM1/17/13
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       PaxTools 4.1.5

      Fixed several bugs in sif-, gsea-, sbgn-, psimi- converters, and biopax reader (e.g., SimpleIOHandler failed on XML comments put above the <rdf:RDF> element); also removed a couple of interesting but experimental modules and moved the BioPAX level converter (biopax-converter) code to paxtools-core (keeping package and class names unchanged). This version also has improved / deprecated some methods in org.biopax.paxtools.controller.ModelUtils. See: all changes. 


      Downloads, documents:

        Emek Demir

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        Jan 17, 2013, 8:36:01 PM1/17/13
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        Arghh - just missed it!

        Igor Rodchenkov

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        Jan 27, 2013, 8:39:20 AM1/27/13
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         PaxTools 4.1.6

        Fixed a bug (null pointer exception) in BindingFeature.isEquivalent logic (e.g., biopax-validator could fail checking some files because of this bug, but most Paxtools's users might have never noticed), improved the auto-generated documentation (new maven site, skin), and improvements in paxtools-pattern module; also paxtools console 'validate' command now works again. Please use this version of Paxtools, as library or from command line (run the jar without arguments, to begin with).

          Igor Rodchenkov

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          May 19, 2013, 2:58:18 AM5/19/13
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           PaxTools 4.2.0

          We improved the documentation, fixed several bugs, cleaned up deprecated/unused code, and also implemented equals and hashCode methods that override default Object's ones in the base BioPAX class, which now makes any two biopax elements having exactly the same class and URI equal. Please, let us know, via this forum or issue tracker, if this causes any problem, e.g., when adding/removing biopax objects to/from java collections. Taking into account all pros and cons, we decided these changes were but minor for most users and not worth waiting till next major (v5) release.

          Igor Rodchenkov

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          Nov 4, 2013, 11:15:25 AM11/4/13
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           PaxTools 4.2.1

          This minor release fixes several bugs in the SIF and SBGN converters, a few concurrency issues, and the paxtools' console 'validate' command (- failed since the biopax.org site moved to SF.net hosting and a new URL-forwarding was there introduced; still, consider using the BioPAX validator directly, online or offline, instead).

            Igor Rodchenkov

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            Nov 5, 2014, 2:38:41 PM11/5/14
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            PaxTools 4.3.0

            Fixes bugs, adds a new (made from scratch) PSI-MI, PSI-MITAB to BioPAX L3 converter, paxtools-trove module (optionally enables memory-efficient java collections), paxtools-archetype (aka Maven project template).

              Cheers,
              Pathway Commons team.

              Igo R

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              Sep 28, 2015, 10:06:00 AM9/28/15
              to BioPAX discussion group
              PaxTools 4.3.1

              Fixes bugs (e.g., eventual infinite loops in the BioPAX traverser or path accessor that occurred when analyzing some pathway data), adds 'pattern' and 'biopax-search' modules, some new command line features.
              • Sources, history: http://github.com/BioPAX/Paxtools (this release tag is "v4.3.1"; the latest code is 5.0.0-SNAPSHOT - not 100% backward compatible with the 4x versions, but quite easy to switch to).
              (Next release will be version 5.0.0, with Hibernate ORM/Search annotations in the paxtools-core, and old sif-converter - removed.)

              Igo R

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              Sep 29, 2015, 2:54:52 PM9/29/15
              to BioPAX discussion group
              Hi BioPAX-ers and Paxtools users,

              If you have already downloaded "fat" paxtools-4.3.1*.jar before today from biopax.org/downloads/paxtools/ (at Sourceforge),
              please download the updated jars now or a.s.a.p.
              (I repackaged to fix the parser error that was simply due to auto-inclusion of old jaxb/stax implementation libs into those jars.)

              PS:

              If you re-build the jars from sources at tag v4.3.1 though, and run the console app or use that as library in your project, you'll get 
              the "...BioPaxIOException: Unexpected element at start: 6" error again; so don't - use the jars from the biopax downloads 
              or build from the latest sources 5.0.0-SNAPSHOT, which do not have the issue).

              If you do not use the "fat" jars neither as console app nor library, i.e., if you only use some of Paxtools modules 
              (e.g., sbgn-converter, psimi-converter, paxtools-jene-io) in your java project as dependencies, then consider 
              explicitly excluding the following from that dependencies (in a maven pom.xml):
              ...
              <exclusions>
                <exclusion>
                  <groupId>com.sun.xml.bind</groupId>
                  <artifactId>jaxb-impl</artifactId>
                </exclusion>
                <!-- if it's the paxtools-jena-io then also - -->
                <exclusion>
                  <groupId>woodstox</groupId>
                  <artifactId>wstx-asl</artifactId>
                </exclusion>
              </exclusions>
              ...

              On Monday, September 28, 2015 at 10:06:00 AM UTC-4, Igo R wrote:
              PaxTools 4.3.1

              Fixes bugs ...

              Igo R

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              Sep 24, 2018, 1:20:45 PM9/24/18
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              PaxTools 5.1.0 release

              Benjamin Good

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              Sep 24, 2018, 2:20:27 PM9/24/18
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              Thanks.  Is there a summary anywhere of changes in this release?


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              Igo R

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              Oct 2, 2018, 11:59:52 PM10/2/18
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              Since 5.0.1, we mostly fixed minor bugs, improved sbgn-converter and pattern implementations, and removed some experimental code. 
              There is no special migration guide or changelog.
              • If you used Paxtools 4 then BioPAXElement getRDFId() must be replaced with getUri() before you compile with Paxtools 5
              • it's MIT licence now instead of LGPL
              • improved sbgn-converter
              • new interfaces in the pattern module
              • updated internal resources, e.g., hgnc.txt, Miriam.xml - used by pattern (incl. SIF converter) and normalizer modules
              • see issues closed
              IR
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