Or change tavtool to tavlang (link) tool, to be consistent with other instances....
On Wed, Feb 3, 2016 at 10:21 AM Gale Naylor <[email protected]> wrote: > Questions and broken links in taverna-scufl2-api/readme.md. > > **************** > INTRODUCTORY PARAGRAPHS > **************** > > (1) LINK ERROR? > Looks like it should be a link ... [SCUFL2][9] "For more information, see > the > [SCUFL2 API][9] pages..." > > **************** > Usage > **************** > > (2) BROKEN LINK - fix? > "Apache Taverna Language" > https://github.com/apache/incubator-taverna-language/blob/master > ---> SHOULD BE?: > https://github.com/apache/incubator-taverna-language/blob/master/README.md > > (3) BROKEN LINK > In table of supported file formats, "RDF Turtle" link gives 403 error > http://www.w3.org/TR/turtle/%22 > > (4) iwir REFERENCE > In table of supported file formats, "scufl2-iwir" > > (5) Change tavtool to tavlang-tool? > "You can use the tavtool command line to perform..." > > > On Wed, Feb 3, 2016 at 9:43 AM Gale Naylor <[email protected]> > wrote: > >> @stian, so, at some point, taverna-wfbundle should be changed to use >> robundle instead of taverna-scufl2-ucfpackage? >> >> On Tue, Feb 2, 2016 at 4:41 PM Stian Soiland-Reyes <[email protected]> >> wrote: >> >>> The UCF documentation even disappeared from adobe.com.. so it's good >>> we are deprecating it. But still the taverna-scufl2-ucfpackage is >>> used by taverna-wfbundle (which should use robundle instead) - so it's >>> needed as an internal dependency. >>> >>> >>> >>> On 2 February 2016 at 18:43, Gale Naylor <[email protected]> >>> wrote: >>> > taverna-robundle, item (12) should be Adobe UCF, not UFC. I see in the >>> > taverna-language readme that the module for Adobe UCF ZIP files is >>> > deprecated. So should we just eliminate the link in the robundle >>> readme? >>> > >>> > On Tue, Feb 2, 2016 at 9:26 AM Gale Naylor < >>> [email protected]> >>> > wrote: >>> > >>> >> >>> >> Java 7 references, broken links, and other notes on taverna-robundle/ >>> >> readme.md: >>> >> >>> >> *********************** >>> >> INTRODUCTORY PARAGRAPHS >>> >> *********************** >>> >> >>> >> (1) Java 7 >>> >> "This API is built on the Java 7 NIO Files and uses the Java 7 ZIP >>> file >>> >> provider to generate the RO Bundle. >>> >> The class org.apache.taverna.robundle.Bundles complements the Java 7 >>> >> java.nio.Files API with more specific helper methods to work with RO >>> >> Bundles." >>> >> >>> >> (2) BROKEN LINK >>> >> Broken "org.apache.taverna.robundle.Bundles" links to >>> >> >>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/main/java/org/purl/wf4ever/robundle/Bundles.java >>> >> >>> >> (3) WRONG LINK? >>> >> "Taverna Data Bundles API" links to non-Apache repo, which says >>> "Moved to >>> >> Apache Taverna." >>> >> (https://github.com/taverna/taverna-databundle) >>> >> >>> >> *********************** >>> >> Usage SECTION >>> >> *********************** >>> >> >>> >> (4) myGRID REFERENCE >>> >> pom.xml code sample says to add "mygrid-repository" and points to >>> >> http://www.mygrid.org.uk/maven/repository >>> >> >>> >> (5) wf4ever REFERENCE >>> >> "robundle releases" links to >>> https://github.com/wf4ever/robundle/releases >>> >> >>> >> (6) myGRID REFERENCE >>> >> "myGrid's Maven repository" links to >>> >> >>> http://repository.mygrid.org.uk/artifactory/mygrid-all/org/purl/wf4ever/robundle/robundle/ >>> >> >>> >> *********************** >>> >> Building SECTION >>> >> *********************** >>> >> >>> >> (7) JAVA 7 >>> >> "should normally work, given a recent version of Maven 3 and Java 7 >>> SDK." >>> >> >>> >> (8) myGRID REFERENCE >>> >> "myGrid's Jenkins installation" links to >>> http://build.mygrid.org.uk/ci/ >>> >> >>> >> (9) BROKEN LINK >>> >> Broken "robundle" link to http://build.mygrid.org.uk/ci/job/robundle/ >>> >> >>> >> (10) myGRID REFERENCE >>> >> "myGrid's snapshot Maven repository" links to >>> >> >>> http://www.mygrid.org.uk/maven/snapshot-repository/org/purl/wf4ever/robundle/robundle/ >>> >> >>> >> (11) myGRID REFERENCE >>> >> pom.xml code sample says to add "mygrid-snapshot-repository" and >>> points to >>> >> http://www.mygrid.org.uk/maven/snapshot-repository >>> >> >>> >> *********************** >>> >> Supported bundle formats SECTION >>> >> *********************** >>> >> >>> >> (12) Question: Is Adobe UFC still relevant? >>> >> The readme link is redirected from " >>> >> https://wikidocs.adobe.com/wiki/display/PDFNAV/UCF+overview"; to a >>> general >>> >> support site: https://helpx.adobe.com/support.html#/top_products, >>> and I >>> >> couldn't find anything when I searched for UFC.. >>> >> >>> >> *********************** >>> >> Example of use SECTION >>> >> *********************** >>> >> >>> >> (13) BROKEN LINK >>> >> Broken "org.apache.taverna.robundle.TestExample" link to >>> >> >>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-robundle/src/test/java/org/purl/wf4ever/robundle/TestExample.java >>> >> >>> >> (14) JAVA 7 >>> >> Code sample includes Java 7 style ("// Or Java 7 style" + code) >>> >> >>> >> -- >>> >> Gale >>> >> >>> >> >>> >> On Tue, Feb 2, 2016 at 8:18 AM Gale Naylor < >>> [email protected]> >>> >> wrote: >>> >> >>> >>> In hindsight, I probably should keep all of the readme reviews as >>> part of >>> >>> this thread. (Sorry for the duplicate email.) >>> >>> >>> >>> taverna-language-commandline/readme.md >>> >>> >>> >>> *********************** >>> >>> INTRODUCTORY PARAGRAPHS >>> >>> *********************** >>> >>> >>> >>> (1) "planned" and "work in progress" should change to reflect code is >>> >>> complete. (Mentioned in "functionality in next release" email.) >>> >>> >>> >>> *********************** >>> >>> License SECTION >>> >>> *********************** >>> >>> >>> >>> (2) BROKEN LINK -- have fix for this >>> >>> Broken "NOTICE" link ( >>> >>> >>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/resources/NOTICE >>> >>> ) >>> >>> ----- SHOULD BE: >>> >>> >>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-language-commandline/src/main/resources/META-INF/NOTICE >>> >>> >>> >>> *********************** >>> >>> Building and install requirements SECTION >>> >>> *********************** >>> >>> >>> >>> (3) JAVA 7 >>> >>> "Java 1.7 or newer" -- change to "Java 1.8" ? >>> >>> >>> >>> *********************** >>> >>> Commands: inspect ---- SECTION >>> >>> *********************** >>> >>> >>> >>> (4) BROKEN LINK >>> >>> Broken "http://ns.taverna.org.uk/2010/activity/constant"; link >>> (Service >>> >>> types used in helloworld.wfbundle) >>> >>> >>> >>> >>> >>> >>> >>> On Tue, Feb 2, 2016 at 7:55 AM Gale Naylor < >>> [email protected]> >>> >>> wrote: >>> >>> >>> >>>> I'm looking at the readme files for Java 7 references. I found >>> several >>> >>>> in taverna-databundle/readme.md, but they are not simple >>> >>>> find-and-replace. For example, "This API is built on the Java 7 NIO >>> Files >>> >>>> and the RO Bundle API, which uses the Java 7 ZIP file provider to >>> generate >>> >>>> the Data Bundle." There is also a Java 7 code sample. In addition, >>> the file >>> >>>> contains several broken links, along with references to myGrid, >>> which >>> >>>> seemed out-of-place to me, but maybe they are okay. If you give me >>> some >>> >>>> direction and help (e.g., for the Java 7 code sample) I can make the >>> >>>> changes. I'm including a list of all the questionable (to me) items >>> in >>> >>>> order: >>> >>>> >>> >>>> taverna-databundle/readme.md >>> >>>> >>> >>>> (1) Says "build failing"? at top of readme >>> >>>> >>> >>>> *********************** >>> >>>> INTRODUCTORY PARAGRAPHS >>> >>>> *********************** >>> >>>> >>> >>>> (1) myGRID REFERENCE >>> >>>> Refers to myGrid data bundle requirements ( >>> >>>> >>> http://dev.mygrid.org.uk/wiki/display/TAVOSGI/2013-02+Data+bundle+requirements >>> >>>> ) >>> >>>> >>> >>>> (2) BROKEN LINK >>> >>>> "TestDataBundles.java" ( >>> >>>> >>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-databundle/src/test/java/uk/org/taverna/databundle/TestDataBundles.java >>> >>>> ) >>> >>>> >>> >>>> (3) JAVA 7 >>> >>>> "This API is built on the Java 7 NIO Files and the RO Bundle API, >>> which >>> >>>> uses the Java 7 ZIP file provider to generate the Data Bundle." >>> >>>> >>> >>>> (4) JAVA 7 >>> >>>> "The class org.apache.taverna.databundle.DataBundles complements the >>> >>>> Java 7 java.nio.Files API with more specific helper methods to work >>> with >>> >>>> Data Bundles." >>> >>>> >>> >>>> (5) BROKEN LINK >>> >>>> Broken "org.apache.taverna.databundle.DataBundles" link ( >>> >>>> >>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-databundle/src/main/java/uk/org/taverna/databundle/DataBundles.java >>> >>>> ) >>> >>>> >>> >>>> **************** >>> >>>> Building SECTION >>> >>>> **************** >>> >>>> >>> >>>> (5) JAVA 7 >>> >>>> "should normally work, given a recent version of Maven 3 and Java 7 >>> SDK." >>> >>>> >>> >>>> (6) myGRID REFERENCE >>> >>>> Refers to "myGrid's Jenkins installation" ( >>> >>>> http://build.mygrid.org.uk/ci/) >>> >>>> >>> >>>> (7) BROKEN LINK >>> >>>> Broken "databundles" link( >>> http://build.mygrid.org.uk/ci/job/databundles/ >>> >>>> ) >>> >>>> >>> >>>> (8) BROKEN LINK >>> >>>> Broken "robundles" link(http://build.mygrid.org.uk/ci/job/robundle/ >>> ) >>> >>>> >>> >>>> (9) myGRID REFERENCE >>> >>>> Refers to "myGrid's snapshot repository" ( >>> >>>> >>> http://build.mygrid.org.uk/maven/snapshot-repository/uk/org/taverna/databundle/databundle/ >>> >>>> ) >>> >>>> >>> >>>> (10) wf4ever LINK >>> >>>> "robundle" links to https://github.com/wf4ever/robundle, which says >>> >>>> "Move to Apache Taverna" >>> >>>> >>> >>>> (11) myGRID REFERENCE >>> >>>> Says to download "robundle" from "myGrid's snapshot repository" ( >>> >>>> >>> http://build.mygrid.org.uk/maven/snapshot-repository/org/purl/wf4ever/robundle/robundle/ >>> >>>> ) >>> >>>> >>> >>>> ********************** >>> >>>> Example of use SECTION >>> >>>> ********************** >>> >>>> >>> >>>> (12) BROKEN LINK >>> >>>> Broken "org.apache.taverna.databundle.TestExample" link ( >>> >>>> >>> https://github.com/apache/incubator-taverna-language/blob/master/taverna-databundle/src/test/java/uk/org/taverna/databundle/TestExample.java >>> >>>> ) >>> >>>> >>> >>>> (13) JAVA 7 >>> >>>> Code sample using "Java 7 style" >>> >>>> >>> >>>> --- >>> >>>> >>> >>>> Gale >>> >>>> >>> >>>> On Mon, Feb 1, 2016 at 9:47 AM Andy Seaborne <[email protected]> >>> wrote: >>> >>>> >>> >>>>> Jena has to turn off Java8 doclint because it fails builds for >>> imperfect >>> >>>>> javadoc. >>> >>>>> >>> >>>>> <profile> >>> >>>>> <!-- Turn of doclint for java8 and later --> >>> >>>>> <id>doclint-java8-disable</id> >>> >>>>> <activation> >>> >>>>> <jdk>[1.8,)</jdk> >>> >>>>> </activation> >>> >>>>> >>> >>>>> <build> >>> >>>>> <plugins> >>> >>>>> <plugin> >>> >>>>> <groupId>org.apache.maven.plugins</groupId> >>> >>>>> <artifactId>maven-javadoc-plugin</artifactId> >>> >>>>> <configuration> >>> >>>>> <additionalparam>-Xdoclint:none</additionalparam> >>> >>>>> </configuration> >>> >>>>> </plugin> >>> >>>>> </plugins> >>> >>>>> </build> >>> >>>>> </profile> >>> >>>>> >>> >>>>> We also have the problem with false warnings >>> >>>>> >>> >>>>> [WARNING] >>> >>>>> >>> >>>>> >>> /home/jenkins/jenkins-slave/workspace/Jena_Development_Deploy/jena-core/src/main/java/org/apache/jena/ontology/OntProperty.java:497: >>> >>>>> warning - @propertyDescription is an unknown tag. >>> >>>>> >>> >>>>> except there is no @propertyDescription in the source! >>> >>>>> >>> >>>>> @propertyDescription can only be used in JavaFX properties getters >>> and >>> >>>>> setters. >>> >>>>> [WARNING] >>> >>>>> >>> >>>>> >>> /home/jenkins/jenkins-slave/workspace/Jena_Development_Deploy/jena-core/src/main/java/org/apache/jena/ontology/OntProperty.java:490: >>> >>>>> warning - Tags @propertyGetter, @propertySetter and >>> @propertyDescription >>> >>>>> can only be used in JavaFX properties getters and setters. >>> >>>>> >>> >>>>> JavaFX ???!!!! >>> >>>>> >>> >>>>> Andy >>> >>>>> >>> >>>>> On 01/02/16 17:01, Stian Soiland-Reyes wrote: >>> >>>>> > Yes, I think ironically we need it to ignore some errors from >>> Java 8's >>> >>>>> > javadoc - this came up as we were doing the 0.15.0 release of >>> >>>>> > taverna-language. >>> >>>>> > >>> >>>>> > See also: >>> >>>>> > https://issues.apache.org/jira/browse/MJAVADOC-387 >>> >>>>> > >>> >>>>> > >>> >>>>> > You can also enable it conditionally with <profile> based on the >>> JDK >>> >>>>> > version like here: >>> >>>>> > >>> >>>>> > >>> >>>>> >>> https://github.com/jai-imageio/jai-imageio-core/blob/master/pom.xml#L195 >>> >>>>> > >>> >>>>> > If we do that we can keep 1.7 support - I mean if we really want >>> to. >>> >>>>> :) >>> >>>>> > >>> >>>>> > >>> >>>>> > >>> >>>>> > Alternatively I guess we can go through and fix the Javadoc >>> warnings.. >>> >>>>> > >>> >>>>> > Some examples: >>> >>>>> > >>> >>>>> > >>> >>>>> > [ERROR] >>> >>>>> >>> /home/stain/src/taverna/incubator-taverna-language/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/impl/odfdom/pkg/OdfPackage.java:910: >>> >>>>> > warning: no description for @throws >>> >>>>> > [ERROR] * @throws Exception >>> >>>>> > [ERROR] ^ >>> >>>>> > >>> >>>>> > [ERROR] >>> >>>>> >>> /home/stain/src/taverna/incubator-taverna-language/taverna-scufl2-ucfpackage/src/main/java/org/apache/taverna/scufl2/ucfpackage/impl/odfdom/pkg/manifest/OdfFileEntry.java:87: >>> >>>>> > warning: no @return >>> >>>>> > [ERROR] public int getSize() { >>> >>>>> > [ERROR] ^ >>> >>>>> > >>> >>>>> > [ERROR] >>> >>>>> >>> /home/stain/src/taverna/incubator-taverna-language/taverna-scufl2-ucfpackage/target/generated-sources/xjc/org/oasis_open/names/tc/opendocument/xmlns/container/ObjectFactory.java:125: >>> >>>>> > warning: no @param for value >>> >>>>> > [ERROR] public JAXBElement<Relationship> >>> >>>>> > createContainerRelationshipsRelationship(Relationship value) { >>> >>>>> > [ERROR] ^ >>> >>>>> > >>> >>>>> > There would be quite a few warnings.. I wonder if the Doclint >>> default >>> >>>>> > has changed with OpenJDK vs Oracle JDK or in different Java patch >>> >>>>> > versions, because if I try on my machine to remove the doclint >>> setting >>> >>>>> > taverna-language still builds, using OpenJDK 1.8.0_72-internal on >>> >>>>> > Ubuntu 14.04.3/x64. >>> >>>>> > >>> >>>>> > (I had to change to -Xdoclint:all to see those warnings) >>> >>>>> > >>> >>>>> > On 1 February 2016 at 14:49, alaninmcr <[email protected] >>> > >>> >>>>> wrote: >>> >>>>> >> On 01/02/2016 12:35, Menaka Madushanka wrote: >>> >>>>> >>> >>> >>>>> >>> Hello, >>> >>>>> >>> I get this error when building tavlang tool.... >>> >>>>> >>> >>> >>>>> >>> [ERROR] Failed to execute goal >>> >>>>> >>> org.apache.maven.plugins:maven-javadoc-plugin:2.9:jar >>> >>>>> (attach-javadocs) on >>> >>>>> >>> project taverna-language-commandline: MavenReportException: >>> Error >>> >>>>> while >>> >>>>> >>> creating archive: >>> >>>>> >>> [ERROR] Exit code: 1 - javadoc: error - invalid flag: >>> -Xdoclint:none >>> >>>>> >>> [ERROR] >>> >>>>> >>> [ERROR] Command line was: >>> >>>>> /usr/lib/jvm/java-7-oracle/jre/../bin/javadoc >>> >>>>> >>> @options @packages >>> >>>>> >> >>> >>>>> >> >>> >>>>> >> Is that option only available in Java 8? >>> >>>>> >> >>> >>>>> >> Alan >>> >>>>> > >>> >>>>> > >>> >>>>> > >>> >>>>> >>> >>>>> >>> >>> >>> >>> -- >>> Stian Soiland-Reyes >>> Apache Taverna (incubating), Apache Commons RDF (incubating) >>> http://orcid.org/0000-0001-9842-9718 >>> >>
