Broken/old links and questions in taverna-scufl2-examples/readme.md: **************** INTRODUCTORY PARAGRAPHS ****************
(1) CORRECT LINK? "SCUFL2 API" links to Download Taverna Language - is this correct? ( http://taverna.incubator.apache.org/download/language/) **************** Build SECTION **************** (2) BROKEN LINK "Maven" http://maven.apache.org/download **************** workflowmaker SECTION **************** (3) myGRID LINK "SCUFL2 wfbundle" http://dev.mygrid.org.uk/wiki/display/developer/Taverna+Workflow+Bundle ---> should be?: http://taverna.incubator.apache.org/documentation/scufl2/bundle **************** t2flowtowfbundle SECTION **************** (4) BROKEN LINK "helloworld.wfbundle" https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloworld.wfbundle?raw=true -->should be?: https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloworld.wfbundle (5) BROKEN LINK "helloanyone.wfbundle" https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloanyone.wfbundle?raw=true --should be?: https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.wfbundle (6) BROKEN LINK "helloworld.t2flow" https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloworld.t2flow?raw=true --> should be?: https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloworld.t2flow (7) BROKEN LINK "helloanyone.t2flow" https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloanyone.t2flow?raw=true --> should be?: https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.t2flow **************** jsonexport SECTION **************** (8) BROKEN LINK "examples/helloworld.json" https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloworld.json --> should be?: https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloworld.json (9) BROKEN LINK "examples/helloanyone.json" https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/helloanyone.json --> should be?: https://github.com/apache/incubator-taverna-language/blob/master/taverna-scufl2-examples/examples/helloanyone.json On Wed, Feb 3, 2016 at 10:27 AM Gale Naylor <[email protected]> wrote: > 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 >>>> >>>
