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 >> >
