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From Gale Naylor <Ga...@noventussolutions.com>
Subject Re: TAVERNA-867 doclint javadoc and Java 7 (was: Snapshot issue when releasing taverna language)
Date Wed, 03 Feb 2016 18:28:00 GMT
Or change tavtool to tavlang (link) tool, to be consistent with other
instances....

On Wed, Feb 3, 2016 at 10:21 AM Gale Naylor <GaleN@noventussolutions.com>
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 <GaleN@noventussolutions.com>
> 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 <stain@apache.org>
>> 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 <GaleN@noventussolutions.com>
>>> 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 <
>>> GaleN@noventussolutions.com>
>>> > 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 <
>>> GaleN@noventussolutions.com>
>>> >> 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 <
>>> GaleN@noventussolutions.com>
>>> >>> 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 <andy@apache.org>
>>> 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 <alaninmcr@googlemail.com
>>> >
>>> >>>>> 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
>>>
>>

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