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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 18:21:11 GMT
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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