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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 18:53:58 GMT
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 <GaleN@noventussolutions.com>
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 <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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