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Posted to user@uima.apache.org by "Pablo N. Mendes" <pa...@gmail.com> on 2016/05/06 22:30:22 UTC
No sofaFS for specified sofaRef found
Folks,
I am getting "No sofaFS for specified sofaRef found" while trying to
deserialize an XMI. I found the message a bit cryptic and didn't find much
help on the lazyweb, so I bit the bullet and spent a few hours poking
around. It seems to be a missing "sofa" attribute. If the sofa attribute
has the wrong value, then you get "xmi id <id> is referenced but not
defined" which is very nice and clear. But if you omit the sofa attribute
you get "No sofaFS for specified sofaRef found" which is less informative
IMHO.
Extra info below.
Cheers,
Pablo
$ diff cas1.xmi cas2.xmi
9c9
< <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
documentId="001"/>
---
> <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
VERSIONS
<uima.version>2.8.1</uima.version>
<uimafit.version>2.1.0</uimafit.version>
JAVA CODE SNIPPET
org.apache.uima.util.XmlCasDeserializer.deserialize(inputStream,
jCas.getCas());
STACK TRACE
Exception in thread "main" org.apache.uima.cas.CASRuntimeException: No
sofaFS for specified sofaRef found.
at org.apache.uima.cas.impl.CASImpl.getSofa(CASImpl.java:806)
at
org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS_common(FSIndexRepositoryImpl.java:2781)
at
org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS(FSIndexRepositoryImpl.java:2763)
at
org.apache.uima.cas.impl.FSIndexRepositoryImpl.addFS(FSIndexRepositoryImpl.java:2068)
at
org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.endDocument(XmiCasDeserializer.java:1486)
at
org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.endDocument(XmlCasDeserializer.java:127)
at org.apache.xerces.parsers.AbstractSAXParser.endDocument(Unknown Source)
at org.apache.xerces.impl.XMLDocumentScannerImpl.endEntity(Unknown Source)
at org.apache.xerces.impl.XMLEntityManager.endEntity(Unknown Source)
at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
at org.apache.xerces.impl.XMLEntityScanner.skipSpaces(Unknown Source)
at
org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at
org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:83)
at
org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:58)
...
CAS1.xmi
<?xml version="1.0" encoding="UTF-8"?>
<xmi:XMI
xmlns:cas="http:///uima/cas.ecore"
xmlns:tcas="http:///uima/tcas.ecore"
xmlns:xmi="http://www.omg.org/XMI"
xmlns:ls="http:///com/example.ecore"
xmi:version="2.0">
<cas:NULL xmi:id="0"/>
<ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
documentId="001"/>
<cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
sofaString="This is a test."/>
<cas:View sofa="1" members="18"/>
</xmi:XMI>
CAS2.xmi
<?xml version="1.0" encoding="UTF-8"?>
<xmi:XMI
xmlns:cas="http:///uima/cas.ecore"
xmlns:tcas="http:///uima/tcas.ecore"
xmlns:xmi="http://www.omg.org/XMI"
xmlns:ls="http:///com/example.ecore"
xmi:version="2.0">
<cas:NULL xmi:id="0"/>
<ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
<cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
sofaString="This is a test."/>
<cas:View sofa="1" members="18"/>
</xmi:XMI>
TYPESYSTEM
<?xml version="1.0" encoding="UTF-8" ?>
<typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
<name>ExampleTypeSystem</name>
<description>Just an example</description>
<vendor>example.com</vendor>
<version>1.0</version>
<types>
<typeDescription>
<name>com.example.DocumentMetadata</name>
<description></description>
<supertypeName>uima.tcas.DocumentAnnotation</supertypeName>
<features>
<featureDescription>
<name>source</name>
<description>Source</description>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
<featureDescription>
<name>documentId</name>
<description>Source</description>
<rangeTypeName>uima.cas.String</rangeTypeName>
</featureDescription>
</features>
</typeDescription>
</types>
</typeSystemDescription>
--
Pablo N. Mendes
http://pablomendes.com
Re: No sofaFS for specified sofaRef found
Posted by "Pablo N. Mendes" <pa...@gmail.com>.
Bingo! I created the posted type system by reverse engineering it from the
XMI provided to me by a third party. I have since requested the type system
XML from them and I can now see that the original DocumentMetadata inherits
directly from uima.cas.TOP! So, yes, the annotation did *not* inherit from
AnnotationBase when it was serialized to XMI but I asked uimaj to create
an annotation that *does* inherit from AnnotationBase when deserializing it
back into a Java object.
Thank you for your time and for the detailed answer. I now see more clearly
the complexity of the issue. Great work!
Cheers,
Pablo
On Fri, May 13, 2016 at 6:33 AM, Marshall Schor <ms...@schor.com> wrote:
> Thanks for your report, analysis, and the data; very thorough and helpful.
>
> I was trying to imagine how the input XMI file could have become
> "corrupted" in
> this manner. I'm guessing that what may have happened is that something
> outside
> of the XMI file changed - for instance, the type system.
>
> This situation (of the sofa attribute being missing) could happen if the
> type
> definition for DocumentMetadata changed.
>
> I searched the source code for UIMA for "DocumentMetadata" as a UIMA type,
> and
> came up empty, so I'm guessing this is some type that was defined in your
> particular application. I see in your note that you included a
> description of
> the type system defining DocumentMeta, and it shows that the supertype
> hierarchy
> of this type is:
>
> uima.tcas.DocumentAnnotation, whose supertype is
> uima.tcas.Annotation, whose supertype is
> uima.cas.AnnotationBase, whose supertype is
> uima.cas.TOP
>
> I'm guessing that at the time the XMI serialized form was created, a
> different
> type system was being used that defined the supertype hierarchy for
> DocumentMetadata such that it did **not** have uima.cas.AnnotationBase in
> it
> super type hierarchy. This would mean that it did not have the "sofa"
> feature.
>
> Can you perhaps confirm that this (changing the type system in this
> manner) was
> probably the cause of this?
>
> -----------------
>
> In figuring out what's the best thing to, it seems there are multiple
> conditions
> to maybe try and catch. To cause this failure:
>
> 1) a type was deserialized where the type system had some features that
> were
> missing in the serialization
>
> 2) the particular feature "sofa" was missing
>
> 3) the feature structure with the missing sofa feature was in a list in
> the
> serialization specifying it was to be added to the indexes
>
> (1) is not generally an error; it is allowed to permit evolution of type
> systems
> (in a compatible way) over time. For example, new features could be
> added. Any
> features not in the serialization are set to their default values.
>
> (2) even this is not (necessarily) an error (but it is bad practice). For
> example, you might be using the initial view, and might have never created
> a
> Sofa. (Sofas are always created if you create a view programatically).
>
> Later versions of UIMA check for the sofa feature missing when attempting
> to add
> a Feature Structure to the indexes; this test was not always there, and,
> for
> backwards compatibility, it can be disabled with a
> -Duima.disable_enhanced_check_wrong_add_to_index JVM property.
>
> ----------------
>
> Because of this, I'm planning to leave the detection of this alone, but
> will
> change the error message to indicate some potential causes of this
> situation,
> including that the type system definition changed for this type from one
> not
> having uima.cas.AnnotationBase in the hierarchy when the serialized form
> was
> created, to the current type system being used for deserialization, which
> does
> (especially, if you can confirm this was the likely cause).
>
> Thank you very much for your report and analysis!
>
> -Marshall
>
>
>
> On 5/6/2016 6:30 PM, Pablo N. Mendes wrote:
> > Folks,
> > I am getting "No sofaFS for specified sofaRef found" while trying to
> > deserialize an XMI. I found the message a bit cryptic and didn't find
> much
> > help on the lazyweb, so I bit the bullet and spent a few hours poking
> > around. It seems to be a missing "sofa" attribute. If the sofa attribute
> > has the wrong value, then you get "xmi id <id> is referenced but not
> > defined" which is very nice and clear. But if you omit the sofa attribute
> > you get "No sofaFS for specified sofaRef found" which is less informative
> > IMHO.
> >
> > Extra info below.
> >
> > Cheers,
> > Pablo
> >
> > $ diff cas1.xmi cas2.xmi
> > 9c9
> > < <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
> > documentId="001"/>
> > ---
> >> <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
> >
> >
> >
> > VERSIONS
> >
> > <uima.version>2.8.1</uima.version>
> > <uimafit.version>2.1.0</uimafit.version>
> >
> > JAVA CODE SNIPPET
> >
> > org.apache.uima.util.XmlCasDeserializer.deserialize(inputStream,
> > jCas.getCas());
> >
> > STACK TRACE
> >
> > Exception in thread "main" org.apache.uima.cas.CASRuntimeException: No
> > sofaFS for specified sofaRef found.
> > at org.apache.uima.cas.impl.CASImpl.getSofa(CASImpl.java:806)
> > at
> >
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS_common(FSIndexRepositoryImpl.java:2781)
> > at
> >
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS(FSIndexRepositoryImpl.java:2763)
> > at
> >
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.addFS(FSIndexRepositoryImpl.java:2068)
> > at
> >
> org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.endDocument(XmiCasDeserializer.java:1486)
> > at
> >
> org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.endDocument(XmlCasDeserializer.java:127)
> > at org.apache.xerces.parsers.AbstractSAXParser.endDocument(Unknown
> Source)
> > at org.apache.xerces.impl.XMLDocumentScannerImpl.endEntity(Unknown
> Source)
> > at org.apache.xerces.impl.XMLEntityManager.endEntity(Unknown Source)
> > at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
> > at org.apache.xerces.impl.XMLEntityScanner.skipSpaces(Unknown Source)
> > at
> >
> org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown
> > Source)
> > at
> >
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
> > Source)
> > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> > at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> > at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> > at
> >
> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:83)
> > at
> >
> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:58)
> > ...
> >
> >
> > CAS1.xmi
> >
> > <?xml version="1.0" encoding="UTF-8"?>
> > <xmi:XMI
> > xmlns:cas="http:///uima/cas.ecore"
> > xmlns:tcas="http:///uima/tcas.ecore"
> > xmlns:xmi="http://www.omg.org/XMI"
> > xmlns:ls="http:///com/example.ecore"
> > xmi:version="2.0">
> > <cas:NULL xmi:id="0"/>
> > <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
> > documentId="001"/>
> > <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
> > sofaString="This is a test."/>
> > <cas:View sofa="1" members="18"/>
> > </xmi:XMI>
> >
> >
> > CAS2.xmi
> >
> > <?xml version="1.0" encoding="UTF-8"?>
> > <xmi:XMI
> > xmlns:cas="http:///uima/cas.ecore"
> > xmlns:tcas="http:///uima/tcas.ecore"
> > xmlns:xmi="http://www.omg.org/XMI"
> > xmlns:ls="http:///com/example.ecore"
> > xmi:version="2.0">
> > <cas:NULL xmi:id="0"/>
> > <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
> > <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
> > sofaString="This is a test."/>
> > <cas:View sofa="1" members="18"/>
> > </xmi:XMI>
> >
> >
> > TYPESYSTEM
> >
> > <?xml version="1.0" encoding="UTF-8" ?>
> >
> > <typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier
> ">
> > <name>ExampleTypeSystem</name>
> > <description>Just an example</description>
> > <vendor>example.com</vendor>
> > <version>1.0</version>
> > <types>
> > <typeDescription>
> > <name>com.example.DocumentMetadata</name>
> > <description></description>
> >
> > <supertypeName>uima.tcas.DocumentAnnotation</supertypeName>
> > <features>
> > <featureDescription>
> > <name>source</name>
> > <description>Source</description>
> >
> > <rangeTypeName>uima.cas.String</rangeTypeName>
> > </featureDescription>
> > <featureDescription>
> > <name>documentId</name>
> > <description>Source</description>
> >
> > <rangeTypeName>uima.cas.String</rangeTypeName>
> > </featureDescription>
> > </features>
> > </typeDescription>
> >
> > </types>
> > </typeSystemDescription>
> >
> >
>
>
--
Pablo N. Mendes
http://pablomendes.com
Re: No sofaFS for specified sofaRef found
Posted by Marshall Schor <ms...@schor.com>.
Thanks for your report, analysis, and the data; very thorough and helpful.
I was trying to imagine how the input XMI file could have become "corrupted" in
this manner. I'm guessing that what may have happened is that something outside
of the XMI file changed - for instance, the type system.
This situation (of the sofa attribute being missing) could happen if the type
definition for DocumentMetadata changed.
I searched the source code for UIMA for "DocumentMetadata" as a UIMA type, and
came up empty, so I'm guessing this is some type that was defined in your
particular application. I see in your note that you included a description of
the type system defining DocumentMeta, and it shows that the supertype hierarchy
of this type is:
uima.tcas.DocumentAnnotation, whose supertype is
uima.tcas.Annotation, whose supertype is
uima.cas.AnnotationBase, whose supertype is
uima.cas.TOP
I'm guessing that at the time the XMI serialized form was created, a different
type system was being used that defined the supertype hierarchy for
DocumentMetadata such that it did **not** have uima.cas.AnnotationBase in it
super type hierarchy. This would mean that it did not have the "sofa" feature.
Can you perhaps confirm that this (changing the type system in this manner) was
probably the cause of this?
-----------------
In figuring out what's the best thing to, it seems there are multiple conditions
to maybe try and catch. To cause this failure:
1) a type was deserialized where the type system had some features that were
missing in the serialization
2) the particular feature "sofa" was missing
3) the feature structure with the missing sofa feature was in a list in the
serialization specifying it was to be added to the indexes
(1) is not generally an error; it is allowed to permit evolution of type systems
(in a compatible way) over time. For example, new features could be added. Any
features not in the serialization are set to their default values.
(2) even this is not (necessarily) an error (but it is bad practice). For
example, you might be using the initial view, and might have never created a
Sofa. (Sofas are always created if you create a view programatically).
Later versions of UIMA check for the sofa feature missing when attempting to add
a Feature Structure to the indexes; this test was not always there, and, for
backwards compatibility, it can be disabled with a
-Duima.disable_enhanced_check_wrong_add_to_index JVM property.
----------------
Because of this, I'm planning to leave the detection of this alone, but will
change the error message to indicate some potential causes of this situation,
including that the type system definition changed for this type from one not
having uima.cas.AnnotationBase in the hierarchy when the serialized form was
created, to the current type system being used for deserialization, which does
(especially, if you can confirm this was the likely cause).
Thank you very much for your report and analysis!
-Marshall
On 5/6/2016 6:30 PM, Pablo N. Mendes wrote:
> Folks,
> I am getting "No sofaFS for specified sofaRef found" while trying to
> deserialize an XMI. I found the message a bit cryptic and didn't find much
> help on the lazyweb, so I bit the bullet and spent a few hours poking
> around. It seems to be a missing "sofa" attribute. If the sofa attribute
> has the wrong value, then you get "xmi id <id> is referenced but not
> defined" which is very nice and clear. But if you omit the sofa attribute
> you get "No sofaFS for specified sofaRef found" which is less informative
> IMHO.
>
> Extra info below.
>
> Cheers,
> Pablo
>
> $ diff cas1.xmi cas2.xmi
> 9c9
> < <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
> documentId="001"/>
> ---
>> <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
>
>
>
> VERSIONS
>
> <uima.version>2.8.1</uima.version>
> <uimafit.version>2.1.0</uimafit.version>
>
> JAVA CODE SNIPPET
>
> org.apache.uima.util.XmlCasDeserializer.deserialize(inputStream,
> jCas.getCas());
>
> STACK TRACE
>
> Exception in thread "main" org.apache.uima.cas.CASRuntimeException: No
> sofaFS for specified sofaRef found.
> at org.apache.uima.cas.impl.CASImpl.getSofa(CASImpl.java:806)
> at
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS_common(FSIndexRepositoryImpl.java:2781)
> at
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS(FSIndexRepositoryImpl.java:2763)
> at
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.addFS(FSIndexRepositoryImpl.java:2068)
> at
> org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.endDocument(XmiCasDeserializer.java:1486)
> at
> org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.endDocument(XmlCasDeserializer.java:127)
> at org.apache.xerces.parsers.AbstractSAXParser.endDocument(Unknown Source)
> at org.apache.xerces.impl.XMLDocumentScannerImpl.endEntity(Unknown Source)
> at org.apache.xerces.impl.XMLEntityManager.endEntity(Unknown Source)
> at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
> at org.apache.xerces.impl.XMLEntityScanner.skipSpaces(Unknown Source)
> at
> org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown
> Source)
> at
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
> Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> at
> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:83)
> at
> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:58)
> ...
>
>
> CAS1.xmi
>
> <?xml version="1.0" encoding="UTF-8"?>
> <xmi:XMI
> xmlns:cas="http:///uima/cas.ecore"
> xmlns:tcas="http:///uima/tcas.ecore"
> xmlns:xmi="http://www.omg.org/XMI"
> xmlns:ls="http:///com/example.ecore"
> xmi:version="2.0">
> <cas:NULL xmi:id="0"/>
> <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
> documentId="001"/>
> <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
> sofaString="This is a test."/>
> <cas:View sofa="1" members="18"/>
> </xmi:XMI>
>
>
> CAS2.xmi
>
> <?xml version="1.0" encoding="UTF-8"?>
> <xmi:XMI
> xmlns:cas="http:///uima/cas.ecore"
> xmlns:tcas="http:///uima/tcas.ecore"
> xmlns:xmi="http://www.omg.org/XMI"
> xmlns:ls="http:///com/example.ecore"
> xmi:version="2.0">
> <cas:NULL xmi:id="0"/>
> <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
> <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
> sofaString="This is a test."/>
> <cas:View sofa="1" members="18"/>
> </xmi:XMI>
>
>
> TYPESYSTEM
>
> <?xml version="1.0" encoding="UTF-8" ?>
>
> <typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
> <name>ExampleTypeSystem</name>
> <description>Just an example</description>
> <vendor>example.com</vendor>
> <version>1.0</version>
> <types>
> <typeDescription>
> <name>com.example.DocumentMetadata</name>
> <description></description>
>
> <supertypeName>uima.tcas.DocumentAnnotation</supertypeName>
> <features>
> <featureDescription>
> <name>source</name>
> <description>Source</description>
>
> <rangeTypeName>uima.cas.String</rangeTypeName>
> </featureDescription>
> <featureDescription>
> <name>documentId</name>
> <description>Source</description>
>
> <rangeTypeName>uima.cas.String</rangeTypeName>
> </featureDescription>
> </features>
> </typeDescription>
>
> </types>
> </typeSystemDescription>
>
>
Re: No sofaFS for specified sofaRef found
Posted by Richard Eckart de Castilho <re...@apache.org>.
The CasCopier was not rewritten for DKPro Core - there are just a few
copies of an old UIMA CasCopier with minor modifications sprinkled
around the DKPro Core source base. At some point, these will be removed
and the canonical UIMA CasCopier will be used.
The CasCopier may not set the sofa in some circumstances, e.g. when
feature structures are copied one-by-one instead of copying whole views.
Marshall recently had started a thread on the developers list about
improving the CasCopier while maintaining backwards compatibility.
See also: https://cwiki.apache.org/confluence/display/UIMA/CasCopier+and+Views
Cheers,
-- Richard
> On 07.05.2016, at 22:15, Pablo N. Mendes <pa...@gmail.com> wrote:
>
> Thanks for your reply. I did not generate the XMI. It was provided to me in
> a file and I could not for the life of me figure out why it wasn't parsing.
> Only after I added the sofa="1" it deserialized perfectly.
>
> So I figured I'd send a comment here to:
> 1) make it easier for others searching for this error message;
> 2) see if the community feels like it's worth changing the error message
> (so it's clearer) or the parsing code so that this is not an issue in the
> future (e.g. couldn't we assume sofa=1 when not specified?)
>
> Is CasCopier known to omit sofa=1 when generating XMI? I noticed you
> rewrote it for DKPro.
>
> Cheers,
> Pablo
>
>
> On Sat, May 7, 2016 at 6:46 AM, Richard Eckart de Castilho <re...@apache.org>
> wrote:
>
>> Were you using a CasCopier for the generation of this XMI?
>>
>> Cheers,
>>
>> -- Richard
>>
>>> On 07.05.2016, at 00:30, Pablo N. Mendes <pa...@gmail.com> wrote:
>>>
>>> Folks,
>>> I am getting "No sofaFS for specified sofaRef found" while trying to
>>> deserialize an XMI. I found the message a bit cryptic and didn't find
>> much
>>> help on the lazyweb, so I bit the bullet and spent a few hours poking
>>> around. It seems to be a missing "sofa" attribute. If the sofa attribute
>>> has the wrong value, then you get "xmi id <id> is referenced but not
>>> defined" which is very nice and clear. But if you omit the sofa attribute
>>> you get "No sofaFS for specified sofaRef found" which is less informative
>>> IMHO.
>>>
>>> Extra info below.
>>>
>>> Cheers,
>>> Pablo
>>>
>>> $ diff cas1.xmi cas2.xmi
>>> 9c9
>>> < <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
>>> documentId="001"/>
>>> ---
>>>> <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
>>>
>>>
>>>
>>>
>>> VERSIONS
>>>
>>> <uima.version>2.8.1</uima.version>
>>> <uimafit.version>2.1.0</uimafit.version>
>>>
>>> JAVA CODE SNIPPET
>>>
>>> org.apache.uima.util.XmlCasDeserializer.deserialize(inputStream,
>>> jCas.getCas());
>>>
>>> STACK TRACE
>>>
>>> Exception in thread "main" org.apache.uima.cas.CASRuntimeException: No
>>> sofaFS for specified sofaRef found.
>>> at org.apache.uima.cas.impl.CASImpl.getSofa(CASImpl.java:806)
>>> at
>>>
>> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS_common(FSIndexRepositoryImpl.java:2781)
>>> at
>>>
>> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS(FSIndexRepositoryImpl.java:2763)
>>> at
>>>
>> org.apache.uima.cas.impl.FSIndexRepositoryImpl.addFS(FSIndexRepositoryImpl.java:2068)
>>> at
>>>
>> org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.endDocument(XmiCasDeserializer.java:1486)
>>> at
>>>
>> org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.endDocument(XmlCasDeserializer.java:127)
>>> at org.apache.xerces.parsers.AbstractSAXParser.endDocument(Unknown
>> Source)
>>> at org.apache.xerces.impl.XMLDocumentScannerImpl.endEntity(Unknown
>> Source)
>>> at org.apache.xerces.impl.XMLEntityManager.endEntity(Unknown Source)
>>> at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
>>> at org.apache.xerces.impl.XMLEntityScanner.skipSpaces(Unknown Source)
>>> at
>>>
>> org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown
>>> Source)
>>> at
>>>
>> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
>>> Source)
>>> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>>> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
>>> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
>>> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
>>> at
>>>
>> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:83)
>>> at
>>>
>> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:58)
>>> ...
>>>
>>>
>>> CAS1.xmi
>>>
>>> <?xml version="1.0" encoding="UTF-8"?>
>>> <xmi:XMI
>>> xmlns:cas="http:///uima/cas.ecore"
>>> xmlns:tcas="http:///uima/tcas.ecore"
>>> xmlns:xmi="http://www.omg.org/XMI"
>>> xmlns:ls="http:///com/example.ecore"
>>> xmi:version="2.0">
>>> <cas:NULL xmi:id="0"/>
>>> <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
>>> documentId="001"/>
>>> <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
>>> sofaString="This is a test."/>
>>> <cas:View sofa="1" members="18"/>
>>> </xmi:XMI>
>>>
>>>
>>> CAS2.xmi
>>>
>>> <?xml version="1.0" encoding="UTF-8"?>
>>> <xmi:XMI
>>> xmlns:cas="http:///uima/cas.ecore"
>>> xmlns:tcas="http:///uima/tcas.ecore"
>>> xmlns:xmi="http://www.omg.org/XMI"
>>> xmlns:ls="http:///com/example.ecore"
>>> xmi:version="2.0">
>>> <cas:NULL xmi:id="0"/>
>>> <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
>>> <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
>>> sofaString="This is a test."/>
>>> <cas:View sofa="1" members="18"/>
>>> </xmi:XMI>
>>>
>>>
>>> TYPESYSTEM
>>>
>>> <?xml version="1.0" encoding="UTF-8" ?>
>>>
>>> <typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier
>> ">
>>> <name>ExampleTypeSystem</name>
>>> <description>Just an example</description>
>>> <vendor>example.com</vendor>
>>> <version>1.0</version>
>>> <types>
>>> <typeDescription>
>>> <name>com.example.DocumentMetadata</name>
>>> <description></description>
>>>
>>> <supertypeName>uima.tcas.DocumentAnnotation</supertypeName>
>>> <features>
>>> <featureDescription>
>>> <name>source</name>
>>> <description>Source</description>
>>>
>>> <rangeTypeName>uima.cas.String</rangeTypeName>
>>> </featureDescription>
>>> <featureDescription>
>>> <name>documentId</name>
>>> <description>Source</description>
>>>
>>> <rangeTypeName>uima.cas.String</rangeTypeName>
>>> </featureDescription>
>>> </features>
>>> </typeDescription>
>>>
>>> </types>
>>> </typeSystemDescription>
>>>
>>>
>>> --
>>> Pablo N. Mendes
>>> http://pablomendes.com
>>
>>
>
>
> --
>
> Pablo N. Mendes
> http://pablomendes.com
Re: No sofaFS for specified sofaRef found
Posted by "Pablo N. Mendes" <pa...@gmail.com>.
Thanks for your reply. I did not generate the XMI. It was provided to me in
a file and I could not for the life of me figure out why it wasn't parsing.
Only after I added the sofa="1" it deserialized perfectly.
So I figured I'd send a comment here to:
1) make it easier for others searching for this error message;
2) see if the community feels like it's worth changing the error message
(so it's clearer) or the parsing code so that this is not an issue in the
future (e.g. couldn't we assume sofa=1 when not specified?)
Is CasCopier known to omit sofa=1 when generating XMI? I noticed you
rewrote it for DKPro.
Cheers,
Pablo
On Sat, May 7, 2016 at 6:46 AM, Richard Eckart de Castilho <re...@apache.org>
wrote:
> Were you using a CasCopier for the generation of this XMI?
>
> Cheers,
>
> -- Richard
>
> > On 07.05.2016, at 00:30, Pablo N. Mendes <pa...@gmail.com> wrote:
> >
> > Folks,
> > I am getting "No sofaFS for specified sofaRef found" while trying to
> > deserialize an XMI. I found the message a bit cryptic and didn't find
> much
> > help on the lazyweb, so I bit the bullet and spent a few hours poking
> > around. It seems to be a missing "sofa" attribute. If the sofa attribute
> > has the wrong value, then you get "xmi id <id> is referenced but not
> > defined" which is very nice and clear. But if you omit the sofa attribute
> > you get "No sofaFS for specified sofaRef found" which is less informative
> > IMHO.
> >
> > Extra info below.
> >
> > Cheers,
> > Pablo
> >
> > $ diff cas1.xmi cas2.xmi
> > 9c9
> > < <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
> > documentId="001"/>
> > ---
> >> <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
> >
> >
> >
> >
> > VERSIONS
> >
> > <uima.version>2.8.1</uima.version>
> > <uimafit.version>2.1.0</uimafit.version>
> >
> > JAVA CODE SNIPPET
> >
> > org.apache.uima.util.XmlCasDeserializer.deserialize(inputStream,
> > jCas.getCas());
> >
> > STACK TRACE
> >
> > Exception in thread "main" org.apache.uima.cas.CASRuntimeException: No
> > sofaFS for specified sofaRef found.
> > at org.apache.uima.cas.impl.CASImpl.getSofa(CASImpl.java:806)
> > at
> >
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS_common(FSIndexRepositoryImpl.java:2781)
> > at
> >
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS(FSIndexRepositoryImpl.java:2763)
> > at
> >
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.addFS(FSIndexRepositoryImpl.java:2068)
> > at
> >
> org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.endDocument(XmiCasDeserializer.java:1486)
> > at
> >
> org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.endDocument(XmlCasDeserializer.java:127)
> > at org.apache.xerces.parsers.AbstractSAXParser.endDocument(Unknown
> Source)
> > at org.apache.xerces.impl.XMLDocumentScannerImpl.endEntity(Unknown
> Source)
> > at org.apache.xerces.impl.XMLEntityManager.endEntity(Unknown Source)
> > at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
> > at org.apache.xerces.impl.XMLEntityScanner.skipSpaces(Unknown Source)
> > at
> >
> org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown
> > Source)
> > at
> >
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
> > Source)
> > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> > at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> > at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> > at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> > at
> >
> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:83)
> > at
> >
> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:58)
> > ...
> >
> >
> > CAS1.xmi
> >
> > <?xml version="1.0" encoding="UTF-8"?>
> > <xmi:XMI
> > xmlns:cas="http:///uima/cas.ecore"
> > xmlns:tcas="http:///uima/tcas.ecore"
> > xmlns:xmi="http://www.omg.org/XMI"
> > xmlns:ls="http:///com/example.ecore"
> > xmi:version="2.0">
> > <cas:NULL xmi:id="0"/>
> > <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
> > documentId="001"/>
> > <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
> > sofaString="This is a test."/>
> > <cas:View sofa="1" members="18"/>
> > </xmi:XMI>
> >
> >
> > CAS2.xmi
> >
> > <?xml version="1.0" encoding="UTF-8"?>
> > <xmi:XMI
> > xmlns:cas="http:///uima/cas.ecore"
> > xmlns:tcas="http:///uima/tcas.ecore"
> > xmlns:xmi="http://www.omg.org/XMI"
> > xmlns:ls="http:///com/example.ecore"
> > xmi:version="2.0">
> > <cas:NULL xmi:id="0"/>
> > <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
> > <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
> > sofaString="This is a test."/>
> > <cas:View sofa="1" members="18"/>
> > </xmi:XMI>
> >
> >
> > TYPESYSTEM
> >
> > <?xml version="1.0" encoding="UTF-8" ?>
> >
> > <typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier
> ">
> > <name>ExampleTypeSystem</name>
> > <description>Just an example</description>
> > <vendor>example.com</vendor>
> > <version>1.0</version>
> > <types>
> > <typeDescription>
> > <name>com.example.DocumentMetadata</name>
> > <description></description>
> >
> > <supertypeName>uima.tcas.DocumentAnnotation</supertypeName>
> > <features>
> > <featureDescription>
> > <name>source</name>
> > <description>Source</description>
> >
> > <rangeTypeName>uima.cas.String</rangeTypeName>
> > </featureDescription>
> > <featureDescription>
> > <name>documentId</name>
> > <description>Source</description>
> >
> > <rangeTypeName>uima.cas.String</rangeTypeName>
> > </featureDescription>
> > </features>
> > </typeDescription>
> >
> > </types>
> > </typeSystemDescription>
> >
> >
> > --
> > Pablo N. Mendes
> > http://pablomendes.com
>
>
--
Pablo N. Mendes
http://pablomendes.com
Re: No sofaFS for specified sofaRef found
Posted by Richard Eckart de Castilho <re...@apache.org>.
Were you using a CasCopier for the generation of this XMI?
Cheers,
-- Richard
> On 07.05.2016, at 00:30, Pablo N. Mendes <pa...@gmail.com> wrote:
>
> Folks,
> I am getting "No sofaFS for specified sofaRef found" while trying to
> deserialize an XMI. I found the message a bit cryptic and didn't find much
> help on the lazyweb, so I bit the bullet and spent a few hours poking
> around. It seems to be a missing "sofa" attribute. If the sofa attribute
> has the wrong value, then you get "xmi id <id> is referenced but not
> defined" which is very nice and clear. But if you omit the sofa attribute
> you get "No sofaFS for specified sofaRef found" which is less informative
> IMHO.
>
> Extra info below.
>
> Cheers,
> Pablo
>
> $ diff cas1.xmi cas2.xmi
> 9c9
> < <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
> documentId="001"/>
> ---
>> <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
>
>
>
>
> VERSIONS
>
> <uima.version>2.8.1</uima.version>
> <uimafit.version>2.1.0</uimafit.version>
>
> JAVA CODE SNIPPET
>
> org.apache.uima.util.XmlCasDeserializer.deserialize(inputStream,
> jCas.getCas());
>
> STACK TRACE
>
> Exception in thread "main" org.apache.uima.cas.CASRuntimeException: No
> sofaFS for specified sofaRef found.
> at org.apache.uima.cas.impl.CASImpl.getSofa(CASImpl.java:806)
> at
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS_common(FSIndexRepositoryImpl.java:2781)
> at
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.ll_addFS(FSIndexRepositoryImpl.java:2763)
> at
> org.apache.uima.cas.impl.FSIndexRepositoryImpl.addFS(FSIndexRepositoryImpl.java:2068)
> at
> org.apache.uima.cas.impl.XmiCasDeserializer$XmiCasDeserializerHandler.endDocument(XmiCasDeserializer.java:1486)
> at
> org.apache.uima.util.XmlCasDeserializer$XmlCasDeserializerHandler.endDocument(XmlCasDeserializer.java:127)
> at org.apache.xerces.parsers.AbstractSAXParser.endDocument(Unknown Source)
> at org.apache.xerces.impl.XMLDocumentScannerImpl.endEntity(Unknown Source)
> at org.apache.xerces.impl.XMLEntityManager.endEntity(Unknown Source)
> at org.apache.xerces.impl.XMLEntityScanner.load(Unknown Source)
> at org.apache.xerces.impl.XMLEntityScanner.skipSpaces(Unknown Source)
> at
> org.apache.xerces.impl.XMLDocumentScannerImpl$TrailingMiscDispatcher.dispatch(Unknown
> Source)
> at
> org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
> Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
> at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
> at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
> at
> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:83)
> at
> org.apache.uima.util.XmlCasDeserializer.deserialize(XmlCasDeserializer.java:58)
> ...
>
>
> CAS1.xmi
>
> <?xml version="1.0" encoding="UTF-8"?>
> <xmi:XMI
> xmlns:cas="http:///uima/cas.ecore"
> xmlns:tcas="http:///uima/tcas.ecore"
> xmlns:xmi="http://www.omg.org/XMI"
> xmlns:ls="http:///com/example.ecore"
> xmi:version="2.0">
> <cas:NULL xmi:id="0"/>
> <ls:DocumentMetadata xmi:id="18" sofa="1" source="file001.txt"
> documentId="001"/>
> <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
> sofaString="This is a test."/>
> <cas:View sofa="1" members="18"/>
> </xmi:XMI>
>
>
> CAS2.xmi
>
> <?xml version="1.0" encoding="UTF-8"?>
> <xmi:XMI
> xmlns:cas="http:///uima/cas.ecore"
> xmlns:tcas="http:///uima/tcas.ecore"
> xmlns:xmi="http://www.omg.org/XMI"
> xmlns:ls="http:///com/example.ecore"
> xmi:version="2.0">
> <cas:NULL xmi:id="0"/>
> <ls:DocumentMetadata xmi:id="18" source="file001.txt" documentId="001"/>
> <cas:Sofa xmi:id="1" sofaNum="1" sofaID="_InitialView" mimeType="text"
> sofaString="This is a test."/>
> <cas:View sofa="1" members="18"/>
> </xmi:XMI>
>
>
> TYPESYSTEM
>
> <?xml version="1.0" encoding="UTF-8" ?>
>
> <typeSystemDescription xmlns="http://uima.apache.org/resourceSpecifier">
> <name>ExampleTypeSystem</name>
> <description>Just an example</description>
> <vendor>example.com</vendor>
> <version>1.0</version>
> <types>
> <typeDescription>
> <name>com.example.DocumentMetadata</name>
> <description></description>
>
> <supertypeName>uima.tcas.DocumentAnnotation</supertypeName>
> <features>
> <featureDescription>
> <name>source</name>
> <description>Source</description>
>
> <rangeTypeName>uima.cas.String</rangeTypeName>
> </featureDescription>
> <featureDescription>
> <name>documentId</name>
> <description>Source</description>
>
> <rangeTypeName>uima.cas.String</rangeTypeName>
> </featureDescription>
> </features>
> </typeDescription>
>
> </types>
> </typeSystemDescription>
>
>
> --
> Pablo N. Mendes
> http://pablomendes.com