[Dspace-tech] Replacing handles with other identifier

2008-03-14 Thread Gary McGath
I'm a relative newbie at DSpace, but I've been asked to look into 
replacing handles with a different persistent identifier for our 
installation (still in the planning stages). From what I've read on the 
archive, this is a somewhat difficult problem, as there are supposedly 
dependencies scattered throughout the code on the syntax of a handle.

 From a quick study of the code, I can't find any dependencies (beyond 
expecting a URI) outside of HandleManager.java. If this is true, we 
could use a different identifier by rewriting HandleManager.java -- not 
a tiny task, but at least a localized one. It's a bit unclean; 
HandleManager.java has to be rewritten rather than overridden because it 
uses static methods.

I'd suggest that a future implementation of DSpace should change 
HandleManager so that an instance is created factory-style. The instance 
could then be a subclass, depending on a configuration setting. All 
references to HandleManager would have to be changed to call the 
instance rather than the static method, so this would be a somewhat 
disruptive change, but not one that would cause major coding difficulties.

Am I on the right track here, or are there other issues which I've missed?

-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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Re: [Dspace-tech] Replacing handles with other identifier

2008-03-14 Thread Gary McGath
Richard Jones wrote:
> Hi Gary,
> 
> Which alternative identifier system were you planning on?

We'd be using Harvard's Name Resolution Service (NRS) URN's, which is 
used for our Digital Repository Service and E-Resources.

> For DSpace 1.6, we have rewritten a lot of the code for handling 
> identifiers, and thus adding new schemes is much much more 
> straightforward.  I'm about to go on holiday, but when I get back I'd be 
> really interested in talking more with you about what you want to do.  
> In the mean time, please feel free to take a look at the trunk in 
> sourceforge.  

Thanks!

-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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[Dspace-tech] Persistent identifiers, again

2008-04-07 Thread Gary McGath
As some of you may recall, I've been looking into implementing a 
non-Handle approach to persistent identifiers in our local version of 
DSpace. My approach has been to replace HandleManager bodily. So far 
I've gotten it to the point where it has the same functionality as 
out-of-the-box DSpace; that is, the handles don't work when accessed as 
external identifiers, but a manual substitution of the URL base produces 
a working URL.

Each time I blow away DSpace (as often happens during early stages of 
code development), I've noticed that the ID's start over from 1. It 
looks to me as if the HandleManager doesn't provide a strong guarantee 
of uniqueness; if DSpace is totally reinitialized, old Handles may be 
recycled. If this happened in a production environment, Handles for 
obsolete objects could point to the wrong object, rather than failing to 
resolve as they should.

This makes me think that for our environment, which stresses the 
"unique" in URN's, I need to add a stronger guarantee of uniqueness. It 
also seems like a minor bug in DSpace.

Have I missed anything? Does something come into play when a live handle 
server is used, which provides a stronger guarantee of uniqueness?

I'm aware, by the way, that DSpace 1.6 has totally new code for 
non-Handle persistent identifiers. Our schedule doesn't let us wait. 
Don't blame me, I'm only the programmer. :)

-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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[Dspace-tech] Adding a jar to a DSpace 1.5 project

2008-04-16 Thread Gary McGath
It's embarrassing that I should have to ask how to make a simple change 
to a makefile, but I'm finding Maven to be one of the most bewildering, 
overly complex pieces of software I've run into.

I've added some Java code within dspace-api, in our own package. Maven 
sees that, with no problem, and tries to compile it. But for it to 
compile successfully, it needs to use a couple of .jar files which we 
have previously developed here. I've put the jars into 
(dspace/target/dspace-1.5.0-build.dir/lib/), but that's not enough to 
get them picked up. I'm guessing that I have to add  tags to 
pom.xml, but can't find any documentation which I can comprehend.

The pom reference page (http://maven.apache.org/pom.html) talks about 
the groupId and artifactId, but neither one of these seems to be the 
name or path of the jar file. The packaging tag tells Maven that it _is_ 
a jar file, but apparently nothing more specific than that. Could 
someone point me at a simple explanation of how to get this to work?



-- 
Gary McGath
Digital Library Software Engineer
Harvard University Libraries, Office for Information Systems

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Re: [Dspace-tech] Adding a jar to a DSpace 1.5 project

2008-04-16 Thread Gary McGath
Mark Diggory wrote:
> 
> On Apr 16, 2008, at 12:11 PM, Gary McGath wrote:
> 
>> It's embarrassing that I should have to ask how to make a simple  change
>> to a makefile, but I'm finding Maven to be one of the most  bewildering,
>> overly complex pieces of software I've run into.
> 
> 
> Well, it is different than most "Make" or "Ant" tools out there  because 
> it is both a build tool and a distribution management tool,  much like 
> Yum/RPM, Gentoo/Emerge, Perl/CPAN, or R/CRAN.  If you can  wrap your 
> head around that, it will save you some frustration.  It is  just a 
> different model.
> 
>> I've added some Java code within dspace-api, in our own package.
> 
> 
> We've moved away from suggesting that you add code to dspace-api or  
> alter code there, this is one of the reasons we aopted MAven, was to  
> modularize the codebase and free the end user from having to alter  this 
> code directly and worry about "merging changes" all the time.
> 
>> Maven sees that, with no problem, and tries to compile it. But for  it to
>> compile successfully, it needs to use a couple of .jar files which we
>> have previously developed here.
> 
> 
> Tell me a little about those tools you've developed? How are they  
> managed, is there a release cycle... I can direct you on how to  install 
> them into Maven and adjust the build dependencies so they are  included.

The starting point of what I'm doing is replacing HandleManager.java in 
place with our own code -- ugly but necessary, since it consists 
entirely of static methods. To make it generate real persistent 
identifiers, it's necessary to add a couple of supporting classes, which 
I've put in an edu.harvard.hul.ois package, and these in turn require 
some jar files.

Should I be creating a new subproject for this code (other than 
HandleManager)? Thanks for any help you can offer.

-- 
Gary McGath
Digital Library Software Engineer
Harvard University Libraries, Office for Information Systems

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Re: [Dspace-tech] Adding a jar to a DSpace 1.5 project

2008-04-16 Thread Gary McGath
Mark Diggory wrote:
> 
> On Apr 16, 2008, at 1:03 PM, Gary McGath wrote:
> 
>> Mark Diggory wrote:
> 
> 
>>> Tell me a little about those tools you've developed? How are they
>>> managed, is there a release cycle... I can direct you on how to   
>>> install
>>> them into Maven and adjust the build dependencies so they are   
>>> included.
>>
>>
>> The starting point of what I'm doing is replacing  HandleManager.java in
>> place with our own code -- ugly but necessary, since it consists
>> entirely of static methods. To make it generate real persistent
>> identifiers, it's necessary to add a couple of supporting classes,  which
>> I've put in an edu.harvard.hul.ois package, and these in turn require
>> some jar files.
> 
> 
> Sounds like your trying to use the Harvard Naming Service? Can you  give 
> me a list of the jars you require? Are any of them third party  to OIS?

The files are nrs.jar and jdbc.jar, both local to OIS. The Java files so 
far are called URNMaker.java and URNException.java. The jar files set up 
a thin JDBC wrapper for talking to our Name Resolution Service database. 
It's not a huge amount of code. There are a few extra items in the 
config file to set up the database connection.

We have the jars set up in a local repository (Unix directory), with 
some simple version management. The repository isn't mounted on the 
machine we're using for DSpace work and isn't available by HTTP, so 
Maven's proclivity for fetching resources from repositories might be 
difficult to satisfy.

> Its a tough call, we are currently rewriting the whole Handle/ 
> Identifier mechanism (as we discussed earlier).  In this case there  may 
> be a mix of approaches,  It might just be better to alter dspace- api 
> (HandleManager) then port over to the new Identifier service when  it 
> comes out in the next major release (but that may very well be  next 
> year). Which would mean that you'd need to port over your  changes to 
> dspace-api on every minor release.
> 
> But if you do, it would save you work later if you encapsulate all  your 
> hul.ois identifier stuff in a separate addon project. This  project 
> would be added as a modules to [dspace-source]/dspace/pom.xml  and added 
> as a dependency in that pom (for CLI applications) and in  
> [dspace-source]/dspace/modules/pom.xml (for webapplications)
> 
> tell me a little more about all the added dependencies and I'll try  to 
> map out the strategy in that context.


-- 
Gary McGath
Digital Library Software Engineer
Harvard University Libraries, Office for Information Systems

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Re: [Dspace-tech] Adding a jar to a DSpace 1.5 project

2008-04-16 Thread Gary McGath
I've managed to get it to compile without errors as a new subproject; 
many thanks! Distributing the jars in a local maven repository is a bit 
more than I want to deal with right now.

Mark Diggory wrote:

> A slight tangent... does OIS consider these jars to be private  
> resources, or do they consider at all sharing them with a larger  
> community at Harvard?  Maybe theres an option for distributing them  in 
> a local maven repository of their own?
> 
>> We have the jars set up in a local repository (Unix directory), with
>> some simple version management. The repository isn't mounted on the
>> machine we're using for DSpace work and isn't available by HTTP, so
>> Maven's proclivity for fetching resources from repositories might be
>> difficult to satisfy.
> 
> 
> I doubt it'd be in the same format anyways. Are you working on  
> deploying just one server, or do you expect this to be What I would  
> recommend
> 
> so, if you wanted to build against these dependencies "right now" yo  
> would do:
> 
> mvn install:install-file -Dfile=location/of/jdbc.jar - 
> DgroupId=edu.harvard.hul.ois -DartifactId=ois-jdbc -Dversion=X.X.X  - 
> Dpackaging=jar
> mvn install:install-file -Dfile=location/of/nrs.jar   - 
> DgroupId=edu.harvard.hul.ois -DartifactId=ois-nrs   -Dversion=X.X.X  - 
> Dpackaging=jar
> 
> where X.X.X is the version you wish to be using (you can make that up  
> if you like or use whatever is already there. then in you pom...  first 
> pass I'd say just do it in dspace-api/pom.xml (later we may  create 
> another maven project if it benefits you).
> 
> 
> ois-jdbc
> edu.harvard.hul.ois
> X.X.X
> 
> 
> 
> ois-nrs
> edu.harvard.hul.ois
> X.X.X
> 
> 
> You'll need to do this again on any server (or user) your running  
> another maven repository in (thus the benefit of deploying instead to  a 
> locally maintained maven repository) which would be added to as a  
>  in the pom and thus the jars could be gotten from on any  
> account/server you were building on.  If you reach this point, it  
> definitely benefits you to consider having a separate maven project  for 
> the nrs HandleManager adapter that preserves this customization  
> independent of the dspace codebase.


-- 
Gary McGath
Digital Library Software Engineer
Harvard University Libraries, Office for Information Systems

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[Dspace-tech] Embargo on DSpace 1.5

2008-04-22 Thread Gary McGath
Has anyone managed to adapt Jose Blanco's embargo fix 
(http://wiki.dspace.org/index.php/Embargo_on_Bitstream_v2_%28JSP%29) to 
DSpace 1.5? I'm starting to go through it, since some form of embargo is 
among our requirements; some directories have moved, which isn't too 
bad, but there may more subtle issues, and something for the XMLUI 
paralleling the JSP appears to be needed.

-- 
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Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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Re: [Dspace-tech] Including a handle for the German national, > library

2008-04-25 Thread Gary McGath

> Date: Fri, 25 Apr 2008 12:38:39 +0200
> From: Robert Roggenbuck <[EMAIL PROTECTED]>
> Subject: [Dspace-tech] Including a handle for the German national
>   library
> 
> Hi all,
> 
> recently we decided to set up our OA-Repository using DSpace.
> Now I have a question regarding special German circumstances: Is it 
> possible to replace the "CNRI Handle"-mechanism by a "DNB-URN"?

We have been working on a similar issue here. I assume you mean that you 
want a permanent link to the Deutsche Bibliothek's own naming repository 
rather than using handle.net?

We have been able to do that by making changes in DSpace 1.5 to 
HandleManager.java and writing some custom code to interface to our own 
naming repository. It's a bit ugly, but not as bad as some people have 
made it out to be. I could send you a copy of what we have done if you 
are interested.


-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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Re: [Dspace-tech] Embargo on DSpace 1.5

2008-05-07 Thread Gary McGath
Elliot Metsger <[EMAIL PROTECTED]> wrote:
> Depending on your timeline for embargo implementation, you may want to take
> a look at http://wiki.dspace.org/index.php/User:Emetsger:Embargo .  Its an
> embargo implementation I'm working on, and hopefully porting to 1.5 this
> summer...  additional eyes/coding/feedback appreciated.

Elliot,

I've been aware of your work for some time. Unfortunately, we're on a 
very tight schedule here. I've found that a significant amount of new 
work is needed to implement embargo in Manakin, and just figuring out 
where the hooks should go is the trickiest part. Right now I'm 
concentrating on the post-processing classes for the steps, which are in 
org.dspace.submit.step under dspace-api.

-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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[Dspace-tech] Item submission details in Manakin

2008-06-10 Thread Gary McGath
I previously asked about general information on finding one's way around 
Manakin, without success. Taking that to mean that there aren't any 
overall road maps available, I'll recast my question in terms of what 
I'm trying to do.

I am attempting to implement an embargo feature on the XMLUI side of 
DSpace 1.5. For this, I'm making some use of "Embargo V2" 
(http://wiki.dspace.org/index.php/Embargo_on_Bitstream_v2_%28JSP%29), 
but that's oriented toward the JSP user interface, so a lot has to be 
re-invented. I've figured out large parts of it, and even added Oracle 
SQL to that page, but need some help on the remaining bits.

I've added an embargo date to the license page. My code subclasses 
dspace-xmlui/dspace-xmlui-api/src/main/java/org/dspace/app/xmlui/aspect/submission/submit/LicenseStep.java
to put the embargo date field into the page, and
dspace-api/src/main/java/org/dspace/submit/step/LicenseStep.java
to process the embargo date.

This ultimately needs to add the ID of the created item to the 
"umrestricted" table which is defined by Embargo V2, and put the embargo 
date into the "date.available" metadata for the item. This can only be 
done at the conclusion of creating the item (or so I assume), but I'm 
having an oddly hard time figuring out where that final step is done.

Can someone give me a pointer on that?

-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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Re: [Dspace-tech] DSpace-tech Digest, Vol 26, Issue 42

2008-06-17 Thread Gary McGath
Sorry about the in-house cross-talk, but this one is under control. For 
some reason we're still working on, the database for the malfunctioning 
instance didn't have the views COMMUNITY2ITEM and DCVALUE, which it was 
supposed to have. This is, we're assuming, an error in the database 
creation process and not any kind of DSpace bug.

Flemion Shafeeq <[EMAIL PROTECTED]> wrote:

>>>We have customised dspace in our development machine and tried to run the 
>>application on a different box, trying some kind of production environment 
>>here.
>>Here the browse functionality particularly for the Authors and the Subject 
>>link is not retrieving any items submitted to the community/collection we 
>>have set up.
>>The browse links such as "By issue date" and "titles" does returns the 
>>item in the collection/community.
>>The entire browse functionality is working fine in our development server.
>>Checked all configurations in the second machine, but its  more or less 
>>the same.
>>Tried re-indexing the production server, by following steps on wiki. But 
>>the script index-all mentioned is absent on [dspace]/bin, Instead there are
>>2 scripts in the name of index-init and index-update
>>Tried running each of them but its throwing the following error



-- 
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Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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[Dspace-tech] DatabaseManager question

2008-06-29 Thread Gary McGath
Sigh ... Implemnting embargo on the Manakin side of DSpace 1.5 is 
proving to be the bane of my life. I appreciate the suggestions I've 
received, but most of them require waiting, and that isn't an option.

Anyway, I've been trying to implement a variant of Embargo v2 
(http://wiki.dspace.org/index.php/Embargo_on_Bitstream_v2_%28JSP%29), 
and making some progress. It comes down to a modification to 
dspace-api/src/main/java/org/dspace/content/InstallItem.java , where I 
add the following code to installItem:

  DCValue[] dateAvailable = item.getDC("date", "available", Item.ANY);
  if (dateAvailable.length > 0)
   {
   DCValue dcDate = dateAvailable[0];
   String dateStr = dcDate.value;
   // Convert -mm-dd to Date object
   int hyph1 = dateStr.indexOf ('-');
   int hyph2 = dateStr.indexOf ('-', hyph1 + 1);
   if (hyph1 > 0 && hyph2 > hyph1) {
   int year = 2000, month = 1, day = 1;
   try {
 year = Integer.parseInt
   (dateStr.substring (0, hyph1 ));
 month = Integer.parseInt
   (dateStr.substring (hyph1 + 1, hyph2 ));
 day = Integer.parseInt
   (dateStr.substring (hyph2 + 1));
   }
   catch (Exception e) {}
   Calendar cal = Calendar.getInstance ();
   cal.set (year, month, day);
   //item.addDC("date", "available", null, now.toString());
   TableRow row = DatabaseManager.create (c, "umrestricted");
   row.setColumn ("item_id", item.getID());
   row.setColumn ("release_date", cal.getTime());
   int n = DatabaseManager.update(c, row);
   }
   }

What I'm finding is that the row is created, but the item_id and 
release_date fields are null. I can add rows with non-null values using 
a desktop database client. I've put debugging code into 
TableRow.setColumn(String, Date), so I know that it's being reached, has 
correct data, and appears to complete correctly. I've stripped out the 
debugging code for readability, but it shows that DatabaseManager.update 
() is returning 0; i.e., it thinks that the row hasn't been modified in 
spite of my setColumn calls.

Obviously I'm doing something wrong, but can't figure out what. Any 
suggestions on what I might try?


-- 
Gary McGath
Digital Library Software Engineer
Harvard University Libraries, Office for Information Systems

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Re: [Dspace-tech] DatabaseManager question

2008-06-30 Thread Gary McGath
Gary McGath wrote:
> Sigh ... Implemnting embargo on the Manakin side of DSpace 1.5 is 
> proving to be the bane of my life. I appreciate the suggestions I've 
> received, but most of them require waiting, and that isn't an option.
> 
> Anyway, I've been trying to implement a variant of Embargo v2 
> (http://wiki.dspace.org/index.php/Embargo_on_Bitstream_v2_%28JSP%29), 
> and making some progress. It comes down to a modification to 
> dspace-api/src/main/java/org/dspace/content/InstallItem.java , where I 
> add the following code to installItem:

I've found the problem, or at least a major part of it. In the Wiki, I'd 
provided Oracle code to set the primary key with a trigger, since the 
DEFAULT clause isn't legal under Oracle. But this was conflicting with 
DSpace's wrapper classes, with the result that the primary key was 
apparently being set twice. This meant that the UPDATE statement 
generated by DatabaseManager.java used a primary key value that didn't 
belong to the row it was trying to update.

I altered my database to remove the trigger, and now at least rows are 
appearing in the UMRESTRICTED table which have actual data. I'm 
wondering if the DEFAULT clause should be there at all, even for 
Postgresql. I'm far from an SQL expert, so my conclusions should be 
treated with caution.

I've updated the wiki page 
(http://wiki.dspace.org/index.php/Embargo_on_Bitstream_v2_%28JSP%29#Create_Database_Tables)
 
to delete the offending trigger, so that now the Oracle code looks just 
like the old SQL except for the absence of a DEFAULT clause.

If there are further issues with this, I'll post again to the list.


-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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[Dspace-tech] Achieving security by obscurity

2008-07-08 Thread Gary McGath
In order to prevent provenance metadata from being easily reached by 
users, and to make embargoing watertight, I'd like to disable the 
"metadata" URLs in Manakin. (I've disabled METS output in the OAI 
provider for the same reason.) Since they're useful for debugging 
purposes, it would be nice to have them available, so changing the path 
component from "metadata" to something else seems like a useful 
approach. To this end, I edited 
(dspace-xmlui/dspace-xmlui-webapp/src/main/webapp/sitemap.xmap) and 
changed the relevant map:match element.  When I restarted DSpace, 
though, it hung. Changing it back let DSpace run normally.

Is there something else that needs to be changed in order to disable or 
modify the metadata URLs?

-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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Re: [Dspace-tech] Achieving security by obscurity

2008-07-08 Thread Gary McGath
Mark Diggory wrote:

> Likewise I've not been very concerned about its exposure (albeit the  
> submitters email address embedded there) Ideally this user info in  
> the provenence metadata should contain obviscated email addresses  
> like the kind that are allowed as sha signatures in FOAF persons.  
> Attaching that signature as metadata to the eperson and allowing  
> lookup via sha signatures would allow the admins to get back to the  
> user that submitted or approved the item from the metadata. and thus  
> there would be no need to hide the actual metadata fields from the  
> public.

Whatever the ideal may be, the reality is that there are e-mail 
addresses in the provenance data. I consider it the basic responsibility 
of any web application not to publish people's e-mail addresses without 
their consent. The second problem, peculiar to us because of the embargo 
requirement, is the inclusion of the bitstream file names, which make it 
easy to access embargoed files. On both counts, the exposure of 
provenance metadata is a serious problem and can't wait for 1.5.1.

> The "metadata/" space is currently being used as a "catch-all" for  
> exposing various types of metadata to the user (at least in my  
> usage), it shouldn't be difficult to block it behind either  
> authentication or drop it entirely using the sitemap.xmap  
> configuration of Cocoon in the dspace/modules/xmlui/src/main/webapp/ 
> sitemap.xmap.  You'll need to obtain a copy from the dspace-xmlui- 
> webapp/src/main/webap/sitemap.xmap.

As I said in my post, that was what I did. My first attempt was to 
change "metadata" to some other string of letters (let's say 
"detamata"). If I do that, Manakin hangs. I then refined the attempt to 
redirect "metadata/**" to something else. Same result.

-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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Re: [Dspace-tech] Achieving security by obscurity

2008-07-09 Thread Gary McGath
Scott Phillips wrote:
> We wanted to expose dspace's metadata in a way that can be used by  
> other applications. They are nice restfull urls that are actionable  
> and easily predictable. There are a few themes that will do client  
> side parsing of those urls in javascript, it opens the possibility for  
> other things to be created. That's not a big argument for handles over  
> internal identifiers, remember manakin is several years in the making  
> and during the most of the design cycle dspace's independence from  
> handles was nothing but a pipedream with no one really working on it.
> 
> As a side note about the protection of Metadata. The DSpace API's data  
> model says that all metadata for any item (withdrawn or in progress)  
> is visible to any anonymous user. In general the dspace model is all  
> objects are visible, but may not be actionable or some parts may be  
> restricted. In my opinion the API should return an authorization  
> errors for attempting to access metadata on restricted items, and then  
> perhaps we could set some kid of security permissions on metadata  
> fields either in the registry or through some dspace.cfg parameter.  
> Although the xslt on the pipelie is a pretty easy hack that solves  
> your problem and is way easier to implement

This still leaves the problem of other ways the metadata can be viewed. 
For instance, we've disabled METS data from the OAI provider because of 
the same problem. I'm considering patching InstallItem.java so that it 
never puts the provenance element into the metadata in the first place. 
Would this cause any problems?


-- 
Gary McGath
Digital Library Software Engineer
Harvard University Library Office for Information Systems
http://hul.harvard.edu/~gary/index.html


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