Metacat

11/23/2011

02:55 PM Bug #5553 (New): setaccess action may have deleting access rule functionality

Currently, setaccess action can only add access rules to the metacat. There is a limitation.
Sometimes, we want to... Jing Tao

02:48 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).

Also i noticed after set the access, the delete, update and set access button disappeared. Only download button can b... Jing Tao

02:36 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).

Since "setaccess" action can add access rules, this will cause problem.
Since the documents' allow rules for public r... Jing Tao

02:23 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).

To a none-public readable document, if we click the set access button with the checked public read check box, the doc... Jing Tao

01:59 PM Bug #5551: Set public access button on the FGDC document display page doesn't work (on sanparks skin).

The kepler_kepler_21 is a FGDC document with the public readable access rule. Here is the record on xml_access:
keple... Jing Tao

11:09 AM Bug #5551 (Resolved): Set public access button on the FGDC document display page doesn't work (on sanparks skin).

When I tried to grant a public readable access to a nonpublic readable document, i got an error:
User public does n... Jing Tao

01:07 PM Bug #5537: Move replication control panel to /admin servlet

There is now a separate /admin screen for replication configuration. Now /replication can require SSL client certific... ben leinfelder

11:00 AM Bug #5530: Sanparks skin shows update and delete action when user public reads a FGDC package

Ben:
Okay. This is the current behavior. I am going to close the bug. Jing Tao

10:44 AM Bug #5530: Sanparks skin shows update and delete action when user public reads a FGDC package

I think the checkbox should reflect the current state of the document. If it is unchecked, that indicates that it is ... ben leinfelder

11/22/2011

05:10 PM Bug #5530: Sanparks skin shows update and delete action when user public reads a FGDC package

If fgdc-root.xsl, it has the control to display the buttons or not. The control is the parameter "enableFGDCediting".... Jing Tao

11/21/2011

02:22 PM Bug #5548 (New): Replace COS Mime multipart library

Here is a comment from Matt in bug 5543:
The COS Mime multipart library is incredibly old, and we should
seriousl... Jing Tao

02:20 PM Bug #5543: Can't upload a FGDC metadata file with a data file in SANParks skin

Ben committed a new version of cos.jar file and modified the MetacatClient.java to handle the file size being -1. In ... Jing Tao

11:33 AM Bug #5543: Can't upload a FGDC metadata file with a data file in SANParks skin

We may not even have to require a known size -- Metacat isn't storing that information. Sure, the new DataONE apis us... ben leinfelder

10:17 AM Bug #5547 (New): Couldn't get the Register Data Form after login under Register Data tab on Sanparks skin

When you click "Register Data" tab on Sanparks skin, it will show a login form if you haven't login. However, it will... Jing Tao

11/18/2011

07:51 PM Bug #5543: Can't upload a FGDC metadata file with a data file in SANParks skin

Jing --
I'm not sure what the right solution is here, but here are some thoughts. First, trying to get the length o... Matt Jones

05:58 PM Bug #5543: Can't upload a FGDC metadata file with a data file in SANParks skin

After dug around the code, i figured out the problem is at the CoientViewHelper.java.
In handlePackageUpload method,... Jing Tao

11/17/2011

04:04 PM Bug #4728: grant document management privileges to admin user

Admin user[s] now have complete control of the Metacata data and metadata. The list of items here (1-6) are covered n... ben leinfelder

02:40 PM Bug #5544 (Resolved): the footer of the output page after clicking TPC status/workflow can't be read on Sanparks skin

The text of the footer of the output page is black and can be read when a user click TPC workflow/status menu. Jing Tao

02:31 PM Bug #5542: Data Package Upload form in SANParks skin missing the description text

In footer, set some text to be regwhitetext. So everything looks fine. Jing Tao

02:30 PM Bug #5542: Data Package Upload form in SANParks skin missing the description text

The text was not missing, but its color was white and couldn't be read.
The regtext class in sanparks.css was set:
.... Jing Tao

12:03 PM Bug #5533: Sanpark skin main page has login issue

For the first issue that a user could not log in on IE, the reason is IE invalid the login form after a div, which co... Jing Tao

11/16/2011

02:55 PM Bug #5543 (Resolved): Can't upload a FGDC metadata file with a data file in SANParks skin

I tried to use the data package upload form to upload a FGDC file, it succeeded. However, if i uploaded a FGDC file w... Jing Tao

02:45 PM Bug #5542 (Resolved): Data Package Upload form in SANParks skin missing the description text

It misses the text like:
Enter the Meta Data File (*.xml)
Enter Data File 1 (*.shp)
Enter Data File 2 (*.dbf)
.... Jing Tao

11/15/2011

01:30 AM Bug #5513: add support for DOI identifiers from EZID

I created a new library called 'ezid' in its own project that can be used to access the EZID REST services from withi... Matt Jones

11/11/2011

09:10 AM Bug #5537 (Resolved): Move replication control panel to /admin servlet

Instead of using the SSL client certificate secured /replication servlet to administer replication settings via the w... ben leinfelder

09:00 AM Bug #5531: Remove/make optional the DataONE MN registration that occurs during Metacat configuration

There is now a separate admin configuration screen for dataone:
-you can bypass it in the same way you can bypass geo... ben leinfelder

11/09/2011

03:19 PM Bug #5353: EcogridWriter doesn't work with the metacat built from trunk.

Both Jing and I were unable to replicate this bug testing against a more recent Metacat trunk build ben leinfelder

02:56 PM Bug #5353: EcogridWriter doesn't work with the metacat built from trunk.

I tried this out with Kepler 2.1, writing sample EML 2.0.0 and EML 2.1.0 metadata (and data files). All worked out fi... ben leinfelder

12:14 PM Bug #5353: EcogridWriter doesn't work with the metacat built from trunk.

Is there a sample Kepler workflow we can use to debug this? ben leinfelder

02:28 PM Bug #3815: Ampersand character not correctly encoded

I just tried the registry on a test machine running most recent Metacat trunk and the ampersand was correctly encoded... ben leinfelder

12:47 PM Bug #5536: Restore replicated data files that are 0 bytes

Matt suggests an alternative approach: delete the files and the DB records for those files so that the next timed rep... ben leinfelder

12:23 PM Bug #5536 (Resolved): Restore replicated data files that are 0 bytes

Due to a replication bug, some data files were not replicated fully. These should be tracked down and restored. ben leinfelder

12:44 PM Bug #4405: PISCO, KNB and LTER have different query result for SBC datasets.

Running the query against the PISCO server returned the expected 14 records. ben leinfelder

12:33 PM Bug #5532: Use strict build tag strategy for 2.0.0 release

Looks good to me. Matt Jones

12:31 PM Bug #5532: Use strict build tag strategy for 2.0.0 release

Proposed tags. Please comment.
-eml schema 2.1.1 (tags/RELEASE_EML_2_1_1)
-eml style sheets (tags/RELEASE_EML_UTILS_1... ben leinfelder

12:22 PM Bug #5519: Replicated data files are 0 bytes

This is fixed. We just need to figure out the files that have not replicated successfully. Any 0-length files on KNB ... ben leinfelder

12:20 PM Bug #3811: Spatial caches should be backed up and restored

The final step in the process should be to _NOT_ regenerate the spatial cache during 2.0 configuration. ben leinfelder

12:13 PM Bug #5288: Metacat got "java.lang.OutOfMemoryError: PermGen space" after new geoserver update

added to word doc ben leinfelder

12:03 PM Bug #5513: add support for DOI identifiers from EZID

I've managed to get UCSB to agree to pay for an EZID account from CDL that we'll be able to use to programatically as... Matt Jones

10:31 AM Bug #5535 (New): The 611 CDR documents replicated to KNB need to be repaired by fixing their inline data.

This bug is the section 4 of the ongoing concerns:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3296
During... Jing Tao

09:59 AM Bug #5534 (Resolved): Replication log somehow doesn't work.

Metacat logged the some important replication information into the metacatreplication.log file which stays in the dir... Jing Tao

09:41 AM Bug #3296: Replication: Many EML documents fail to replicate

Follow-up to the previous comment of 2008-06-05:
1. There are still 94 documents that fail to replicate. These are a... Duane Costa

11/08/2011

08:19 AM Bug #5533: Sanpark skin main page has login issue

An additional message from judith:
Jing
I notice that when you login through the web page on firefox You get the me... Jing Tao

11/07/2011

05:43 PM Bug #4356: knb website query result shows old version of a document

Ben and I tested the updating and query on both forced replication and timed replication between two metacats. We cou... Jing Tao

04:07 PM Bug #4356: knb website query result shows old version of a document

I used a morpho to create a eml document and insert it to metacat. Then i did a search and records was added to xml_q... Jing Tao

11/04/2011

04:33 PM Bug #5533 (Resolved): Sanpark skin main page has login issue

Hi Jing
Yes I see that it works on firefox the problem is that all our staff have to use IE So is there a way to f... Jing Tao

03:18 PM Bug #5532 (Resolved): Use strict build tag strategy for 2.0.0 release

Currently Metacat relies on a number of external projects and repositories. We should take this opportunity to finali... ben leinfelder

10:26 AM Bug #5531 (Resolved): Remove/make optional the DataONE MN registration that occurs during Metacat configuration

Right now when I [re]configure Metacat I hit the DataONE CN in an attempt to register myself as a MN. This should be ... ben leinfelder

11/01/2011

02:10 PM Bug #5499: citation format odd for metacat data sets

added to EML project and updated the Metacat build to pull from that tagged style update. ben leinfelder

01:57 PM Bug #5499: citation format odd for metacat data sets

Close. All that needs to change is delete #3 -- if BOTH are provided, only list the individualName and omit the orga... Matt Jones

12:43 PM Bug #5499: citation format odd for metacat data sets

After looking more closely at the code, I think we already have what you propose -- it just depends on the content of... ben leinfelder

10/31/2011

05:21 PM Bug #2495: Charset bug: Internationalization

Moving this to 2.0.0.
Also, I think relying on the XML-declared encoding is a much safer (easier) bet than inspectin... ben leinfelder

05:13 PM Bug #5519: Replicated data files are 0 bytes

After installing Metacat 1.9.5 on fred.msi.ucsb.edu I was able to see the failure point. It was something that I fixe... ben leinfelder

02:18 PM Bug #5519: Replicated data files are 0 bytes

There's no difference between 1.9.5 tag and trunk for the ReplicationService.handleGetDataFileRequest() method -- may... ben leinfelder

02:06 PM Bug #5519: Replicated data files are 0 bytes

Now with BOTH servers using Apache certificate/SSL mechanisms the replication is still successful.
bespin.nceas.ucsb.... ben leinfelder

01:25 PM Bug #5519: Replicated data files are 0 bytes

Switching bespin.nceas.ucsb.edu to use Apache for the SSL handling still left the data replication working as expecte... ben leinfelder

12:34 PM Bug #5519: Replicated data files are 0 bytes

I set up one-way replication from bespin.nceas.ucsb.edu --> fred.msi.ucsb.edu.
Using the Tomcat-only certificate gene... ben leinfelder

02:27 PM Bug #5530: Sanparks skin shows update and delete action when user public reads a FGDC package

also see: http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5394 ben leinfelder

02:21 PM Bug #5530 (Resolved): Sanparks skin shows update and delete action when user public reads a FGDC package

Here is an email from Judith:
Hi Jing
I have successfully uploaded a number of GIS layers What concerns me is
th... Jing Tao

02:27 PM Bug #5394: FGDC interface does not correctly show controls and permission settings

consolidating into one bug ben leinfelder

08:40 AM Bug #5499: citation format odd for metacat data sets

No, I don't think that's quite right. If a Creator contains an individualName, use that and not the organization. If ... Matt Jones

10/28/2011

04:25 PM Bug #5499: citation format odd for metacat data sets

Does there need to be an XSLT parameter that allows different skins to specify whether they want organizations treate... ben leinfelder

04:21 PM Bug #5499: citation format odd for metacat data sets

Okay, what's the final decision here?
We have givenName, surName and an organizationName. It sounds like the citatio... ben leinfelder

02:48 PM Bug #5526 (Resolved): final test issue

One final test, sorry for the spam. Matt Jones

02:46 PM Bug #5525: test issue again

Test bug. Matt Jones

02:36 PM Bug #5525 (Resolved): test issue again

Another test to be ignored. Matt Jones

02:36 PM Bug #5524: test issue

Test bug. Closing. Matt Jones

02:34 PM Bug #5524 (Resolved): test issue

Please ignore -- this is a test issue. Matt Jones

02:23 PM Bug #5522: download linked KNB data and convert links in EML to ORE packages

Creation of SystemMetadata when no SystemMetadata is provided (i.e. any object creation not through the DataONE API) ... Chris Jones

02:06 PM Bug #5522 (New): download linked KNB data and convert links in EML to ORE packages

The KNB data sets, and EML data in general, represent linkages to data as online/url linkages in EML documents. When... Matt Jones

02:16 PM Bug #5523 (Resolved): setting authoritative MN and rightsHolder for KNB data on conversion

When EML and data in the NCEAS and LTER metacat is converted to use in the new KNB MN, we need to generate system me... Matt Jones

01:28 PM Bug #5515: change version to 2.0.0 in prep for release

db version scripts and properties are updated to 2.0.0 ben leinfelder

01:23 PM Bug #3815: Ampersand character not correctly encoded

I only see delNormalize() being called from the deleteData() function in register-dataset.cgi -- but perhaps similar ... ben leinfelder

01:11 PM Bug #3815: Ampersand character not correctly encoded

The specific example looks to have its origins in delNormalize (sic) within register-dataset.cgi -- the first regex o... Shaun Walbridge

01:17 PM Bug #4907: Replication error stops insert/update of valid EML document

Added clearer error handling when replication lock requests cannot be gotten ben leinfelder

01:01 PM Bug #4083: Metacat doesn't declare XML document encoding

For incoming XML files, Metacat will inspect the encoding specified in the prolog and use that if found; defaulting t... ben leinfelder

12:48 PM Bug #2236: metacat parser allows eml with missing content

I tried inserting this document as is: it was fine because it validates against the 2.0.1 schema.
I tries modifying i... ben leinfelder

10/27/2011

10:23 PM Bug #3815: Ampersand character not correctly encoded

Using the Java MetacatClient API to insert a document with & also worked fine (no additional encoding of the & sy... ben leinfelder

08:23 PM Bug #3815: Ampersand character not correctly encoded

Using the dev skin to load an XML document with an ampersand encoded as: & kept the character intact. To me, this... ben leinfelder

07:41 PM Bug #5054: Unable to insert large EML documents and no error status returned

On first inspection, it appears that the request is coming into Metacat with no parameters set when I use the dev ski... ben leinfelder

07:00 PM Bug #5273: docs with inline-data allow invalid xml into metacat

I tried this with the attached inline.xml file that has an invalid unescaped ampersand in the inline section -- Metac... ben leinfelder

06:58 PM Bug #5273: docs with inline-data allow invalid xml into metacat

This file uses unescaped ampersand (&) in the inline data section. ben leinfelder

04:05 PM Bug #5515: change version to 2.0.0 in prep for release

updated docs and the source tree to use tomcat6 rather than tomcat5.5 ben leinfelder

01:30 PM Bug #3811: Spatial caches should be backed up and restored

If someone wants to put the spatial cache in /var/metacat they will have to do it manually, then configure metacat (w... ben leinfelder

01:01 PM Bug #2084: Pathquery support for temporal search on date fields

Will exercise this during testing for release. ben leinfelder

10/26/2011

06:59 PM Bug #5520 (Resolved): Create replication integration test suite

Replication integration tests should include:
-force replication between two servers -- A, B (write, update, delete)... ben leinfelder

06:31 PM Bug #5519 (Resolved): Replicated data files are 0 bytes

We set up 2-way replication between PPBio and PELD (Brazilian Metacat instances) and have since seen that the replica... ben leinfelder

04:30 PM Bug #2084: Pathquery support for temporal search on date fields

This should be in 2.0.0 since it is already in the trunk. The upgrade script is the only thing I am worried about -- ... ben leinfelder

04:11 PM Bug #5262: EML document owner can't read the document

Probably solution is to use Java's canonicalization routines to normalize the DN, as Ben has done on the DataONE DNs.... Matt Jones

03:59 PM Bug #5244: ldapweb.cgi shouldn't report ou=Account accounts since they're unusable

Need to check with Shaun if this is actually fixed. Matt Jones

03:54 PM Bug #4651: data packages losing data tables (and then finding them again)

Unable to replicate. Please reopen if more details emerge. Matt Jones

03:48 PM Bug #4442: Spatial indexing should not run and block metacat

Related to bug #3811. Matt Jones

03:47 PM Bug #5518 (In Progress): Track down the performance issue of metacat query.

Matt queried knb with the word "water". It took one minute and half. We need to figured out why it so slow. Jing Tao

03:46 PM Bug #3811: Spatial caches should be backed up and restored

Decided that its best to move these files to /var/metacat by default. Matt Jones

03:44 PM Bug #5234: Replication -- user does not have permission to update access rule for data file

In v1.9.5 we use a null replication user to perform replication (rather than the user_owner from the xml_documents ta... ben leinfelder

03:17 PM Bug #4900: LDAP referral connection timeout

Decided that #3 is not feasible since accounts may be in groups defined on various LDAP servers. ben leinfelder

01:20 PM Bug #5517 (Resolved): mark EcoGrid and Servlet APIs as deprecated

EcoGrid and Servlet APIs in metacat are being replaced (gradally) by the DataONE services. Mark these older APIs as ... Matt Jones

01:19 PM Bug #5516 (Resolved): continue updating user documentation

Documentation needs editing to describe new 2.0.0 features, including support for new DataONE APIs, deprecation of ol... Matt Jones

01:15 PM Bug #5515 (Resolved): change version to 2.0.0 in prep for release

To prepare for the release, change te version number to 2.0.0 for all documentation, including README, Sphinx docs, etc. Matt Jones

01:01 PM Bug #5288: Metacat got "java.lang.OutOfMemoryError: PermGen space" after new geoserver update

Not sure if there is an action here. Maybe add this information to the Metacat documentation/faq? Matt Jones

12:47 PM Bug #4083: Metacat doesn't declare XML document encoding

I think these encoding issues have been fixed by Ben in trunk, but we need to discuss it to see if anything further n... Matt Jones

12:38 PM Bug #1601: Metacat will add default value for optional parameter into eml 2 document

Marking as complete, because the read problem is fixed based on now reading original from disk. The insert problem i... Matt Jones

12:34 PM Bug #4275: Earthgrid REST API Implementation

Task now being handled via #5011 DataONE service API implementation. This original work on interfaces has been obsol... Matt Jones

12:17 PM Bug #5514: implement DataONE service API

Duplicate bug to #5011. Matt Jones

12:15 PM Bug #5514 (Resolved): implement DataONE service API

Support the new DataONE service API for interoperable data repositories:
http://mule1.dataone.org/ArchitectureDocs... Matt Jones

12:10 PM Bug #5513 (Resolved): add support for DOI identifiers from EZID

DOI identifiers can be created through the EZID service run by the California Digital Library. See:
http://n2t.ne... Matt Jones