Activity
From 09/19/2013 to 10/18/2013
10/18/2013
- 04:01 PM Bug #6161 (Closed): Add access_log indexes to support DataONE log retrieval
- These are in the trunk now. For large repositories, it may be necessary to increase postgres configuration values so ...
- 12:14 PM Bug #6161 (Closed): Add access_log indexes to support DataONE log retrieval
- 12:16 PM Revision 8335 (metacat): add 2 indexes to speed up dataONE log retrieval. https://projects.ecoinformatics.org/ecoinfo/issues/6161
- 09:38 AM Revision 8334 (metacat): Added Lauren to contributors list in the metacat guide, and made the two lists match in sort order.
10/17/2013
- 04:04 PM Bug #6123: Rework on the IndexGenerator class in the metacat-index module
- I am thinking of the issues about moving the class to Metacat:
This class is a backup plan. If we move it to Metac... - 01:43 PM Bug #6157 (Resolved): Couldn't control the log level in solr
- It turned out that the solr-core.jar and other solr jar files are using the slf4j logging mechanism. It comes with tw...
- 01:36 PM Bug #6157 (Resolved): Couldn't control the log level in solr
- Our current log control didn't work with the log from solr. It has the default value - INFO. The log message was very...
- 01:33 PM Revision 8333 (metacat): 1.Remved the dependency on solr-core since the metacat-common alreay has the dependency.
- 2.Excluded the slf4j-log jar files since we are using slf4j-log4j jar file.
- 12:26 PM Revision 8332 (metacat): Use the slf4j-log4j jar to replace slf4j-jdk one.
10/16/2013
- 05:27 PM Revision 8328 (metacat): Change the version to 2.2.2
- 05:24 PM Bug #6154 (Resolved): The metacat configuration showed that it was done even though the dataONE configuration hadn't been touched
- Add a new class DataONEConfigUtil. It has a method to determine if the configuration for DataONE is done or not.
Thi... - 05:23 PM Bug #6154 (Resolved): The metacat configuration showed that it was done even though the dataONE configuration hadn't been touched
- It seems the configuration ignore the dataONE part.
- 05:19 PM Revision 8327 (metacat): Fixed a bug that the configuration page shows complete even though the DataONE configuration hadn't done yet.
- 05:18 PM Revision 8326 (metacat): Add a util class for dataone configuration.
- 05:17 PM Revision 8325 (metacat): Change the button from Cancel to Bypass. So it is consistent with the Geoserver configuration page.
- 04:31 PM Revision 8324 (metacat): Add a jsp file to display the schema modification exception.
- 04:29 PM Revision 8323 (metacat): Add code the display the SchemaModification exception.
10/15/2013
- 08:46 PM Revision 8321 (metacat): Fixed a catch clause syntax which is only compatible with java 1.7.
- 03:39 PM Revision 8320 (metacat): Add code the overwrite the schema.xml in the solr-home/conf.
- 03:37 PM Revision 8319 (metacat): Add two scripts to update the db to 2.2.2
- 10:34 AM Bug #6141 (Closed): Permission denied to update/publish metadata for group member on Gulfwatch
- 10:31 AM Bug #6141 (In Progress): Permission denied to update/publish metadata for group member on Gulfwatch
- In the branch - being included in 2.2.1 patch for MN and CNs
- 08:36 AM Bug #6141: Permission denied to update/publish metadata for group member on Gulfwatch
- Yes, she was logged in fully. I was tailing the logs and watched her log in, and could see the entry scroll by. Als...
- 06:47 AM Bug #6141: Permission denied to update/publish metadata for group member on Gulfwatch
- My first guess is that there is something not quite right with the login/session since the error message only mention...
- 10:34 AM Bug #6136 (Closed): files left open causes too many file descriptors on OS
- 10:33 AM Bug #6142: Metacat.property guid.ezid.unitemplate.metadata includes context
- This is in the 2.2 branch.
- 06:47 AM Bug #6142: Metacat.property guid.ezid.unitemplate.metadata includes context
- This should be included in the upcoming patch release.
- 10:31 AM Bug #6138 (Closed): Metacat-index assumes default "knb" context
10/14/2013
10/11/2013
- 05:39 PM Bug #6142 (Resolved): Metacat.property guid.ezid.unitemplate.metadata includes context
This has been changed to just be the hostname only.
The metacat.properties file on the Gulfwatch server is also ...- 05:36 PM Bug #6141 (Closed): Permission denied to update/publish metadata for group member on Gulfwatch
- Sarah Clark was unable to publish metadata on Gulfwatch even though she is a member of the evos group which has permi...
- 04:35 PM Revision 8313 (metacat): Change the guid.ezid.uritemplate.metadata property value to the hostname only, with no context
- 02:57 PM Revision 8312 (metacat): Add properties to keep the hash values for the schema.xml of the solr.
- 02:42 PM Revision 8311 (metacat): Fixed compile error that an ioexception should be caught.
- 11:07 AM Revision 8310 (metacat): Use the setting from the metacat-common component.
- 11:06 AM Revision 8309 (metacat): Some settings will be shared between metacat and metacat-index components.
10/10/2013
- 01:01 PM Revision 8307 (metacat): prep project for 2.2.1 patch release -- will also merge to the 2.2.x branch.
- 12:43 PM Bug #6136: files left open causes too many file descriptors on OS
- A brief overview of how I was inspecting memory, threads, file descriptors, etc. while stress testing Metacat. This ...
- 12:27 PM Revision 8306 (metacat): correctly configure metacat-index to use metacat context/deployment location. https://projects.ecoinformatics.org/ecoinfo/issues/6138
- 12:12 PM Bug #6138 (Closed): Metacat-index assumes default "knb" context
- 09:39 AM Task #6040: Metacat-index does not handle <references>
- Even with a SAX parser, the implementation could keep track of all elements with "id" attributes and anytime a "refer...
- 09:36 AM Task #6040: Metacat-index does not handle <references>
- Skye said that the sax parser is used to parse those information. This change may require to use DOM parser. It is a...
- 09:37 AM Bug #6137 (Resolved): Add a new action reindexall to reindex all the solr index
- Just leave as it is.
- 09:33 AM Task #6110 (Resolved): Use a new schema of dataone solr index so that the author last name can be sortable
- Skype released a "buildout" component DATAONE-CN-INDEX_v1.2.1. It only has the schema change. Now our schema is using...
- 09:20 AM Revision 8305 (metacat): Change the svn location of the schema.xml file to d1_cn_index_processor 1.2.1. The 1.2.1 release is a "buildout" release. There was no code change.
- Skye change the attribute "stored" to be true for the authorSurNameSort and authorGivenNameSort. Otherwise the sortin...
10/09/2013
- 11:57 PM Bug #6136: files left open causes too many file descriptors on OS
- Checked all instances of FileInputReader and ensured that close() was being called properly. See commit r8304.
- 03:05 PM Bug #6136: files left open causes too many file descriptors on OS
- After looking into this, its not just file handles that are left open, but many InputStream and OutputStream instance...
- 01:53 PM Bug #6136: files left open causes too many file descriptors on OS
- Switched to using IOUtils.closeQuietly() which handles nulls and already closed file handles in r8299.
- 01:28 PM Bug #6136: files left open causes too many file descriptors on OS
- Also added a close() to the finally block in DocumentImpl.readFromFileSystem() in r8298. This is probably not causin...
- 01:05 PM Bug #6136: files left open causes too many file descriptors on OS
- Closed file handles in DocumentImpl and ReplicationService in commit r8297.
- 01:03 PM Bug #6136 (Closed): files left open causes too many file descriptors on OS
- Metacat writes temp files to disk, and in the process has been failing to close file handles. Over time, especially ...
- 11:52 PM Revision 8304 (metacat): Reviewed code for all uses of FileInputStream, checking to see if the method should be closing the stream, and if so, closing it in the method as well as in the finally clause to ensure we don't leak file descriptors.
- 10:03 PM Bug #6137: Add a new action reindexall to reindex all the solr index
- I read this message after i committed the change :)
I still think we should give an expensive process a dedicated ... - 04:52 PM Bug #6137: Add a new action reindexall to reindex all the solr index
- I think this would be redundant and it would be better to just leave it as is, and have administrators use care. The...
- 04:14 PM Bug #6137 (Resolved): Add a new action reindexall to reindex all the solr index
- Currently we have an action named reindex. If the action has a parameter pid, it will reindex the solr index of the s...
- 08:53 PM Revision 8303 (metacat): Sparate the action reindex and reindexall.
- 05:49 PM Revision 8302 (metacat): The checked-out schema.xml will overwrite the one in src/main/resource/solr-home/conf.
- 04:02 PM Story #6114: Include updated D1 indexing library
- After changing the version depency on the metacat-index pom.xml and some code change, the new version works.
Ther... - 03:27 PM Task #6110: Use a new schema of dataone solr index so that the author last name can be sortable
- Won't this be included in the next (1.2.1) release of the library as well? Could just wait for that if it is coming u...
- 03:23 PM Task #6110: Use a new schema of dataone solr index so that the author last name can be sortable
- After adopting the d1_cn_index_processor 1.2.0, the authorSurNameSort field is sortable. But it doesn't work very wel...
- 03:20 PM Feature #6109 (Resolved): Keep the SOLR index for obsoleted objects
- Removed the code which excluded the obsoleted objects from indexing. Next release, we need to notice the metacat owne...
- 03:17 PM Bug #6122 (Resolved): Metacat-index can't index taxon information
- Adopted d1_cn_index_processor 1.2.0 into metacat. The new version processor can index taxon information.
- 02:42 PM Revision 8301 (metacat): Closing some more streams that were left open. This Bug #6136 seems to be pervasive and is going to require an extensive audit to find all of the places where streams are not closed properly.
- 01:52 PM Revision 8300 (metacat): Adding build files to ignore.
- 01:47 PM Revision 8299 (metacat): Refactor to use IOUtils.closeQuietly() which handles nulls and streams that are already closed.
- 01:26 PM Revision 8298 (metacat): Added close() to finally block for readFromFileSystem() call.
- 12:44 PM Revision 8297 (metacat): Closing FileOutputStream handles so that the OS limits on filehandles are not exceeded.
- 12:10 PM Revision 8296 (metacat): Use the d1_cn_index_processor 1.2.0 version.
- 12:09 PM Revision 8295 (metacat): Remove those files. They will be get from the d1_cn_index_processor 1.2.0 jar.
- 12:07 PM Revision 8294 (metacat): Use the schema for the d1_cn_index_processor 1.2.0
10/08/2013
- 05:51 PM Revision 8293 (metacat): combine the index code for failed ids and other ids.
- 04:49 PM Revision 8292 (metacat): Clean up the code.
- 02:22 PM Revision 8291 (metacat): The IndexGenerator will index the obsoleted data objects as well.
- 12:05 PM Revision 8290 (metacat): add sample SSLCertificateChainFile directive to DataONE section.
- 12:04 PM Revision 8289 (metacat): add sample SSLCertificateChainFile directive to DataONE section.
- 11:33 AM Revision 8288 (metacat): Remove the obsoletes chain from the update method in the SolrIndex class.
10/07/2013
- 05:56 PM Revision 8287 (metacat): When an object is archvied, the solr index will not be removed.
- 04:09 PM Story #6128 (Closed): Wait for MetacatUI 1.1.0 release
- Using MetacatUI 1.1.0 tag.
https://github.com/NCEAS/metacatui/tree/METACATUI_1_1_0
10/04/2013
- 05:32 PM Story #6128 (Closed): Wait for MetacatUI 1.1.0 release
- 11:39 AM Bug #6123 (Rejected): Rework on the IndexGenerator class in the metacat-index module
- The IndexGenerator class has two purpose - first, to create the solr index for all data objects for a Metacat which i...
- 11:20 AM Bug #6122: Metacat-index can't index taxon information
- This will be fixed by adopting d1_cn_index_processor 1.2 in the 2.2.1 release.
- 09:26 AM Revision 8283 (metacat): merge from 2.2 branch: remove the index queue item when it is being processed. https://projects.ecoinformatics.org/ecoinfo/issues/6117
10/03/2013
- 09:54 PM Bug #6117 (Resolved): Reindexing (action=reindex) only works once
- I installed a metacat from the 2.2.0 branch. It works very well for the reindex action.
I also deleted the solr in... - 12:46 PM Bug #6117 (In Progress): Reindexing (action=reindex) only works once
- Added code to remove from the queue when responding to the add event. Testing now.
- 12:39 PM Bug #6117 (Resolved): Reindexing (action=reindex) only works once
- 05:47 PM Bug #6122: Metacat-index can't index taxon information
- I committed those files to the trunk and it works. I haven't committed to the 2.2.0 branch.
- 05:46 PM Bug #6122 (Resolved): Metacat-index can't index taxon information
- With the help of Skye, we patched 5 files: application-context-eml-base.xml, application-context-eml201.xml, applicat...
- 05:38 PM Revision 8282 (metacat): Add a patch for d1_cn_index_processor 1.1.2 version. So it can index taxon information.
- Those files will overwrite the ones in the d1_cn_index_process-1.1.2.jar.
- 12:17 PM Task #6040: Metacat-index does not handle <references>
- Spaces aren't really sufficient as a solution, and there are a lot of references fields in EML. We probably need to ...
- 12:01 PM Task #6040: Metacat-index does not handle <references>
- This is included in the 1.2.0 d1 index release. It will not include || but instead will use blanks. Not a very great ...
- 11:07 AM Task #6040: Metacat-index does not handle <references>
- Apparently this is fixed in cn-index-processor v1.2.0 -- so we will need to pull in this newer dependency in metacat-...
- 11:59 AM Task #6110: Use a new schema of dataone solr index so that the author last name can be sortable
- This is included in the v1.2.0 release of d1 indexing -- called "authorSurNameSort"
Schema:
https://repository.da... - 11:47 AM Feature #6031 (Rejected): Add rendered metadata to Bagit package contents
- Duplicate of 6053
10/02/2013
- 05:55 PM Revision 8279 (metacat): Fixed a bug that the code copied the solr-home to the target directory before it checked out the schema from the dataone svn repository.
- 11:41 AM Story #6062 (Closed): Deprecate skin configuration
- 11:40 AM Task #6067 (Closed): Update documentation to reflect the new metacatui theme mechanism
- 11:40 AM Revision 8272 (metacat): minor edits to the UI theme section. https://projects.ecoinformatics.org/ecoinfo/issues/6067
- 11:36 AM Bug #5243: ldapweb.cgi crashes with invalid password characters
- move it to 2.2.1
- 10:58 AM Bug #5243: ldapweb.cgi crashes with invalid password characters
- I agree to add guidelines for users.
- 10:55 AM Bug #5243: ldapweb.cgi crashes with invalid password characters
- While we do allow someone to create an account with special characters as the password, I am unable to login using th...
- 11:12 AM Story #6063 (Closed): ldapweb.cgi enhancements
- 10:50 AM Task #6113 (Resolved): Getting "Bad header" error when similar accounts are present
- the new installation fixed the issue.
- 10:24 AM Task #6115 (Resolved): ldapweb.cgi - default configuration should use o=unaffiliated
- I change the configuration in the metacat.properties and nceas.properties. The default value now is unaffiliated.
- 09:48 AM Task #6115 (Resolved): ldapweb.cgi - default configuration should use o=unaffiliated
- We are not yet ready to use ou=Account by default in our ldapweb skin configurations.
- 09:46 AM Bug #6086 (Closed): publish service call fails to authenticate properly
- 09:23 AM Story #6114 (Closed): Include updated D1 indexing library
10/01/2013
- 05:59 PM Task #6113: Getting "Bad header" error when similar accounts are present
- i installed a new metacat with the trunk code. The ldap server points to ldap-dev. It works great with similar accou...
- 05:08 PM Task #6113 (Resolved): Getting "Bad header" error when similar accounts are present
- WHen I try to register with an account that has similar info as an existing one (email, last name etc) on dev2.nceas....
- 05:43 PM Revision 8271 (metacat): Change the default org from Account to unaffilicated in the account creation.
- 05:41 PM Revision 8270 (metacat): Change the default org from Account to unaffiliated in the account creation.
- 04:59 PM Task #6096 (Closed): Add reCaptcha library instructions to admin docs
- Added to the registry installation section.
- 04:59 PM Revision 8269 (metacat): include reCaptcha instructions, albeit briefly. https://projects.ecoinformatics.org/ecoinfo/issues/6096
- 04:22 PM Task #6110 (Resolved): Use a new schema of dataone solr index so that the author last name can be sortable
- Ben said skye developed a new schema of the dataone solr index so that the author last name can be sortable. We need ...
- 04:09 PM Feature #6109 (Closed): Keep the SOLR index for obsoleted objects
- Currently, metacat only keeps the solr index for the current objects. The solr index for the obsoleted objects are re...
- 01:27 PM Feature #6107 (Rejected): Make publication year in search results less prominent
- Should have put this in MetacatUI project
09/30/2013
- 02:25 PM Feature #6107 (Rejected): Make publication year in search results less prominent
- Move to the end of the citation line and preface with "Published:"
09/27/2013
09/24/2013
- 04:34 PM Bug #6101 (Closed): MN.update() fails but modifies revision chain
- Moved the call "existingSysMeta.setObsoletedBy(newPid);" to after the insert/update in Metacat is called.
- 04:09 PM Bug #6101 (Closed): MN.update() fails but modifies revision chain
- Hello Ben, Chris,
I was trying to update two data and metadata files for some old subtidal data today and ran int... - 04:21 PM Revision 8267 (metacat): do not modify existing SystemMetadata on MN.update() if something goes wrong during content insertion. https://projects.ecoinformatics.org/ecoinfo/issues/6101
09/23/2013
- 04:36 PM Story #6082 (Closed): Rename knb.war to ???.war
- Using metacat.war now.
- 04:35 PM Task #6087 (Closed): Change all default configurations to use new context
- 04:34 PM Task #6088 (Closed): Update documentation to use new context name
- 04:21 PM Revision 8266 (metacat): add note about restarting Tomcat when using Metacat indexing.
- 03:54 PM Revision 8265 (metacat): Refer to metacat.war deployments since those are now the default. https://projects.ecoinformatics.org/ecoinfo/issues/6082
- 01:21 PM Bug #6100 (Closed): Metacat search does not work for Chinese characters
- Now forcing UTF-8 if the request does not specify and encoding.
- 10:33 AM Bug #6100 (Closed): Metacat search does not work for Chinese characters
- Hi Ben,
We found there is a searching problem on Metacat Home page. We can search Chinese characters correctly on ... - 01:20 PM Revision 8264 (metacat): use UTF-8 if request encoding not given. https://projects.ecoinformatics.org/ecoinfo/issues/6100
- 12:03 PM Task #6067 (Feedback): Update documentation to reflect the new metacatui theme mechanism
- 11:51 AM Feature #6080 (Closed): Update Metacat admin screen using cues from the new default look and feel
- Went through a review and it looks complete.
- 11:50 AM Bug #6094 (Closed): Replace all screenshot images in the documentation with screenshots of the new documentation style
- Added new screenshot images.
- 11:48 AM Revision 8263 (metacat): Added the documentation for the new MetacatUI theming mechanism. Make some styling changes to the documentation and configuration pages and added Bootstrap and FontAwesome.
- 10:30 AM Task #6066 (Closed): Add email verification for new accounts
- I made the activation link accessible via a configured #external url in the metacatui.properties file. This let's us ...
09/20/2013
- 04:36 PM Revision 8262 (metacat): Remove an extra print content type statement.
- 03:26 PM Revision 8261 (metacat): Add a print statment for "content type". Otherwise, the html can't show up.
- 02:58 PM Revision 8260 (metacat): Use https to replace http. Otherwise, the recapatcha code can't show up in a https link.
- 02:42 PM Revision 8259 (metacat): do not email a specific account reset URL so that the emails can be used in multiple UI contexts. https://projects.ecoinformatics.org/ecoinfo/issues/6066
- 01:17 PM Revision 8258 (metacat): Comment out some extral "contet type".
- 12:48 PM Revision 8257 (metacat): add "btn" class as stop-gap for metacatUI styled email links. https://projects.ecoinformatics.org/ecoinfo/issues/6066
- 12:47 PM Revision 8256 (metacat): comment out the "forgot password?" link so that we can use the reset page in different UI locations.
- 12:30 PM Revision 8255 (metacat): remove unused JS that was only throwing an error when loaded via ajax
- 12:20 PM Revision 8254 (metacat): ensure all emailed links make sense for the UI that initiated them. also format referrals using the same options as the primary accounts (recursive call needed the html parameter). https://projects.ecoinformatics.org/ecoinfo/issues/6066
- 11:46 AM Revision 8253 (metacat): include optional email.overrideURL property for the account management page to send an email link that will result in a styled response. https://projects.ecoinformatics.org/ecoinfo/issues/6066
- 11:20 AM Task #6066 (In Progress): Add email verification for new accounts
- This working great - only issue is that using the metacatui cfg we get an un-styled "Activation Successful!" page. Th...
- 11:06 AM Task #6065 (Closed): Add reCaptcha widget to initial registration page
- 11:06 AM Revision 8252 (metacat): remove the NCEAS-specific admin db connection properties from the metadata config so they do not show up in the metacatui configuration.
- 10:59 AM Task #6098 (Closed): Make reCaptcha work with AJAX include
- Works as expected now.
- 08:33 AM Task #6098: Make reCaptcha work with AJAX include
- This is now rendering on dev2. I did not know the private key for our recaptcha config, so it needs to be tested when...
- 07:50 AM Task #6098: Make reCaptcha work with AJAX include
- I included the ajax-style of recaptcha, but need to verify that it works. Jing - do you foresee any issues with using...
- 07:45 AM Task #6098 (Closed): Make reCaptcha work with AJAX include
- Instead of having the perl code generate the catcha content, the template can include the ajax-style of constructing ...
- 10:47 AM Feature #6099 (Closed): Remove temporary LDAP accounts after X amount of time has passed
- Users are added to a temporary LDAP tree until they activate their account via email. We should remove these accounts...
- 10:44 AM Task #3306 (Closed): NCEAS skin account creation needs more thought
- We've now made the text more generic so that the LDAP account creation feature can be used in multiple contexts and i...
- 10:40 AM Task #2635 (Closed): Look up for forgotten KNB account names
- This is working nicely.
- 08:32 AM Revision 8251 (metacat): include link to show the captcha - ensures we have all the divs loaded when the script runs to generate the code. https://projects.ecoinformatics.org/ecoinfo/issues/6098
- 07:48 AM Revision 8250 (metacat): use AJAX method of including the captcha. https://projects.ecoinformatics.org/ecoinfo/issues/6098
09/19/2013
- 05:04 PM Revision 8249 (metacat): Fixed a typo.
- 05:03 PM Revision 8248 (metacat): Remove an extra space in the email message.
- 01:52 PM Revision 8247 (metacat): use correct id for the lookupAccount link - used in metacatui view.
- 12:38 PM Task #6096 (Closed): Add reCaptcha library instructions to admin docs
- THis is a new dependency and should be documented in the registry install docs.
- 12:16 PM Revision 8246 (metacat): More screenshots for the docs
- 11:59 AM Revision 8245 (metacat): FontAwesome and Bootstrap are imported locally rather than via CDN. Updated the docs screenshots to the new style.
- 11:39 AM Story #6082: Rename knb.war to ???.war
- [11:34am] matt: ben: the more I think about it, I still think we should go with metacat.war, despite the duplicate pa...
- 11:30 AM Revision 8244 (metacat): correct table formatting for sphinx
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