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From 12/28/2012 to 01/26/2013

01/26/2013

08:17 AM Bug #5799: publish using DOI feature
Move to 2.1 - after site review and a stable 2.0 release. Coincides with DOI reservation/registration supporton Metacat. ben leinfelder
08:15 AM Bug #5757: Add identifier scheme drop down to id conflict window
Moving this to 2.1 where we couple it with Metacat DOI+EZID support. The window does have a drop down now, but I have... ben leinfelder
08:13 AM Bug #5798: ORE documents generated by Morpho do not include obsolescence chain
I think the best we can do right now is to check for an existing ORE object to obsolete by using the standard id patt... ben leinfelder

01/25/2013

10:17 PM Bug #5801: Test Morpho against GMN
This (system metadata byte size vs actual) will be interesting. I wonder if it will always be 8 bytes different. One ... ben leinfelder
05:39 PM Bug #5801: Test Morpho against GMN
I created a simple data package by the new data package wizard, then saved it to a GMN node https://mn-stage-orc-1.te... Jing Tao
10:13 PM Bug #5794: Cannot add only Genus with Common Name
This looks good now - keeps the common name for Genus in the place it was entered. ben leinfelder
05:25 PM Bug #5796: D1Object in Morpho still uses byte array as data source
I am thinking about the two methods we will add (in comment 1):
getDataInputStream() and setDataInputStream()
I th...
Jing Tao
02:12 PM Bug #5825 (Resolved): Call CN.setReplicationPolicy() when editing replication policy
This should act the same as the access policy edits. For network packages, we call the CN.setReplicationPolicy() and ... ben leinfelder
02:08 PM Bug #5824 (Resolved): Call CN.setAccessPolicy() when editing access
Currently Morpho edits the SystemMetadata.AccessPolicy for an EML and/or data file and uploads a new version of those... ben leinfelder
01:21 PM Bug #5823: Improve save-to-network performance
With my NCEAS network connection I did a small and big data file:
big (50 MB) -- 18.5 s
small (119 bytes) -- 8.3 s
ben leinfelder

01/24/2013

11:38 PM Bug #5823: Improve save-to-network performance
I think in all cases we have the following calls:
-check if EML file exists
-generate new ID if so
-check if data fi...
ben leinfelder
11:37 PM Bug #5823 (New): Improve save-to-network performance
Jing saved data packages with binary data entities from Morpho to a Metacat MN to test the performance of those save ... ben leinfelder
11:29 AM Bug #5788: It is confusing that the "Save Dialog" comes back again when a user clicks okay in the id collision dialog
I think it is good to have the save dialog showing while we wait for the save to complete rather than throwing away t... ben leinfelder
11:22 AM Bug #5809 (New): Default save behavior to always include local store
Currently you can opt to save your datapackage changes to either LOCAL, NETWORK, or BOTH. This means you can make cha... ben leinfelder
11:12 AM Bug #5808 (Resolved): Evaluate "Synchronize" feature for potential removal
Synchronize is very similar to the Save action. I think the only difference right now is that you can invoke synch fr... ben leinfelder
11:04 AM Bug #5807 (Resolved): Update LaTEX user guide to reflect new 2.0 changes
Notably:
-Probably need a new D1 section to explain it.
-Preferences (CN/MN selection)
-Authentication (potentiall...
ben leinfelder
10:13 AM Bug #5806: NPE when creating profile on fresh Morpho install
Actually, the order can be changed. Now initializing the *DSS classes before loading/creating the new profile. ben leinfelder
10:07 AM Bug #5806: NPE when creating profile on fresh Morpho install
The LDSS is null because the profile dialog is presented before the LDSS is initialized. LDSS relies on the profile s... ben leinfelder
10:04 AM Bug #5806 (Resolved): NPE when creating profile on fresh Morpho install
If I remove my .morpho2 directory, I get an NPE at the final step of creating the first new profile. This is when the... ben leinfelder
09:59 AM Bug #4418: "about" box displays incorrect version number
Compiled and ran on linux. ben leinfelder
09:48 AM Bug #4418: "about" box displays incorrect version number
We can use the AppleJavaExtensions.jar and set our own About... behavior. I've been reading about this and I think we... ben leinfelder

01/23/2013

05:01 PM Bug #5792: In some situation, morpho uses the same frame to display two data package with different ids (one in local and one in network)
This is no longer an issue now that we do the identifier resolution in one place before saving to local+network. ben leinfelder
04:43 PM Bug #5804: Need to prompt for login when attempting to save as "public" user
Now prompting during network save. If you skip it no save to the network will be attempted. ben leinfelder
03:09 PM Bug #5804 (Resolved): Need to prompt for login when attempting to save as "public" user
I get an error when trying to save when I forget that my certificate has expired. We should prompt user to login in t... ben leinfelder
04:31 PM Bug #5805 (In Progress): Local and Network revisions show at same time in search results
I can see an older local version of a package in the search results along with the newer network version by doing the... ben leinfelder
04:23 PM Bug #5797: LocalDataStoreService.generateIdentifier() seems to be called twice
Found the faulty logic: too many "lastId++" statements. ben leinfelder
04:21 PM Bug #5795: Centralize identifier conflict resolution during save LOCAL+NETWORK
I have moved this into the DataStoreServiceController. Now the identifiers are generated as needed before either the ... ben leinfelder
10:22 AM Bug #5757: Add identifier scheme drop down to id conflict window
We should consider this feature in the larger "publish" paradigm. ben leinfelder
10:21 AM Bug #5803 (Resolved): Tag a release of ECP client code
Before we release, I would like to have a tagged (stable) version of the simple-ecp-client building in hudson. Right ... ben leinfelder
10:18 AM Bug #5741: Decide on login procedure
We are going with ECP. There are other, more operations-based, tasks that will need to be done to support this in a p... ben leinfelder
07:52 AM Bug #5802 (Resolved): Use UUID for local identifiers
Currently in Morpho 2.x development we are using a "scope.XX" format for our local identifiers. The "XX" is increment... ben leinfelder
07:45 AM Bug #5622: Modify morpho package id management when we switch to dataone
Revision handling is finished. We are still discussing an alternative local Id scheme (UUID) and this will be address... ben leinfelder
07:41 AM Bug #5801 (Resolved): Test Morpho against GMN
Specifically:
-create (save new package)
-update (save another revision of same package)
-read (open by id)
-sear...
ben leinfelder
07:37 AM Bug #5800 (Resolved): Search support should degrade gracefully when MN.query is not supported
Morpho currently relies on the new-ish and optional MN.query() method and only understands the "pathquery" engine. De... ben leinfelder
07:22 AM Bug #5796: D1Object in Morpho still uses byte array as data source
We discussed the following changes to D1Object.
-add: getDataInputStream() and setDataInputStream()
-modify: getData(...
ben leinfelder

01/22/2013

10:48 PM Bug #5799 (New): publish using DOI feature
Morpho currently uses local identifiers that are not necessarily globally unique for data objects and metadata docume... Matt Jones
02:56 PM Bug #5798 (Resolved): ORE documents generated by Morpho do not include obsolescence chain
Because there is currently no good way for Morpho to know if an ORE package exists for a given set of EML+data, we en... ben leinfelder
02:49 PM Bug #5797 (Resolved): LocalDataStoreService.generateIdentifier() seems to be called twice
When saving packages we see local Ids that have been incremented by 2 rather than 1. We should find out why the local... ben leinfelder
12:21 PM Bug #5794: Cannot add only Genus with Common Name
Jing made a change to this, but I still cannot add a row with Genus+Common Name and get Morpho to remember it. Am I d... ben leinfelder
10:29 AM Bug #5788: It is confusing that the "Save Dialog" comes back again when a user clicks okay in the id collision dialog
Yes, I believe the collision windows is on the top of the save dialog. But it covers it and make users think the save... Jing Tao
10:19 AM Bug #5788: It is confusing that the "Save Dialog" comes back again when a user clicks okay in the id collision dialog
Isn't it just that the collision window is on top of the save dialog? It doesn't really "go away" it is just hidden w... ben leinfelder
10:14 AM Bug #5788: It is confusing that the "Save Dialog" comes back again when a user clicks okay in the id collision dialog
Yes.
If there is no id collision window disrupting it, it is fine that the destination selection window remains visi...
Jing Tao
09:43 AM Bug #5788: It is confusing that the "Save Dialog" comes back again when a user clicks okay in the id collision dialog
Do you mean that the destination selection window remains visible during the save? ben leinfelder

01/18/2013

04:43 PM Bug #5786: Open command only shows the local packages even though the user has logged in
Somehow, the open command only search the local. I have to specify the open command to search the network as well in ... Jing Tao
04:23 PM Bug #5796 (Resolved): D1Object in Morpho still uses byte array as data source
When morpho reads and saves the data package to the DataONE network, it handle the D1Objects. The entities, metadata ... Jing Tao
04:17 PM Bug #5795 (Resolved): Centralize identifier conflict resolution during save LOCAL+NETWORK
After splitting the identifier conflict resolution code into separate Local and Network classes, it turns out this ca... ben leinfelder
04:13 PM Bug #5128: access list does not show all dns in the LTER LDAP tree
This is a symptom of a server-side issue -- defer to that bug. ben leinfelder
04:11 PM Bug #4418: "about" box displays incorrect version number
At the very least there must be someway to change the 1.0 to a more meaningful number ben leinfelder
03:12 PM Bug #5793: SystemMetadata missing for updated EML doc
Two pronged approach to this:
-updated Metacat's MN.update() implementation to set the SM.serialVersion to default va...
ben leinfelder
01:54 PM Bug #5793: SystemMetadata missing for updated EML doc
It looks like this is because the SM.serialVersion value was null.
We can fix this in Morpho by using a real value, b...
ben leinfelder
01:51 PM Bug #5793: SystemMetadata missing for updated EML doc
Here is the full stacktrace:
knb 20130118-19:28:04: [ERROR]: Error while creating systemmetadata record: tao.392 [ed...
ben leinfelder
01:41 PM Bug #5793 (Resolved): SystemMetadata missing for updated EML doc
Following the procedure outlined in #5792, we do not see the record for SystemMetadata in the Metacat systemMetadata ... ben leinfelder
01:45 PM Bug #5794 (Resolved): Cannot add only Genus with Common Name
In the taxonomic import screen, Sarah Clark tried to add a Genus+Common Name without including a corresponding Specie... ben leinfelder
11:35 AM Bug #5792 (Resolved): In some situation, morpho uses the same frame to display two data package with different ids (one in local and one in network)
Here are steps to duplicate the issue:
1. Use the new data package wizard to create a new data package and save it t...
Jing Tao
10:30 AM Bug #1508: New Data Table Wizard: Last Step does not add Table every time
Sounds like no one can reproduce this... ben leinfelder
10:18 AM Bug #1708: data import wizard crashes when you click finish
I have not seen this behavior in the modern generation of Morpho (last 5 years). ben leinfelder
10:14 AM Bug #5791: The login window shows the subject of name as the login user name
now the DN will not show up in the username field. ben leinfelder
10:04 AM Bug #5791: The login window shows the subject of name as the login user name
Yeah, I think it should just be blank since we are not saving the username or organizational affiliation in the profi... ben leinfelder
09:55 AM Bug #5791 (Resolved): The login window shows the subject of name as the login user name
Everyday, when i started morpho and opened the login dialog. It shows:
Orgnaization: knb -Ecoinformatics:
Username:...
Jing Tao
10:07 AM Bug #2465: new lines are displayed in the text boxes but do not show after text entries saved
The whitespace is preserved, but when displayed online (or in Morpho using the EML stylesheets) the newlines are not ... ben leinfelder
09:16 AM Bug #1514: Citation DPW
Leaving this as is - seems to be a conscious decision that only Authors are added to this section. ben leinfelder
09:05 AM Bug #1514: Citation DPW
I believe the buttons are "Move up" and "Move down" and are readable in the current generation of Morpho (1.10/2.0). ... ben leinfelder

01/17/2013

05:25 PM Bug #5141: offer a choice to "cancel" from any save
In the LocalDataStoreService and DataONEStoreService class, if the user clicks cancel button on the id collision dial... Jing Tao
03:24 PM Bug #5141: offer a choice to "cancel" from any save
I opened a local package and edited the title. The location of the data package is blank. Then I chose "save to local... Jing Tao
12:03 PM Bug #5141: offer a choice to "cancel" from any save
There is now a "Cancel" button on the id conflict screen. If you choose to cancel at that point you can. I agree it i... ben leinfelder
04:58 PM Bug #5788 (Resolved): It is confusing that the "Save Dialog" comes back again when a user clicks okay in the id collision dialog
After edits a data package, a user click the "save" button and a destination selection dialog will show up. The user ... Jing Tao
02:35 PM Bug #942: wrong icon appears for data in package from metacat
Modern versions of EML (2.0.1-2.1.1) do not use this multiple-file/triples business for packaging. Closing this. ben leinfelder
02:29 PM Bug #1502: Text on dpw screen 4 of 15 makes it sound like associated party info is required
I can kind of see that from the overview page, but the actual associated party page, as dan mentioned, does not have ... ben leinfelder
02:21 PM Bug #1228: Open command not working correctly on older versions of Morpho
very old problem ben leinfelder
02:20 PM Bug #1239: morpho fails when lastId gets out of sync
Sounds like it correctly checked for the last id, but on a different server. At any rate, this is all different in v ... ben leinfelder
02:17 PM Bug #2795: The delete selected row feature does not always work.
Deleting blank rows that I added seems to work. ben leinfelder
02:03 PM Bug #2799: Access List doesn't include groups at LDAP root
We changed to use the CN account and group listing for this rather than Metacat.getPrincipals(). ben leinfelder
02:01 PM Bug #1773: Importing code table results in display of ID numbers, not code values
Morpho renders this reference correctly. Perhaps this was never closed when it was completed. ben leinfelder
01:51 PM Bug #1848: Error message when exporting data package without saving it
Tried this on trunk (upcoming morpho 2.0.0) and it works as expected. ben leinfelder
12:50 PM Bug #5787: Morpho Help build fails
Fixed now. But be warned -- when building a release you must build the help jar and commit it to SVN as it is not par... ben leinfelder
12:23 PM Bug #5787 (Resolved): Morpho Help build fails
I noticed the help is stale and started looking into it. I'm having errors when building the morphohelp.jar ben leinfelder
12:09 PM Bug #1521: Column name labels in Morpho Data Table Display disappear
The bold faced headers show even if the column width is made smaller than the width of the text. Assume some improvem... ben leinfelder
11:55 AM Bug #5139: morpho "preferences" and query speed
Sounds like we will punt on this. We are moving to a newer search mechanismin Metacat a la DataONE that will use SOLR... ben leinfelder
11:52 AM Bug #5128: access list does not show all dns in the LTER LDAP tree
Link the the ticket is dead.
We can't really provide a complete list of all the IP addresses that might follow the ld...
ben leinfelder
11:46 AM Bug #5613: Consolidate the metacat code in morpho
Update to 2.0.0 ben leinfelder
11:46 AM Bug #4961: user guide error re: how to import taxonomic coverage from file
Will be in v2.0.0 ben leinfelder
11:37 AM Bug #5622: Modify morpho package id management when we switch to dataone
Moving to 2.0.0 milestone -- I believe this feature is addressed in another bug and is well underway. ben leinfelder
11:35 AM Bug #4625: authenticate against KNB, switch source to DEV, and still have access
Morpho is switching to certificate-based authentication and will not be tied to any particular Member Node (Metacat) ... ben leinfelder
11:30 AM Bug #4031: More features in supporting SSL in morpho
I think our understanding and use of SSL has improved over the past three years. For Morpho 2.0 we have removed the c... ben leinfelder
11:28 AM Bug #5786 (Resolved): Open command only shows the local packages even though the user has logged in
If the user clicked the Open button, the dialog only shows the local data packages even the user has logged in. I bel... Jing Tao
11:26 AM Bug #3873: "Enter Information about Owners" wizard reorders dataset creators
This just got fixed - it came up with our EVOS users and percolated to the top of the pile. ben leinfelder
11:20 AM Bug #2210: Displaying taxonomic information imported from table
I am updating the EML documentation (embedded in the eml-coverage.xsd source) to use species binomial in the red mapl... ben leinfelder
11:12 AM Bug #2094: "New Profile" keyboard navigation skips page 2
There is no longer a Metacat screen, so this is probably a moot point. (tested key navigation in os x and it worked w... ben leinfelder
11:10 AM Bug #1992: DP Wizard: lat/long coordinates not displayed correctly or saved
Editing geographic coordinates and then re-editing them works for me with no loss or perceived loss of user-entered d... ben leinfelder
10:59 AM Bug #1555: Unable to open data files of local data packages that are created in another profile
I cannot open a datapackage from a different profile than my current profile. Closing. ben leinfelder
10:55 AM Bug #5117: Add an "Edit Profile..." dialog
In Morpho 2.0, the profile will no longer be tied to any specific log-in. The profile will still store a scope for id... ben leinfelder
10:52 AM Bug #5264: EML 2.1.1 support
This has been in Morpho since 1.10.0 ben leinfelder
10:50 AM Bug #5238: Use UTF-8 for file reading and writing
This should be closed. UTF-8 is used exclusively in Morpho - especially important now that we have so much internatio... ben leinfelder

01/16/2013

05:31 PM Bug #5785: Morpho doesn't set obsoletes correctly for the local data package when a user saves a package to both local and network
Currently, the step to increase revisions is separated into the local and network service. If we save to the both loc... Jing Tao
04:29 PM Bug #5785 (Resolved): Morpho doesn't set obsoletes correctly for the local data package when a user saves a package to both local and network
I created a data package by the new data package wizard and saved it to the both local and network.
Then I updated a...
Jing Tao
03:06 PM Bug #5783: Import Taxonomic coverage does not allow quoted column values
this is committed ben leinfelder
02:31 PM Bug #5783: Import Taxonomic coverage does not allow quoted column values
Now stripping the escape quotes from the values when importing them. This is both in trunk and the 1.10.0 branch ben leinfelder
12:53 PM Bug #5779: Owners list reorders its entries
This is in trunk and also was merged into the 1.10.0 branch in case we want to do a minor 1.10.1 release. ben leinfelder
12:52 PM Bug #5784: Import Taxonomic coverage does not handle code/definition enumerations very well
There was a slight bug in how the code/def values were retrieved from attributes that provided them. We were processi... ben leinfelder

01/15/2013

03:06 PM Bug #5784 (Resolved): Import Taxonomic coverage does not handle code/definition enumerations very well
In a data package where some columns were annotated to use an enumerated domain (code=definition) the taxonomic impor... ben leinfelder
03:04 PM Bug #5783 (Resolved): Import Taxonomic coverage does not allow quoted column values
WHen importing taxonomic coverage from a data table, the import process includes the quotes around each field if the ... ben leinfelder

01/14/2013

05:17 PM Bug #5779: Owners list reorders its entries
(Meant to close this the last time) ben leinfelder
05:17 PM Bug #5779: Owners list reorders its entries
Turns out the order was entirely the luck of the draw in terms of Map implementations. I forced the use of a TreeMap ... ben leinfelder
05:08 PM Bug #5779: Owners list reorders its entries
This also happens for Associated Parties and Contacts ben leinfelder
03:28 PM Bug #5779 (In Progress): Owners list reorders its entries
When 4 or more parties are listed in the Owners wizard page, they reorder themselves when you click 'Ok'.
It seems t...
ben leinfelder
04:55 PM Bug #5780 (New): DataONE object listing doesn't show the updated data package by morpho
I created a data package by the morpho new data package wizard. Then i saved it to the DataONE and got the id tao.284... Jing Tao
11:58 AM Bug #5777: Can't save a data package which was created by the new data pacakage wizard to the DataONE network
THe metadata map was being updated to reflect the new EML identifier, but the map that has D1Objects keyed by identif... ben leinfelder
10:48 AM Bug #5777 (Resolved): Can't save a data package which was created by the new data pacakage wizard to the DataONE network
After creating a data package by the new data package wizard, I tried to save it to the dataONE directly. However, I ... Jing Tao

01/11/2013

02:42 PM Bug #5758: Morpho revision handling is fragile
After the change, morpho has worked very well for me. I am closing the bug. If there is any problem happen again, we ... Jing Tao
02:40 PM Bug #5776: No resource map was generated when uses use the new data package wizard and the new data table wizard to create a data package
When a new entity was created, the entity information will be added to MorphoDataPackage object. Also if any id is up... Jing Tao

01/10/2013

01:52 PM Bug #5776: No resource map was generated when uses use the new data package wizard and the new data table wizard to create a data package
I opened the data package and updated the entity access rules. Then I saved it. Now i can get the resource map. Howev... Jing Tao
12:06 PM Bug #5775: Morpho doesn't allow users to modify the entity access rules at the second time
In the serializeData method of LocalDataStoreService class, the code to use a wrong order to look up the latest version. Jing Tao

01/09/2013

05:13 PM Bug #5776 (Resolved): No resource map was generated when uses use the new data package wizard and the new data table wizard to create a data package
I used the data package wizard and data table wizard to create a new data package. This data package has a data file ... Jing Tao
05:06 PM Bug #5775 (Resolved): Morpho doesn't allow users to modify the entity access rules at the second time
I created a data package with a data file successfully. The docid of eml was tao.112 and data file id was tao.110. I ... Jing Tao
04:56 PM Bug #5774 (New): Only save the system metadata to local and network if users only modify the system metadata rather than the data or eml
This issue has come from modifying the access rules for the entities.
After the user modify the access rules for a...
Jing Tao
04:44 PM Bug #5737: Refactor Access page to use SystemMetadata rather than EML
Ben and I discussed the issue about how to save the the entity only with the system metadata modification. We came up... Jing Tao
11:57 AM Bug #5737: Refactor Access page to use SystemMetadata rather than EML
adding D1Object.isSystemMetadataDirty might be tricky since it is in the d1 library ben leinfelder
11:52 AM Bug #5737: Refactor Access page to use SystemMetadata rather than EML
Maybe we need to add the method - MN.saveSystemMetadata().
Actually i want to add the flag - isSystemMetadataDirty i...
Jing Tao
11:22 AM Bug #5737: Refactor Access page to use SystemMetadata rather than EML
Saving the SM for entities when the access policy has changed (but the actual data file has not) is fine for local sa... ben leinfelder
11:13 AM Bug #5737: Refactor Access page to use SystemMetadata rather than EML
Now the access page will read and store the access information from the SystemMetadata object in both the data packag... Jing Tao

01/08/2013

04:33 PM Bug #5773: Morpho doesn't generate the system metadata for a data table created by data table wizard.
In the EntityWizardListener class, I added code to initialize the system metadata base on the eml's system metadata a... Jing Tao
12:01 PM Bug #5773 (Resolved): Morpho doesn't generate the system metadata for a data table created by data table wizard.
I created a data package by the data package wizard. At the end, i used the data table wizard to generate a data tabl... Jing Tao

01/03/2013

01:59 PM Bug #5741: Decide on login procedure
I have Morpho using the Java ECP (simple-ecp-client) to get a client certificate. the library is in my github and I h... ben leinfelder

12/31/2012

02:45 PM Bug #5741: Decide on login procedure
I have the "simple-ecp-client" java library in use in Morpho now. I'm working with the developer for that project to ... ben leinfelder
 

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