Morpho

01/28/2013

05:26 PM Bug #5824: Call CN.setAccessPolicy() when editing access

This needs to be done for data entities as well. I don't currently see any changes to edit SystemMetadata for these d... ben leinfelder

05:21 PM Bug #5824: Call CN.setAccessPolicy() when editing access

Matt suggested that we _not_ save the access rules in EML anymore since they can drift out of synch with what is in t... ben leinfelder

05:19 PM Bug #5824: Call CN.setAccessPolicy() when editing access

I'll take this -- should be just like doing the setReplicationPolicy bug. ben leinfelder

05:13 PM Bug #5825: Call CN.setReplicationPolicy() when editing replication policy

Now doing the same for data objects. ben leinfelder

04:55 PM Bug #5825: Call CN.setReplicationPolicy() when editing replication policy

Now calling the CN for changes to the EML ReplicationPolicy. Note that Morpho calls the CN first to retrieve the late... ben leinfelder

11:37 AM Bug #5801: Test Morpho against GMN

We were not recalculating size and checksum of the EML before saving. Now we are. ben leinfelder

10:36 AM Bug #5796: D1Object in Morpho still uses byte array as data source

create an issue on the dataone redmine. So the dataone persons can know what we will do.
https://redmine.dataone.org/... Jing Tao

10:00 AM Bug #5826 (Resolved): Show identifier conflict prompt when conflict is detected

I removed this window from the save workflow because it seemed like there was no logical question to ask the user - i... ben leinfelder

09:29 AM Bug #5141: offer a choice to "cancel" from any save

We allow you to cancel if/when the identifier conflict screen shows. If the save is canceled at this stage, neither t... ben leinfelder

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