Activity
From 08/08/2006 to 09/06/2006
09/06/2006
- 11:35 PM Bug #2539: Test new VegBranch XML upload
- preassigned accession codes required a few tweaks to LoadTree... and AccessionGen.
These are now tested and work ok.... - 08:58 PM Bug #2539: Test new VegBranch XML upload
- works on aldo, but denorms broke when we got to them. Not sure how to get around that. Email didn't get to me, eith...
- 05:57 PM Bug #2539: Test new VegBranch XML upload
- includes test of preassigned XML
- 05:57 PM Bug #2539 (Resolved): Test new VegBranch XML upload
- test new VegBranch 1.0.5 upload to Aldo.
In progress several plots sent. - 09:07 PM Bug #2164: allow southern hemisphere UTM conversions.
- not so important right now
- 09:07 PM Bug #1804: export data from VegBranch into several formats
- not hugely important right now.
- 05:56 PM Bug #2002: add VegBranch downloads to cache and fix infinite loop problem
- VegBranch downloads now work on aldo. Need to stress test a bit. If plots aren't in cache, it does time out on the ...
- 03:12 PM Bug #2434: Profiling of XML Loader's Performance
- this is as done as it's going to get. the only way this is going to get faster is to significantly change the code b...
- 03:11 PM Bug #833: Management page needed with full ability to modify accounts
- we can now run accessionGen and denormGen, plus keyword gen from the /usr/vegbank/bin dir. This should work for admi...
- 03:11 PM Bug #2482: automate caching of data for homepage -- replace ant function
- cron job now does this.
- 03:10 PM Bug #2478: Implement Nightly/Weekly Cron (SQL)
- this is now running with a cron job.
- 01:04 PM Bug #2488: NPS-PLOTS import Growth Form Bug
- growthForm and rounding now fixed version 1.7
- 10:14 AM Bug #2488: NPS-PLOTS import Growth Form Bug
- Cover values now rounded to 6th digit after decimal, fixing the single to double data type bug.
- 10:03 AM Bug #2488: NPS-PLOTS import Growth Form Bug
- custNPS_intGF12() is updated but needs testing
- 01:03 PM Bug #2538: Recent PRojects page not spitting out right data
- denorm issue. Now updated the denorms for that new project. Fixed. Might set some denorms to run on "metadata" wit...
- 11:49 AM Bug #2538 (Resolved): Recent PRojects page not spitting out right data
- it didn't update to include the new stuff on aldo: the Alvar plots, also not on vEgBank.
- 11:48 AM Bug #1877: Alvar data: denorms, keywords, xml cache
- downloaded ok into vegbank and denorms run. Keywords may still need running.
- 09:42 AM Bug #1877: Alvar data: denorms, keywords, xml cache
- The Alvar data are there on VegBank now, but need denorms and keywords run on them. Also, xml cache probably isn't g...
- 11:31 AM Bug #2537: update closed lists before distributing VegBank Modules 105
- done
- 11:25 AM Bug #2537 (Resolved): update closed lists before distributing VegBank Modules 105
- please
- 09:46 AM Bug #2477: Login forwarding problems
- This is a mere annoyance, and it no longer breaks anything. The user does get logged in, just forwarded to the wrong...
- 09:45 AM Bug #2525: implement "request accessionCode" that is now available on VegBank
- User can use local VegBranch accessionCodes or VegBank preassigned ones. Works well, but takes a bit longer to get a...
- 09:44 AM Bug #2528: Import from VegBank doesn't work for VegBranch
- VegBranch 1.7 now imports VegBranch csv from VegBAnk. Just need to have that downloadable again.
09/05/2006
- 04:31 PM Bug #1877: Alvar data: denorms, keywords, xml cache
- I have begun to load this to vegbank, and it appeared to work, but the subsequence threads and denorms, etc, seem to ...
- 04:04 PM Bug #2535: run Accession Generation on VegBank
- completed with a full clean install. Then ran ok.
Loading those jars and setting classpath still doesn't work well ... - 04:02 PM Bug #2536: XML download files must validate
- the error was in the ZipUtility class. it was erroneously writing an int to the zipoutputstream which should have be...
- 01:20 PM Bug #2536: XML download files must validate
- To test download of weird characters, delete the xml for an observation on aldo:
delete from dba_xmlCache where acces... - 01:18 PM Bug #2536 (Resolved): XML download files must validate
- dateTime format was fixed, but nulls still throw it for a loop- the field should either be omitted, or we could redef...
09/04/2006
- 05:18 PM Bug #2528: Import from VegBank doesn't work for VegBranch
- There are now more fields in the import tables. Plant and Comm Name matching is highly improved. A bit more close Q...
- 05:00 PM Bug #2525: implement "request accessionCode" that is now available on VegBank
- this now works, and there is an option to turn it off and generate them locally only. It's a bit slow, but it does w...
- 04:34 PM Bug #2535 (Resolved): run Accession Generation on VegBank
- I tried to run accessionCode generation from /usr/vegbank/bin with ./runAccGen vegbank VB, but either the code isn't ...
- 11:11 AM Bug #2519: Tracking bug for upgrade of vegbank
- Server Updates
-----------
DONE 1) upgrade postgres to version 8.1.4
DONE 2) modify backup procedures so that older b... - 11:09 AM Bug #2395: Fix Backup Strategy -- delete extra backups from time to time
- the backup script now keeps 5 backups (from the last 5 days) around but deletes older ones so that the disk does not ...
09/03/2006
- 01:12 PM Bug #2519: Tracking bug for upgrade of vegbank
- Server Updates
-----------
DONE 1) upgrade postgres to version 8.1.4
2) modify backup procedures so that older backup...
09/02/2006
- 11:49 AM Bug #2519: Tracking bug for upgrade of vegbank
- Server Updates
-----------
DONE 1) upgrade postgres to version 8.1.4
2) modify backup procedures so that older backup... - 11:48 AM Bug #2519: Tracking bug for upgrade of vegbank
- (In reply to comment #5)
> Vegbank Software Upgrade
> ------------------------
> 1) tag cvs for the release
> XXX 2)...
09/01/2006
- 10:35 PM Bug #2533 (New): temp tables need to be part of denormalization update
- temptbl* tables need to be kept up to date. Currently they aren't.
- 09:20 PM Bug #2532: When users aren't logged in, prompt to do so in popup form
- This could be done with by linking to a struts form that requires log in. Since the user isn't logged in, it prompts...
- 09:13 AM Bug #2532 (New): When users aren't logged in, prompt to do so in popup form
- currently users have to login with a regular link and they lose where they were. It would be great if we could pop-u...
- 09:05 PM Bug #2477: Login forwarding problems
- I have a potential solution to this, if I can only figure out how to wrestle struts into submission. If I can add a ...
- 05:01 PM Bug #2477: Login forwarding problems
- this no longer results in an error screen, because the bug 2476 is fixed. Still, it is disorienting to get forwarded...
- 12:23 PM Bug #2476: when you try to submit data without certification, you can get to the upload screen
- fixed by replacing three characters with four different ones in the struts-config file. If only all bugs were so eas...
- 12:16 PM Bug #2475: If not certified, but logged in, should prompt to certify, not login
- now it tells you to get certified if you are logged in, otherwise to log in. Also link is provided in case you want t...
- 11:38 AM Bug #2474: After users register, they need to know it worked
- now they do. Plus they know when they log in and log out that those worked, too.
- 11:10 AM Bug #2074: Login on IE doesn't work (use aldo.msi.ucsb.edu, works there)
- works now
- 12:08 AM Bug #1975: Iteratively query to narrow or broaden query results
- this could be done by 1.2
- 12:06 AM Bug #1975: Iteratively query to narrow or broaden query results
- this should be doable, and is very useful functionality.
- 12:07 AM Bug #821: Notes: add new note form, link from views of things to note
- oops, changed the milestone on the wrong bug
08/31/2006
- 08:36 PM Bug #2483: Link into site the new searchable data dictionary (and glossary?)
- Done. Data dictionary now searchable and you can do negative searches too, plus it highlights the found terms in the...
- 03:27 PM Bug #2519: Tracking bug for upgrade of vegbank
- Server Updates
-----------
DONE 1) upgrade postgres to version 8.1.4
2) modify backup procedures so that older backup...
08/30/2006
- 10:47 AM Bug #2002: add VegBranch downloads to cache and fix infinite loop problem
- I think I've fixed the infinite loop problem within soilTaxon. There is a marker tag in the db_model_vegbank.xml fil...
- 10:12 AM Bug #2002: add VegBranch downloads to cache and fix infinite loop problem
- I think I've finally tracked down what's going on with the soilTaxon infinite recursion problem. SoilTaxon has a rec...
- 01:54 AM Bug #2483: Link into site the new searchable data dictionary (and glossary?)
- Searchable data dictionray now exists on aldo:
http://aldo.vegbank.org/vegbank/views/dba_tabledescription_summary.jsp...
08/29/2006
- 04:23 PM Bug #2520: XML Doesn't validate: DateTime invalid
- Fixed this bug in the xsl stylesheet that generates the java code for the beans. the date is now xml compliant.
- 02:51 PM Bug #2526: Denorms run 26 times on XML Loading
- This bug was due to an errant embedded for loop that was not removing items from a vector as it should have. it is n...
- 11:54 AM Bug #833: Management page needed with full ability to modify accounts
- Would it be possible to add to the management page at:
http://aldo.vegbank.org/vegbank/AdminMenu.do
the ability to r... - 11:50 AM Bug #1862: treat plantConcept and commConcept matching accCodes differently
- plantStatus and commStatus are now handled this way. These entities plus taxonInterpretation are added to userDAtase...
08/28/2006
- 05:38 PM Bug #1828: Process AccessionCode receipt fromVegBank
- don't need this any more.
- 05:38 PM Bug #2530 (Resolved): export data for "interpretations" in VegBranch
- need to export "new" interpretations from VegBranch so that one can bulk interpret data in VegBank.
- 05:37 PM Bug #1862: treat plantConcept and commConcept matching accCodes differently
- observation is now handled-- you can add new taxonInterpretations and commClass records to old observations via the X...
- 01:15 PM Bug #2406: Automate homepage map- color by number of plots per state
- later! For now, MLee will just update it.
08/26/2006
- 04:52 PM Bug #2528 (Resolved): Import from VegBank doesn't work for VegBranch
- There are new fields and new tables to digest (and a new number of fields (75))
- 04:05 PM Bug #1862: treat plantConcept and commConcept matching accCodes differently
- sure, I'll take a shot at this
- 04:04 PM Bug #2002: add VegBranch downloads to cache and fix infinite loop problem
- Also, if we have time, it would be great to add a new field to dba_xmlCache called vegbranchCSV which is just a style...
- 03:40 PM Bug #2002: add VegBranch downloads to cache and fix infinite loop problem
- We have a slight problem in the caching system as plots with soilTaxon Records don't cache because of an infinite loo...
- 04:01 PM Bug #2522: XML comments should be turned off
- Note, though that download will still have comments in them as they are read from the xml cache. I manually deleted ...
- 04:00 PM Bug #2522: XML comments should be turned off
- comments turned off (these are part of autogenerated files, so change was in xsl)
- 03:50 PM Bug #2521: XML needs to reference new xsd
- Done, with a new series of variables, properties, filters and constants.
- 03:38 PM Bug #2435: Store XML file's AccessionCodes in userDatasetItem
- no longer needed, as accessionCodes from VegBranch are generated on VegBank!
- 01:59 PM Bug #2453: Empty DB created, add necessary population + verify
- ant dbVerify now validates default values and also checks that certain tables are prepopulated.
- 11:22 AM Bug #2527: Plots don't load if missing project, coverMethod, stratumMethod
- they are now required in the XML (beefy version) but aren't in the VegBranch version... but VegBranch requires them t...
08/25/2006
- 07:33 PM Bug #2527 (Resolved): Plots don't load if missing project, coverMethod, stratumMethod
- So we either need to require those in the XML (and we need to require PK's, too), or we need to make the loader add p...
- 07:32 PM Bug #2526 (Resolved): Denorms run 26 times on XML Loading
- When I load a simple XML file to Aldo, the denorms run through the complete cycle of denorms, in order, but they run ...
- 07:28 PM Bug #2303: TEST: Misc model changes
- yes, all the new fields get added successfully to the database!
- 11:40 AM Bug #2453: Empty DB created, add necessary population + verify
- dbVerify now validates sequences and views. Last bit that would be nice to check is to see that certain tables (dba ...
- 02:39 AM Bug #2453: Empty DB created, add necessary population + verify
- ant dbverify that Chad did is now working to create all tables and ant dbVerify verifies that they have been created ...
- 01:50 AM Bug #2453: Empty DB created, add necessary population + verify
- aux_role is now properly populated in the vegbank_populate_configtables.sql
This is also called with the build scrip... - 02:41 AM Bug #2515: Loader gets sequence values when loading old data
- not anymore!
Loader now doesn't get the new PK value until it is SURE it is a new record (i.e. not already in XML, a... - 01:30 AM Bug #2523: We need a mechanism to require properties to be set in build.properties
- Added a set of
<fail unless="[propertyName]" message="'[propertyName' is required in build.properties" />
statemen... - 01:01 AM Bug #2524: keywords not generating: ambiguous referencE_ID
- added sql views and now we don't see an error about ambiguous reference_ID
- 12:11 AM Bug #2524 (Resolved): keywords not generating: ambiguous referencE_ID
- keywords are not generating due to some complexity in gathering info on the extras (I assume). This is probably best...
- 12:21 AM Bug #2525 (Resolved): implement "request accessionCode" that is now available on VegBank
- Use URLs like so: http://aldo.vegbank.org/vegbank/views/getNewRequestID.jsp?tablename=reference&recordcount=4
to get... - 12:20 AM Bug #1860: XML Loader: need to read incoming accessionCodes from user and check to see if already loaded to VegBank
- no longer needed as bug 2442 is now resolved, making this unneeded.
- 12:19 AM Bug #1859: XML Loader: need receipt for VegBranch to update user's local AccessionCodes
- this is no longer needed as I fixed bug 2442
- 12:18 AM Bug #2442: Create a "request new AccessionCode" function for VegBranch in VegBank
- Works now. New data that are loaded into VegBank accept accessionCodes that are in the dba_preassignAccCode table. ...
08/24/2006
- 11:41 PM Bug #2523 (Resolved): We need a mechanism to require properties to be set in build.properties
- We used to compare build.properties with build.properties.compare and anything that was in the latter but not the for...
- 07:00 PM Bug #2521: XML needs to reference new xsd
- http://vegbank.org/vegdocs/xml/vegbank-data-ver1.0.5-full.xsd now exists, as referencing in the above description/com...
- 06:46 PM Bug #2521 (Resolved): XML needs to reference new xsd
- At the top of our XML documents, we have a declaration:
<VegBankPackage xmlns:xsi="http://www.w3.org/2001/XMLSchema-... - 06:52 PM Bug #2522 (Resolved): XML comments should be turned off
- currently the XML is created with a lot of debugging statements inserted. While these aren't horrible, it would be a...
- 06:44 PM Bug #2520 (Resolved): XML Doesn't validate: DateTime invalid
- In our XML stream, we have tons of date fields that are now being output like so:
<observation.obsStartDate>2001-1... - 02:46 PM Bug #2519: Tracking bug for upgrade of vegbank
- -possibly add a link on the vegbank homepage describing how one would get the vegbank software if they wanted it.
- 02:39 PM Bug #2519: Tracking bug for upgrade of vegbank
- -install awstats
- 01:09 PM Bug #2519: Tracking bug for upgrade of vegbank
- -tag cvs for the release
- 01:08 PM Bug #2519: Tracking bug for upgrade of vegbank
- -Send a message to users that vegbank will be down for a day or two while we get this done.
- 12:46 PM Bug #2519 (In Progress): Tracking bug for upgrade of vegbank
- Tasks that need to be done on vegbank for the upgrade (in no particular order):
-modify backup procedures so that ... - 11:59 AM Bug #821: Notes: add new note form, link from views of things to note
- changing the milestone
- 11:43 AM Bug #2002: add VegBranch downloads to cache and fix infinite loop problem
- The xml cache is now working as far as I can tell. xml cache items get created upon upload to the system. If an ite...
- 11:41 AM Bug #1975: Iteratively query to narrow or broaden query results
- changing milestone
- 11:40 AM Bug #1860: XML Loader: need to read incoming accessionCodes from user and check to see if already loaded to VegBank
- changing milestone and reassigning to mlee
- 11:39 AM Bug #1859: XML Loader: need receipt for VegBranch to update user's local AccessionCodes
- changing the milestone and re-assigning to mlee
- 11:36 AM Bug #833: Management page needed with full ability to modify accounts
- I'm going to close this bug because I don't think there is anything else left to do with it. Restarting tomcat from ...
08/17/2006
- 01:31 PM Bug #2497: Denorm utility incorrect in order of statements (based on tables, not sequence)
- the denormutility now builds a vector of all of the keys in the sqlStore.properties file and sorts them by the sort v...
08/15/2006
- 03:31 PM Bug #2515 (Resolved): Loader gets sequence values when loading old data
- The XML Loader appears to get the next sequence value for each element it encounters, even if the element is not adde...
08/14/2006
- 04:50 PM Bug #2481: Fix Backup Strategy: where backups go
- colby has confirmed that this is working. //vegbank/usr/vegbank/backup/latest is being backed up to tape with NCEAS ...
- 04:49 PM Bug #1862: treat plantConcept and commConcept matching accCodes differently
- I don't think this would be all that complex for new commClasses of an observation -- it's just one table to look up ...
- 04:47 PM Bug #1946: try to use "commTypeID" for Z_USER_I
- not needed at all. Can change label of field if that's helpful
- 04:46 PM Bug #1352: choose which comms from commInterpretation - higher level obs summary
- allow std view of plots to be configurable as to which comms to see (most recent, best fit, original) and what names ...
- 04:45 PM Bug #2406: Automate homepage map- color by number of plots per state
- now that we have no more funding after August, we need this to be done. Matt Jones has been emailed to try to get id...
- 04:44 PM Bug #2468: show error estimates of mapped plots
- Error is estimated using colored icons.
- 04:42 PM Bug #675: Evaluate Tutorial
- Lots has changed since the tutorial was written. Probably needs to be updated. But is this a good format for it?
- 04:41 PM Bug #2402: Strategy to update denormalized data, cache, pages
- I think we decided against triggers as they proved to be slow and potentially circular. This bug remains of high imp...
- 04:40 PM Bug #2483: Link into site the new searchable data dictionary (and glossary?)
- Mlee can do this after Chad leaves if need be.
- 04:40 PM Bug #2435: Store XML file's AccessionCodes in userDatasetItem
- will not be needed if we can get bug 2394 working.
- 04:39 PM Bug #2282: Confirm that "taxonAlt" loads via XML Loader
- yup, it does.
- 04:39 PM Bug #2002: add VegBranch downloads to cache and fix infinite loop problem
- So when does the bootstrapper function? Does it search the DB periodically? What if we update a plot- how/does the ...
- 04:38 PM Bug #1860: XML Loader: need to read incoming accessionCodes from user and check to see if already loaded to VegBank
- will not be necessary if we can get bug 2394 working!
- 04:37 PM Bug #1859: XML Loader: need receipt for VegBranch to update user's local AccessionCodes
- will not be necessary if we can get bug 2394 working!
- 04:36 PM Bug #2484: add min cover % and max cover % to constancy table
- donE!
- 04:35 PM Bug #2482: automate caching of data for homepage -- replace ant function
- Very important! Perhaps we could set a cron job to run the right ant task to get this done? Or somehow else just ge...
- 04:34 PM Bug #2478: Implement Nightly/Weekly Cron (SQL)
- caching of homepage data is CRITICAL that it be done somehow without ant.
Perhaps we could set a cron-job to run ant... - 04:32 PM Bug #2442: Create a "request new AccessionCode" function for VegBranch in VegBank
- getPKFromAccessionCode() needs to be modified to look for the accessionCode in the "lookup table" if it isn't already...
- 04:08 PM Bug #2453: Empty DB created, add necessary population + verify
- aux_roles need to be prepopulated, as the loader doens't allow new ones (correct behaviour)
- 04:02 PM Bug #1877: Alvar data: denorms, keywords, xml cache
- This dataset is now ready to go, and has been loaded onto Aldo as a test. It can be loaded to VegBank after the rein...
08/09/2006
- 11:31 AM Bug #2444: user passwords are stored in clear text in the database
- The email password function now works. It creates a random password and emails that the the user asking him/her to c...
08/08/2006
- 03:42 PM Bug #2444: user passwords are stored in clear text in the database
- I've altered the password system so that it now accepts and stores MD5 digests instead of clear text passwords. I've...
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