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From: SourceForge.net <no...@so...> - 2004-05-09 16:44:27
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Bugs item #950854, was opened at 2004-05-09 10:42 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950854&group_id=16453 Category: Bio::Genex Perl API Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: centralize mechanism for setting table/view permissions Initial Comment: There are currently too many seperate paths to setting the permissions for newly created tables/views. Have everything available as an API method(s) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950854&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 16:44:27
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Bugs item #949671, was opened at 2004-05-06 23:38 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=949671&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Add Preferences table Initial Comment: We need a way to configure user preferences for the WWW apps ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=949671&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 16:44:27
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Bugs item #848040, was opened at 2003-11-24 00:26 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848040&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Nobody/Anonymous (nobody) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Scratch wants to have it's float fields turned into ints Initial Comment: Scratch wants to have it's float fields turned into ints - this is for indexing performance reasons (how many do we need? Just one I think) perhaps create a SELECT trigger so that the columns are returned correctly as floats? Probably not, since that would probably really confuse the DBI. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848040&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 16:43:16
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Bugs item #948977, was opened at 2004-05-06 02:01 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948977&group_id=16453 Category: Administrative Apps Group: Genex-2 >Status: Closed >Resolution: Duplicate Priority: 7 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: mbad-load.pl does not associate PBA with Experiment Initial Comment: The MBA is added to the ExperimentLink table but the PBA is not. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948977&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 16:42:40
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Bugs item #945399, was opened at 2004-04-30 10:10 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945399&group_id=16453 Category: Administrative Apps Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: mbad-insert.pl is not adding the PBA to ExperimentLink Initial Comment: The PhysicalBioAssay entry is being created, but it is not being associated with the experiment ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=945399&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 16:42:40
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Bugs item #950703, was opened at 2004-05-09 01:05 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950703&group_id=16453 Category: Administrative Apps Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: fix mba-filter.pl to support destination column names Initial Comment: currently the source table columns must match the destination columns exactly. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950703&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 16:42:19
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Bugs item #950854, was opened at 2004-05-09 10:42 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950854&group_id=16453 Category: Bio::Genex Perl API Group: Genex-2 Status: Open Resolution: None Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: centralize mechanism for setting table/view permissions Initial Comment: There are currently too many seperate paths to setting the permissions for newly created tables/views. Have everything available as an API method(s) ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950854&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 16:32:24
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Bugs item #947522, was opened at 2004-05-04 01:54 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=947522&group_id=16453 Category: Bio::Genex Perl API Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Ensure that Bio-Genex 'make test' is functional Initial Comment: We have not been running the automated regression tests on the DB in a long time. To ensure that changes are not breaking existing code we need to resume testing. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=947522&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 16:32:24
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Bugs item #950852, was opened at 2004-05-09 10:26 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950852&group_id=16453 Category: Bio::Genex Perl API Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Connect::new() is including single quote in user name Initial Comment: perl applications using Getopt::Long are getting arguments like: --username='some_user' and when they call Connect->new() the single quotes are getting passed as part of the username. This does not confuse DBI, but it does confuse other methods that are accessing user(). I would like to know why Getopt::Long is including the quotes. In the meantime, new() should filter any strange characters. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950852&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 16:26:25
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Bugs item #950852, was opened at 2004-05-09 10:26 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950852&group_id=16453 Category: Bio::Genex Perl API Group: Genex-2 Status: Open Resolution: None Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Connect::new() is including single quote in user name Initial Comment: perl applications using Getopt::Long are getting arguments like: --username='some_user' and when they call Connect->new() the single quotes are getting passed as part of the username. This does not confuse DBI, but it does confuse other methods that are accessing user(). I would like to know why Getopt::Long is including the quotes. In the meantime, new() should filter any strange characters. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950852&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-09 07:05:24
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Bugs item #950703, was opened at 2004-05-09 01:05 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950703&group_id=16453 Category: Administrative Apps Group: Genex-2 Status: Open Resolution: None Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: fix mba-filter.pl to support destination column names Initial Comment: currently the source table columns must match the destination columns exactly. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=950703&group_id=16453 |
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From: <ja...@op...> - 2004-05-07 11:41:41
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Hey All, While adding the Preferences table to the DB - for storing user preferences for the Mason WWW interface in the DB - I re-discovered the really ugly tangle of how the initial DB users and groups were created. I've wanted to overhaul it for a long time but haven't been willing to bite the bullet, and instead I've been bandaiding it over for a year or so. Today I finally overhauled it completely, and it is now *much* simpler to maintain. Now all the processes that create users all go through the exact same mechanism - instead of having three different mechanisms that were all slowly getting out of synch with one another. Also, I've added a GENEX_VERSION parameter to Config.pm. This way we can now support an update script. So to test it I added some version dependent pieces to the 'make uninstall' script. Just an FYI. Back to finishing the schema changes, jas. |
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From: SourceForge.net <no...@so...> - 2004-05-07 05:39:01
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Bugs item #949671, was opened at 2004-05-06 23:38 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=949671&group_id=16453 Category: DB Schema Group: Genex-2 Status: Open Resolution: None Priority: 9 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Add Preferences table Initial Comment: We need a way to configure user preferences for the WWW apps ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=949671&group_id=16453 |
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From: Harry J M. <hj...@ta...> - 2004-05-06 18:16:22
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Hi All,
Here's the 1st (text) draft of the GeneX-ODBC doc. I tested it on Linux,
windows on OOo(both) and Excel(win). Both can connect fine (I tried
connecting to both my local DB and to the one on matrix. Performance (on an
empty DB) is fine ;). We need to do some work on profiling on big data, of
course. Soon.
Please try to run thru it to see what's interpretable and what's not.
the only bit missing is how to provide pre-built queries to others. I've
found out how the queries are stored (as XML of course) in the file
DataAccess.xcu, deep in the guts of your local OOo file tree. The problem is
how to slice it out of there and make it available to other people in usable
chunks. This, I'm still trying to figure out.
--
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
<<plain text preferred>>
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From: SourceForge.net <no...@so...> - 2004-05-06 16:45:27
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Bugs item #889535, was opened at 2004-02-02 23:54 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=889535&group_id=16453 Category: DB Schema Group: None >Status: Closed >Resolution: Fixed Priority: 5 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Shouldn't make update trigger on abstract table views Initial Comment: Abstract tables should not allow any data insert or update ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=889535&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-06 16:35:46
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Bugs item #848040, was opened at 2003-11-24 00:26 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848040&group_id=16453 Category: DB Schema Group: Genex-2 Status: Open Resolution: None >Priority: 9 Submitted By: Nobody/Anonymous (nobody) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Scratch wants to have it's float fields turned into ints Initial Comment: Scratch wants to have it's float fields turned into ints - this is for indexing performance reasons (how many do we need? Just one I think) perhaps create a SELECT trigger so that the columns are returned correctly as floats? Probably not, since that would probably really confuse the DBI. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848040&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-06 16:34:19
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Bugs item #948983, was opened at 2004-05-06 02:09 Message generated for change (Settings changed) made by jason_e_stewart You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948983&group_id=16453 Category: DB Schema Group: Genex-2 >Status: Closed >Resolution: Fixed Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Fix administrative user names Initial Comment: user names should begin with genex to identify them as local to genex and not conflict with other parts of Postgres. add a test user with curator priveleges. add back the switch from 'readonly' to 'sessions' user that was lost. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948983&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-06 10:37:49
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Bugs item #949062, was opened at 2004-05-06 04:37 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=949062&group_id=16453 Category: Mason GUI Group: Genex-2 Status: Open Resolution: None Priority: 7 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: For Annotation apps, document red column names Initial Comment: Black column names mean optional. Red column names are required. It should say so somewhere on the interface pages ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=949062&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-06 10:36:18
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Bugs item #949061, was opened at 2004-05-06 04:36 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=949061&group_id=16453 Category: Mason GUI Group: Genex-2 Status: Open Resolution: None Priority: 7 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Annotation apps should have better column order Initial Comment: The order of the columns in the annotation applications is random. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=949061&group_id=16453 |
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From: <ja...@op...> - 2004-05-06 09:18:56
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Hey Diane, Wow, this one got buried long ago... I had some questions for you about how you used this feature. Just recently I ran into trouble that needed this solution - but came up with a slightly different (and not as nice approach). "Diane Trout" <di...@ca...> writes: > The one change that I'd made to the table.dtd file was the following: > > *************** > *** 78,83 **** > --- 77,84 ---- > foreign_table_pkey > CDATA #REQUIRED > fkey_type CDATA #REQUIRED > + local_association_name CDATA #IMPLIED > + foreign_association_name CDATA #IMPLIED > can_cascade > (true|false) "false" > write_sql (true|false) "true" > > The local and foreign association names are used to override the names > of the getters and setters in the classes. (Basically I grabbed the > concept from UML). > > Here's the explination for those that need it. > > For instance if you have a Tree table where records can point to > another record in the same table, my code would've origionaly > generated two different getTree member functions--one to get the > children and one to get the parent. > > With the association name construct I can rename them to getParent and > getChildren. I see, so it's basically describing the two ends of what would be a UML association, correct? Is this only useful for tables that reference themselves, or did you find other uses for it? > Another thing, I've also considered using association semantics in the > table.dtd file instead of specific foregin key references. Basically I > think the current foreign_key tag is a bit challenging to use, and > that having an association_end tag in the tables that are being linked > together might be easier for the schema developer. Agreed. But Since I'm moving genex-3 to have full UML support, I think I will wait until then. Cheers, jas. |
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From: SourceForge.net <no...@so...> - 2004-05-06 08:13:37
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Bugs item #948987, was opened at 2004-05-06 02:13 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948987&group_id=16453 Category: Mason GUI Group: Genex-2 Status: Open Resolution: None Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Need data component for annotation apps Initial Comment: Users don't know how add dates ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948987&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-06 08:11:46
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Bugs item #948986, was opened at 2004-05-06 02:11 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948986&group_id=16453 Category: Mason GUI Group: Genex-2 Status: Open Resolution: None Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Order of columns in annotation applications is random Initial Comment: The ordering of the columns should be determined by the order that the columns are listed in the XML schema files. Perhaps we will need some better grouping - for example associating a measurements column with a units column, but at least this ordering is needed. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948986&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-06 08:09:31
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Bugs item #948983, was opened at 2004-05-06 02:09 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948983&group_id=16453 Category: DB Schema Group: Genex-2 Status: Open Resolution: None Priority: 8 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: Fix administrative user names Initial Comment: user names should begin with genex to identify them as local to genex and not conflict with other parts of Postgres. add a test user with curator priveleges. add back the switch from 'readonly' to 'sessions' user that was lost. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948983&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-05-06 08:01:41
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Bugs item #948977, was opened at 2004-05-06 02:01 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948977&group_id=16453 Category: Administrative Apps Group: Genex-2 Status: Open Resolution: None Priority: 7 Submitted By: Jason E. Stewart (jason_e_stewart) Assigned to: Jason E. Stewart (jason_e_stewart) Summary: mbad-load.pl does not associate PBA with Experiment Initial Comment: The MBA is added to the ExperimentLink table but the PBA is not. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=948977&group_id=16453 |
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From: <ja...@op...> - 2004-05-06 07:54:33
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jw...@gm... writes: > 2. Comments on Data Loading Workflow skeleton I think medium-sized is > a good way to express the assumption about skill sets - there is no > reason why a correctly staffed individual lab could not use it, but we > are not making self-extracting installing out-of-the box whee! > software. Yes - we really need to make that clear or we will be up to our necks in grumpy users and silly genex-user messages asking what a GNU is, and where can they buy one. > I think we seek other funding if we decide there is a call for > this. NIH has particular programs to facilitate exactly this. Ok. > For repetitive workflow-another things we really need is to > establish antecedents so that you know what to enter first so you can > build on previous entries. Also, you want to be able to see what > already exists, so you can re-enter or modify entries rather than > repeat them. Yes. With web applications going back and forth and all around is challenging - but we have a dedicated DB behind our apps, so we can store any intermediate data we want in a temporary space until the user has finished the work, and then commit it to the actual annotation tables. > On the MAGE vocabulary - could we separate into array-associated > and analysis-associated concepts? Or object-related? The straight > alphabetical list doesn't let me see which things are major ideas and > which are examples that should be in particular controlled > vocabularies. I'll leave that up to others. Cheers, jas. |
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