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From: Harry M. <hj...@ta...> - 2004-08-11 18:44:07
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The URL: http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html is the one that is supposed to be used. Where did you see/get this one: http://matrix.binf.gmu.edu/genex/mason/workspace/workspace.html This is the reason I postedthat maybe we should put a referer link at http://host/genex/index.html Otherwise it can be difficult to find the right starting URL. hjm jw...@gm... wrote: > Task: Login GUI > Error: link to workspace in new browser window. > Actions: >>From a new browser window > Use this URL to log in: > http://matrix.binf.gmu.edu/genex/mason/authenticate.html?caller=http://matrix.binf.gmu.edu/genex/mason/workspace/workspace.html > Result: the login screen appears. > Enter name and password. > The URL that appears is to: > http://matrix.binf.gmu.edu/genex/mason/workspace/workspace.html > And this gives a error (can?t find page) > > If the login screen URL is modified: > http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html > > Result: you find that you are logged in and at the workspace screen. > > If you logout you are taken to the login screen at > http://matrix.binf.gmu.edu/genex/mason/authenticate.html?caller=http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html > > and this time after filling in name and password you are taken to the workspace at > http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html > > > > End JWW -- Cheers, Harry Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta... <<plain text preferred>> |
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From: <jw...@gm...> - 2004-08-11 18:43:09
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Test: Logout and browser window Error: closing browser window does not logout user. Actions: Pull up login screen and enter name and password Close window without logging out Open a new browser window. Result: you are given an active window showing you being logged in. It requires active logging out. end JWW |
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From: <jw...@gm...> - 2004-08-11 18:42:15
|
Test: Change user password as normal user
Error: same system error as with admin change password for any window, not just logout
Actions: Log in as standard user
Tab: Admin
Menu: Account options, Change password
Result: a message that the change was accepted (and if you log in again the new password must be used).
Result 2: going to the Workspace tab gave the following error message
A subsequent attempt to simply logout gave the same error message.
error: Can't "next" outside a loop block at /usr/local/share/perl/5.8.4/Bio/Genex/StorePostgres.pm line 98.
context: ...
94: my $self = shift;
95: my $session = shift;
96:
97: # if the user doesn't have permission to update, we skip this
98: next unless defined $session->{data}->{username};
99: 100: $self->connection($session); 101:
102: local $self->{dbh}->{RaiseError} = 1;
End:JWW
|
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From: <jw...@gm...> - 2004-08-11 18:27:25
|
Task: Login GUI Error: link to workspace in new browser window. Actions: From a new browser window Use this URL to log in: http://matrix.binf.gmu.edu/genex/mason/authenticate.html?caller=http://matrix.binf.gmu.edu/genex/mason/workspace/workspace.html Result: the login screen appears. Enter name and password. The URL that appears is to: http://matrix.binf.gmu.edu/genex/mason/workspace/workspace.html And this gives a error (can?t find page) If the login screen URL is modified: http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html Result: you find that you are logged in and at the workspace screen. If you logout you are taken to the login screen at http://matrix.binf.gmu.edu/genex/mason/authenticate.html?caller=http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html and this time after filling in name and password you are taken to the workspace at http://matrix.binf.gmu.edu/genex/mason/login/workspace/workspace.html End JWW |
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From: <jw...@gm...> - 2004-08-11 18:15:35
|
GUI Test: Change password error
Log in as admin
Tab: Select Admin
Side menu: select Account options
Submenu: select Change password
Upon submission the message says Password Successfully Changed
Logout (in order to log in again and check use of new password) and the following error results:
error: Can't "next" outside a loop block at /usr/local/share/perl/5.8.4/Bio/Genex/StorePostgres.pm line 98. context: ...
94: my $self = shift;
95: my $session = shift;
96:
97: # if the user doesn't have permission to update, we skip this
98: next unless defined $session->{data}->{username};
99:
100: $self->connection($session);
101:
102: local $self->{dbh}->{RaiseError} = 1; ...
End -JWW
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From: Harry J M. <hj...@ta...> - 2004-08-11 17:12:12
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post-installation of genex on matrix - only 1 error in whole process. - looks like a error in MANIFEST than anything else. now trying to add a user via the mason gui http://matrix.binf.gmu.edu/genex/mason/login/admin/admin.html clk on Insert DB user -> http://matrix.binf.gmu.edu/genex/mason/login/workspace/insert/user-insert.html got down to affiliated inststitution and tried to edit it in another window so wouldn't lose work..was able to edit it in another window but had to reload the frame to see it so lost work anyway. Looks like this will be an introductory irritation until all the Orgs, institutions, etc get filled in, unless there's some way to push a refreshed form to the user to pick up the changes without losing data already entered. inserted jweller as DB user, pass xxxxx insert jwwadmin as admin user, pass xxxxx insert jwwcurat as curator, pass xxxxxx insert hrishi as DB user, pass xxxxxx gui for changing group affiliation works well, except that it refuses to add jwwadmin to the superuser group. (can it only have one member?) Hmmm - yes, I guess it can only have one member - I could change it to jwwadmin, if I unchecked genex. So strictly, it should have pushbuttons rather than checkboxes for superuser - well not really - see below *** (it appears to be some kind of delayed bug or problem with a fresh login) ditto genex_test_curator public can be set to any number of members tho. *** (from above) however, when I logged in as jwwadmin and tried to make some changes that only a superuser could make, I saw that the superuser group has both genex and jwwadmin in it and I can (theoretically) remove genex. when I set the superuser to hrishi, tho, after logging in as hrishi, I only see hrishi as a superuser tho and as hrishi, I couldn't set/unset anyone as part of the superuser group now after clicking and unclicking various people several times, after having the page reset to show both jwwadmin and genex as superusers, I logged in as genex again and now see all 3 (hrishi, jwwadmin, and genex) as superusers. logging in as jwwadmin, I see all 3 as superusers still, so this seems to be the final situation. and jwwcurat still seems to be a member of the genex_test_curator group. I changed the genex_test_curator group to 'curator' successfully via gui: http://matrix.binf.gmu.edu/genex/mason/login/workspace/edit/groupsec-edit.html?mode=edit even tho the read/write group was genex_test_curator as I was changing the name to 'curator' - going back to that screen, the name of the read/write group was correctly changed to 'curator' so I set them all to jww username to see if it would work as set. Will wait to hear from JWW. -- Cheers, Harry Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta... <<plain text preferred>> |
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From: Harry J M. <hj...@ta...> - 2004-08-11 16:19:18
|
Hi Jason,
In refreshing the installation on matrix, the only error in the whole thing
was:
!! System Error: No such file or directory @ line: 286 (cp
Mason/login/workspace/comps/exp-analyze.mason /var/www/genex/mason/login/workspace/comps)
Since the source file itself is missing, this looks like an error in the
MANIFEST file - right?
Otherwise it looks like a clean install and all dependencies are still current
relative to Deb unstable and the INSTALL doc.
--
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
<<plain text preferred>>
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From: <ja...@op...> - 2004-08-11 02:24:41
|
jw...@gm... writes: > Test: insert DB User > Start in Admin tab > Go to insert side bar > Go to DB User heading > Type in information on each line (the only symbols used were > hyphens in the telephone numbers). > Upon submission the return message is Error: No such File or > Directory, which appears as a message within GUI. Um. we need the output from the Apache error log. It would be nice if I could trap it somehow, but I don't right now. Whenever you get an error like that - the "no such file or directory" - go to a command line shell on matrix and type: tail -40 /var/log/apache/error.log That tail command looks at the end of the log file, and the -40 says to print out 40 lines. That should tell me what I need to know. It's probably the same Bio::Genex::Connect version problem though. Cheers, jas. |
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From: <ja...@op...> - 2004-08-11 02:19:28
|
jw...@gm... writes: > Test: Browse tab > Select a table, in this case GeneX_User_sec > Response: > Error during compilation of /var/www/genex/mason/comps/objs2table.mason: > Bio::Genex::Connect version 20040519 required--this is only version 20040509.2 at /var/www/genex/mason/comps/objs2table.mason line 11. > Hi Jennifer, This is a matrix-specific problem. We need to update your copy of Bio::Genex::Connect. The required version numbers is a useful means of avoiding meaningless bug reports. If Mason didn't die because of the version mismatch - you might have been able to do some work, but then fail later on with some random error message. Cheers, jas. |
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From: <ja...@op...> - 2004-08-11 01:56:25
|
jw...@gm... writes: > Test: Edit Experiment > Select Trials 1 > If selected from browse experiment view a system error is displayed. > If selected from drop-down list the correct experiment is displayed > > OntologyEntry still gives a system error when you try to save it, even with very simple single words entered. If the system errors are still that "Version blah-blah expected, but this is only version nuff-nuff" then we will have to update matrix's Perl modules to be the current SVN. > Select treatment type: if selected from drop-down list this is accepted > > GeneX DB DatabaseEntry Edit Page > What is the accession number version? Mostly there is no such > critter (some sequences in GenBank, but I am not aware of any in > microarray land). It is not required. It might be reasonable to > include the date of download instead. Um, good question. You are in annotation never-never-land. This was added by the MAGE folks, and I added it to be compatible with MAGE. In short - it's optional, ignore it. > Insert DB Entry worked, then I went back a screen and hit > refresh. This does allow you to see the new entry in the drop-down > list but all other previously entered data disappears. Either the DB > Entry should be first, so you don?t lose your work, or there should > be a way to save what you have entered before you refresh the > screen. This type of stuff probably wants to be bulk loaded by curators so that ArrayDesign's can be loaded. This stuff should *never* be hand inserted (there's just too damn many of them). This Mason app exists because there is one for every table, not because I thought it was a good idea. Cheers, jas. |
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From: <jw...@gm...> - 2004-08-10 21:13:43
|
Test: Browse tab Select a table, in this case GeneX_User_sec Response: Error during compilation of /var/www/genex/mason/comps/objs2table.mason: Bio::Genex::Connect version 20040519 required--this is only version 20040509.2 at /var/www/genex/mason/comps/objs2table.mason line 11. From: JWW |
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From: <jw...@gm...> - 2004-08-10 21:06:23
|
FYI, I have a prioritized list of interfaces to test from Jason Stewart, I will be submitting an error report for each. In some cases there will be design issues intertwined, since as a user the way the interface appears can be misleading about what needs to be inserted. I will give as a subject heading GUI Test: xxxx so if this not your cup of tea it will be easy to ignore. Cheers, Jennifer |
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From: <jw...@gm...> - 2004-08-10 21:06:23
|
Test: insert DB User Start in Admin tab Go to insert side bar Go to DB User heading Type in information on each line (the only symbols used were hyphens in the telephone numbers). Upon submission the return message is Error: No such File or Directory, which appears as a message within GUI. Cheers, Jennifer |
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From: <ja...@op...> - 2004-08-10 03:16:06
|
Hrishikesh Deshmukh <gen...@ya...> writes: > That's a strange place for genex to be installed - I don't remember > installing it at root, tho I may be mistaken. yuck. Genex shouldn't be installed in '/' - that's icky. Cheers, jas. |
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From: <ja...@op...> - 2004-08-10 03:14:35
|
Hrishikesh Deshmukh <gen...@ya...> writes: > Yes in deed thats the last line in the file but what does it mean > and how do i fix it! Hey Hrishi, Did this happen after we talked? If so, this is what I meant by needing to rewrite fix-array.pl for each type of input file. It is set up to only handle quantarray data files for input. You'll notice there are 5 different scripts: * fix-array-cel.pl - .cel file input * fix-array-mas4.pl - mas4 input * fix-array-mas5.pl - mas5 input * fix-array.pl - quantarray input * fix-array-qa.pl - yet another version of quantarray input You should probably look at the other ones, they are most recent - the original fix-array.pl was for mangling the probe names in one of Karen's original data files. There are two ways to fix this: 1) put a sample input file on genex2 and tell me where to find it so I can write a script to handle it 2) read the comments in the script to understand what the program does, and modify it to work with your input. This are very simple scripts. All it does is go through every line of the input file and writes out a simplified version that only has the necessary pieces. The script needs to know: 1) when to start reading in the spot data (that's what the two perl regular expressions $data_start_regexp and $reading_data_regexp are for 2) what data columns to keep in the output file 3) how to create a unique spot_identifier for each row of data. Affy files have a unique probe name, quantarry files use a concatenation of the four values: row, column, grid_row, and grid_column. Requiring ArrayDesign's is a *painful* part of data loading - but this is something that only curators should ever have to do. It is needed by the system because we have to map every expression value in the data table to a spot on a chip - and to do that we need a uniform way of creating spot_identifiers. If someone comes up with a better approach I will be forever grateful. Cheers, jas. > Harry Mangalam <hj...@ta...> wrote: > Hi Hrishi, > > That's a strange place for genex to be installed - I don't remember installing > it at root, tho I may be mistaken. > > Also, it's an odd error - there is no '==' at line 230 - I'm assuming it's the > one that finished the stanza at 232. > > I think this implies that the input is at line 3195 - is that the end of the > file or does that line look peculiar in any way relative to the rest of the file? > > > > Hrishikesh Deshmukh wrote: >> Hi All, >> >> Here is the error which i get when i try to run fix-array.pl script on a >> cDNA file. >> >> $ perl /genex/bin/fix-array.pl --in mssm.txt --design /tmp/mssm_fix.txt >> Use of uninitialized value in numeric eq (==) at /genex/bin/fix-array.pl >> line 230, line 3195. >> Finished >> Thanks, >> Hrishi >> >> ------------------------------------------------------------------------ >> Do you Yahoo!? >> Yahoo! Mail Address AutoComplete >> >> - You start. We finish. > > -- > Cheers, Harry > Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta... > < >> > > > ------------------------------------------------------- > SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media > 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 > Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. > http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 > _______________________________________________ > Genex-dev mailing list > Gen...@li... > https://lists.sourceforge.net/lists/listinfo/genex-dev > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com |
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From: <ja...@op...> - 2004-08-10 02:19:04
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jw...@gm... writes: > OK. This is a good priority list and goes along with what has been our > goals as I have been reviewing them. However, `what' to do does not > tell us `how' or `where'. > > Your list included four points: > 1) Test the core system (regardless of how poor the existing > interfaces are) until we are pretty sure all major schema changes > are in place. > What changes have been made to the schema since May? Your invoices > seem to indicate that there have been some. I'm embarrassed to admit that I don't remember the details - it's been so long. Luckily subversion comes to the rescue - the 'svn log' command prints out the log messages I entered when committing the changes to the repository. So on a high level here they are: * a number of tables didn't get their ControlledVocabulary entries converted to use the new OntologyEntry method (the old method didn't ensure that a the value was actually in the vocabulary - the new method enforces it). * Some further testing of the Scratch table revealed I missed some important integer => floating point stuff. * all the QT sub-tables became CURATOR privelege tables instead of USER tables * the Preference table got added to hold user preferences across sessions * the external_reference column was added to tables in which data can be acquired by some outside source * in testing the Protocol/Step/Procedure stuff, I added some important columns to the Parameter and Procedure table to make it possible to re-use Protocols on different data sets * added the Image table to track image files In summary, none of these changes are user-visible in any important way. > A. Should these get moved over to matrix now? Then we can > reinstitute the freeze. Harry and I talked about this today. Unfortunately, because I've been away from the system for some time, I have to take a while to reorient exactly where things stand. The short answer is "yes" you need these changes, but give me another day to test it all, and make sure I've got all the modifications to the interfaces to work with my most recent changes. > B. What exactly needs to be tested and how should we go about > this? Here were my initial thoughts on that subject: https://sourceforge.net/mailarchive/forum.php?thread_id=4562876&forum_id=3186 the relevant bit is: That leaves part 2) [test Mason Components - ed.] . We should test: - insert DB User - change password - set user preferences - all required docs available - Full data load path: * insert Experiment (user) * insert Biomaterial (user) * load ArrayDesign (curator) * insert ArrayManufacture (user) * insert Array (user) * load MBA Data (user) - also adds MBA and PBA * add Image to PBA (user) * copy MBA Data to Scratch (user) * run processing protocol on Scratch data * add scratch view (curator)??? * add processing protocol (curator)??? * annotate BiomaterialCharacteristics (user)??? - export DBA/MBA data to tab file - other??? Let me know what you think. > The way I understand this is to use upload interface components that > put data in specific tables or groups of tables. In a sense we need > a site map from forms to tables, and some idea that this is > complete. Or we use some other database tool to directly put data > into tables when interfaces have not yet been developed. Or a > combination of these methods as needed. I hope that users of the system never have to think about tables. Ever. If they do, then I've done a bad job. We have to because we're writing the system. But from the testing standpoint, we need to begin thinking about how users are going to want to use the system - what do they want to do, what are they going to want to see, and how are they going to want to do things. That said, I *do* think that users are going to care about *types* of data - like the numeric spot data, maybe they'll care about adding Biomaterial annotations, and maybe they'll care about Protocols for processing their data. Maybe they might care about annotating the BioAssays like the PhysicalBioAssay data - but probably they won't :-( All the needed apps should be in place - if they are missing that is a bug. We should *never* be using any external tool to load data or manipulate the DB unless we're doing it on purpose (like OO.o). > 2) Fix the most critical interface issues - data loading, limited data > processing possibilities. 3) Document the existing interfaces and > core system so that other people can use the system. 4) Make a > release > > Comments: As far as I can see, if we are careful to document as we go > through data loading we will end up fixing the data loading and > interface problems (or we will be stuck) and by having a test plan we > will have a site map as well as an understanding of any deficits in > interface (not bugs, we have to use them in order to find those). Hopefully you are right. > Hrishi and I will spend several hours loading data today, and get back > to you on first-pass problems. This will be data from Karen and the > Stenger lab since we have array layouts to match. Hrishi will look > into the array layout code to see about producing a couple for data > sets we are interested in actually doing some analysis with - he will > have questions no doubt. Great! In the begining, I expect that you will discover things I've missed - so far I'm the only person to really put the system through it's paces, and since I wrote big chunks of it, I'm not a very good tester. This is likely to mean that things are frustrating and not clear - because my documentation sucks (or doesn't exist), or because the interfaces I wrote are obtuse or even broken if you do things in a different order than I've tested. I'm hoping that we can push hard on the system in the next two weeks and identify any obvious mistakes I've made in the core, and after that make the schema freeze complete. After that, only interface issues can be fixed. I'm happy to have such a flurry of activity. Cheers, jas. |
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From: Hrishikesh D. <gen...@ya...> - 2004-08-09 21:24:48
|
Hi Harry, Yes in deed thats the last line in the file but what does it mean and how do i fix it! Thanks, Hrishi Harry Mangalam <hj...@ta...> wrote: Hi Hrishi, That's a strange place for genex to be installed - I don't remember installing it at root, tho I may be mistaken. Also, it's an odd error - there is no '==' at line 230 - I'm assuming it's the one that finished the stanza at 232. I think this implies that the input is at line 3195 - is that the end of the file or does that line look peculiar in any way relative to the rest of the file? Hrishikesh Deshmukh wrote: > Hi All, > > Here is the error which i get when i try to run fix-array.pl script on a > cDNA file. > > $ perl /genex/bin/fix-array.pl --in mssm.txt --design /tmp/mssm_fix.txt > Use of uninitialized value in numeric eq (==) at /genex/bin/fix-array.pl > line 230, line 3195. > Finished > Thanks, > Hrishi > > ------------------------------------------------------------------------ > Do you Yahoo!? > Yahoo! Mail Address AutoComplete > > - You start. We finish. -- Cheers, Harry Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta... < > ------------------------------------------------------- SF.Net email is sponsored by Shop4tech.com-Lowest price on Blank Media 100pk Sonic DVD-R 4x for only $29 -100pk Sonic DVD+R for only $33 Save 50% off Retail on Ink & Toner - Free Shipping and Free Gift. http://www.shop4tech.com/z/Inkjet_Cartridges/9_108_r285 _______________________________________________ Genex-dev mailing list Gen...@li... https://lists.sourceforge.net/lists/listinfo/genex-dev __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com |
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From: Harry M. <hj...@ta...> - 2004-08-09 20:05:39
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Hi Hrishi, That's a strange place for genex to be installed - I don't remember installing it at root, tho I may be mistaken. Also, it's an odd error - there is no '==' at line 230 - I'm assuming it's the one that finished the stanza at 232. I think this implies that the input is at line 3195 - is that the end of the file or does that line look peculiar in any way relative to the rest of the file? Hrishikesh Deshmukh wrote: > Hi All, > > Here is the error which i get when i try to run fix-array.pl script on a > cDNA file. > > $ perl /genex/bin/fix-array.pl --in mssm.txt --design /tmp/mssm_fix.txt > Use of uninitialized value in numeric eq (==) at /genex/bin/fix-array.pl > line 230, <IN> line 3195. > Finished > Thanks, > Hrishi > > ------------------------------------------------------------------------ > Do you Yahoo!? > Yahoo! Mail Address AutoComplete > <http://us.rd.yahoo.com/mail_us/taglines/aac/*http://promotions.yahoo.com/new_mail/static/ease.html> > - You start. We finish. -- Cheers, Harry Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta... <<plain text preferred>> |
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From: Hrishikesh D. <gen...@ya...> - 2004-08-09 19:12:39
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Hi All, Here is the error which i get when i try to run fix-array.pl script on a cDNA file. $ perl /genex/bin/fix-array.pl --in mssm.txt --design /tmp/mssm_fix.txt Use of uninitialized value in numeric eq (==) at /genex/bin/fix-array.pl line 230, <IN> line 3195. Finished Thanks, Hrishi --------------------------------- Do you Yahoo!? Yahoo! Mail Address AutoComplete - You start. We finish. |
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From: <tf...@nc...> - 2004-08-06 19:46:04
|
The latest version of NCGR's GeneX-Lite has been released. This version has an improved user interface and enhanced annotation capabilities. Visit http://www.ncgr.org/genex to download. Todd Peterson GeneX-Lite Technical Lead The National Center for Genome Resources Santa Fe, New Mexico USA |
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From: <jw...@gm...> - 2004-08-06 17:24:31
|
Hi Harry, Use case for short oligo-based microarray data For a H sapiens array, select those probes showing signal in the ?linear range? or intensity between 200-30,000 fluorescent units, including both perfect match and mismatch where these distinctions are relevant, that are annotated as having an associated SNP. Return the gene name, probe id, probe sequence, match or mismatch status, LocusLink id, SNP position within the probe, SNP bases characterized, and the intensity associated with the probe. Cheers, Jennifer |
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From: Harry M. <hj...@ta...> - 2004-08-05 23:28:16
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Jennifer - did you get this? Reply only to me direct..
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Cheers, Harry
Harry J Mangalam - 949 856 2847 (vox; email for fax) - hj...@ta...
<<plain text preferred>>
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From: SourceForge.net <no...@so...> - 2004-07-05 05:05:40
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Bugs item #985186, was opened at 2004-07-04 23:05 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=985186&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: comp for running external applications should grab STDERR Initial Comment: instead of needing to check the apache error logs all the time, we should grab STDERR and display it directly in the browser when there is an error from an external application ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=985186&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-07-05 05:02:37
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Bugs item #985184, was opened at 2004-07-04 23:02 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=985184&group_id=16453 Category: Mason GUI 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: error handling cleanup Initial Comment: There are a number of distinct issues with how the Mason interface handles errors: 1) Mixing direct DB interaction with external applications which insert data - if the external app succeeds, but the Mason GUI generates an error you will have partial data entry 2) should autohandler define $SIG{__DIE__} and allow apps to simply call die() or $dbh->error() 3) decide what errors are recoverable, e.g. required parameters not defined, and which errors are fatal, e.g. bad data type specified for a column. Handle recoverable errors using /comps/error.mason and handle fatal errors using $SIG{__DIE__} handler? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=985184&group_id=16453 |
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From: SourceForge.net <no...@so...> - 2004-07-05 04:41:53
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Bugs item #985176, was opened at 2004-07-04 22:41 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=985176&group_id=16453 Category: Mason GUI 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: analyze-experiment.html must handle ProtocolApplication's Initial Comment: Currently this app is not inserting ProtocolApplication, ProtocolStepApplication, or ParameterValue's when running a protocol. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=116453&aid=985176&group_id=16453 |
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