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[Genex-cvs-commit] genex-server TODO,1.22,1.23 ChangeLog,1.128,1.129
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From: <jas...@us...> - 2003-04-26 23:28:24
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Update of /cvsroot/genex/genex-server
In directory sc8-pr-cvs1:/tmp/cvs-serv29854
Modified Files:
TODO ChangeLog
Log Message:
usual
Index: TODO
===================================================================
RCS file: /cvsroot/genex/genex-server/TODO,v
retrieving revision 1.22
retrieving revision 1.23
diff -C2 -d -r1.22 -r1.23
*** TODO 16 Apr 2003 23:30:23 -0000 1.22
--- TODO 26 Apr 2003 23:28:20 -0000 1.23
***************
*** 1,14 ****
TODO
=======
Wed Apr 16 14:57:39 MDT 2003
* Make a synonym table for DB table names and column names
* start removing all the unnecessary '%%FOO%%' flags and .in files now
that we can use $Bio::Genex::Config->{FOO} directly
Mon Apr 7 10:20:59 MDT 2003
! * why is quantitationdimension and quantitationdimension_view in the
DB?
! * add return to index to all mason apps
! * need to quote groupname in 'create-experiment.html'
Thu Oct 17 13:41:31 MDT 2002
--- 1,64 ----
TODO
=======
+ Sat Apr 26 15:30:10 MDT 2003
+ * fix protocol-insert.html to indicate required fields
+ * fix Mason apps to use ro_rw_group.mason and other components
+ * fix Mason apps to show error properly
+ * fix Mason apps to show primary key after insert
+ * start entering todo items into SF bug tracker
+ * document how to rename the default perl installation:
+ /usr/bin/perl Configure --GENEX_DIR
+ * added GENEX_NAME and use it instead of GENEX_DIR for the default
+ names of the DB, etc.
+ * document how to install the Perl API in a private location
+ /usr/bin/perl Configure --PRIVATE_PERL_API
+
+
+ Thu Apr 24 09:40:30 MDT 2003
+ * handle GENEX_EXTRALIBS by using a BEGIN block:
+ begin {
+ use Bio::Genex::Config;
+ use lib $Bio::Genex::Config->{GENEX_EXTRALIBS};
+ }
+ this will eliminate all pl.in substitutions except START_PERL
+ * fix the subroutine in Install that checks the perl version to use GENEX_EXTRALIBS
+
+ Mon Apr 21 10:22:59 MDT 2003
+ * add emission energy to channel table
+ * add PhysicalBioAssay insertion program and GUI
+ * fix schema html pages
+ * add archive_data_uri column to PhysicalBioAssay to be the directory
+ that holds all on-disk but not in DB data for the PBA, like the .DAT,
+ .CEL, .RPT files
+ * add per-user upload directories
+ - add Unix user when creating new Genex user (for samba)
+ * for scripts like group-create.html that have a link to a
+ followup program, check that the user has the privelege to modify
+ the newly created data, otherwise, they get a wierd error
+ * start identifying permission groups for various tables, e.g. admin,
+ curator, user
+ * investigate the --controlled flag for create_genex_class.pl, and see
+ if things are happening as they should
+ * fix ProtocolStep table so that there is a unique index on
+ protocol_fk, order
+
+ Sun Apr 20 13:50:13 MDT 2003
+ * data-sources.html broken
+ * query.html broken because Provider is gone
+ fixed => * add ParameterValue insertion program and GUI
+ fixed => * add Sample insertion program and GUI
+
Wed Apr 16 14:57:39 MDT 2003
* Make a synonym table for DB table names and column names
* start removing all the unnecessary '%%FOO%%' flags and .in files now
that we can use $Bio::Genex::Config->{FOO} directly
+ * fix install so that Perl API files can be installed into a private
+ directory
Mon Apr 7 10:20:59 MDT 2003
! fixed => * why is quantitationdimension and quantitationdimension_view in the
DB?
! fixed => * add return to index to all mason apps
! fixed => * need to quote groupname in 'create-experiment.html'
Thu Oct 17 13:41:31 MDT 2002
***************
*** 24,141 ****
- QC: test data sets (Affy - MAS4/5, QuantArray, GenePix)
- talk to Brandon about Caltech MAGE work
-
- Sat May 26 23:38:47 MDT 2001
- * update INSTALL to explain Xerces installation
-
- Mon Feb 5 21:04:50 MST 2001
- * fix db-update script to use Genex.pm classes instead of raw SQL
-
- Tue Jan 23 09:17:48 MST 2001
- fixed ==> * remove CSF
- fixed ==> * fix broken DTD's
- fixed ==> * remove default passwords for readonly/genex
- * get rid of jpywork dir from CVS
- fixed ==> * add Term::ReadKey to required mods for install-all
- * fix MANIFEST
-
- Tue Jan 16 11:21:14 MST 2001
- fixed ==> * Move over to Class::ObjectTemplate::DB
-
- Fri Jan 12 14:57:30 MST 2001
- fixed ==> * db2xml shouldn't check passwords
- fixed ==> * make sure no CVS files get copied
- * why don't GNU apps get reset accepting cache defaults?
-
- Sat Jan 6 14:33:43 MST 2001
- fixed ==> * DTD shouldn't copy CVS
- fixed ==> * use $^X if it's a full path (check with -x), use startperl otherwise.
- fixed ==> * add checks for DB actually existing
- fixed ==> * add Genex.pm html into html installation tree
- fixed ==> * add dtd2html
- fixed ==> * must crap out if required perl modules not installed
-
- Fri Jan 5 16:42:54 MST 2001
- fixed ==> * GENEX_CGIDIR/samples must be created by install-all.pl
- fixed ==> * runa.so isn't created by the time install-all tries to install it
- fixed ==> * SUBMISSION_HOME should be set automatically after local root
- fixed ==> * questions should go to STDOUT, diagnostics should go to STDERR
-
- Thu Dec 28 13:45:54 MST 2000
- * Get rid of global variables and just use %Vars
-
- = change --SLOW to --FAST and invert the tests so that it it will by defulat go
- slow unless youwant it to go fast...
-
- fixed ==> = need to move the graphics subdir URLS to refer to /genex/graphics rather than
- /graphics
-
- fixed ==> = add mergem utility
-
- fixed ==> = note that we need the INSTALLATION GUIDE that is mentioned
- in the 1st splash screen
-
- fixed ==> = submission home directory? [/tmp/submission] (if chose
- /tmp/genex in 1st ?, this should be /tmp/genex/submission
-
- fixed ==> = #### Sorry, user /tmp/submission doesn't work, try again ####
- this should ask whether you want me to create it
- fixed ==> = What DBMS driver should DBI use by default?
- should we give some alternatives at this point?
- fixed ==> = What username should DBI use for the readonly user?
- [add some explanatory text about this - maybe decide on a format for
- allowing each answer to have additional help avialable, as in
- linux kernel config procedure...]
- fixed ==> = What username should DBI use for the super-user account?
- [more help needed]
- = http://cx408397-a.irvn1.occa.home.com/genex/index.html
- [indicated at end as the home URL, isn't installed there]
-
- 11.11.00 - CyberT Ananlyses (from the gxfetchpage) help needs more
- docs in the CyberT help file to explain what the Paired and
- C+E need in terms of minimum number of arrays, etc. should
- really collapse the CyberT form script into 1 - the analytical
- scripts should also be collapsed bu they might be a bit more
- complex to do so.
-
- 11.10.00 - Need to relabel or add help to note that the Current "Retrieve"
- Column in gxfetch_array1.pl indicates to "select for Retrieve or Paired
- Analysis" maybe "Paired / <BR>Retrieve" ? And add matching docs to the
- "What can I do with this Array Table" Should probably rename it to "What do
- the selections allow you to do in the Array Table Below"
-
- 11.01.00 - not going to skip these - might change the GetOrSetGNU() to stop
- only if there's a failure to find one of the GNU Apps; ditto GetOrSet()
-
- 10.31.00 - rationalize how to treat the GeneX-ified stuff to be able to use
- the the regular CyberT files without a huge amount of hand-editing. Talk
- to William about this..? Use Frames and then include other files into the
- frames instead of tables and requireing hand-editing?
-
- what about the samples subdir? on genex??
- referenced in curation-tool/generate-cb.pl
- ? Setting $JobDir in curation-tool/generate-cb.pl
-
- ? htdocs/download dir? bundle with curation-tool? Probably keep separate
- and just cp everything to the right place. Isn;t really related to the
- C-T except as a download access site.
- should use it for all downloads, instead of breaking all the bits up into
- a zillion places...? except that each of the zillion different files are more
- related to the function rather than the download thingie itself... Hmmmmm
-
- still need to be able to skip those stanzas whose vars have been defined
- already. Easy, but tedious. Save til tomorrow.
-
- 10.29.00 - replace all the shebang perl stuff with %%START_PERL%% to make
- sure all the scripts work OK..
- - also have to replace all the substitution var pre/suffixes in the CyberT with
- '%%' instead of '__'
-
-
- 10-28-00 recursion works; now have to edit the .in files to insert the
- correct the !!VARS!! Only have to do the CyberT and gxquery scripts
- (and then mod the query script to allow the addition of the C&E
- script... After that, only have to finish the install-all script
- (rename to install-analyses?) and package.. submit to CVS..
-
### *** emacs file mode definition ***
--- 74,77 ----
Index: ChangeLog
===================================================================
RCS file: /cvsroot/genex/genex-server/ChangeLog,v
retrieving revision 1.128
retrieving revision 1.129
diff -C2 -d -r1.128 -r1.129
*** ChangeLog 20 Apr 2003 02:10:56 -0000 1.128
--- ChangeLog 26 Apr 2003 23:28:20 -0000 1.129
***************
*** 1,2 ****
--- 1,84 ----
+ 2003-04-26 Jason E. Stewart <ja...@op...>
+
+ * Install (Repository):
+ now copies the genex-2.conf file to LOCAL_ETC
+ added creation of LOCAL_ETC *before* installing MANIFEST files
+
+ * Configure (Repository):
+ Added LOCAL_ETC, GENEX_MASON_HANDLER, PRIVATE_PERL_API
+ renamed GENEX_MASON_DIR => GENEX_MASON_COMP_ROOT
+ brought back the ability to install the Perl API to a private
+ location, but like modifying the default name of the genex
+ installation, it can only be indicated by runing the script as:
+ /usr/bin/perl Configure --PRIVATE_PERL_API
+ Changed how GENEX_EXTRALIBS is used, it no longer includes the
+ 'use lib' portion, and is instead a list of directory names
+ that must be wrapped like: 'use lib qw(%%GENEX_EXTRALIBS%%')
+
+ * Mason/workspace/protocol-step-insert.html.in (Repository):
+ fixed 'order' => 'protocol_order'
+
+ * Mason/workspace/comps/contacts.mason (Repository):
+ * Mason/workspace/comps/authenticate.mason.in (Repository):
+ * Mason/workspace/add_user_to_group.html.in (Repository):
+ * Mason/workspace/array-design.html.in (Repository):
+ * Mason/workspace/authenticate.html.in (Repository):
+ * Mason/workspace/autohandler.in (Repository):
+ * Mason/workspace/bioassay.html.in (Repository):
+ * Mason/workspace/contact-insert.html.in (Repository):
+ * Mason/workspace/data-loader.html.in (Repository):
+ * Mason/workspace/data-sources.html.in (Repository):
+ * Mason/workspace/experiments.html.in (Repository):
+ * Mason/workspace/experimentset-create.html.in (Repository):
+ * Mason/workspace/generate_group.html.in (Repository):
+ * Mason/workspace/generate_user.html.in:
+ * Mason/workspace/group-create.html.in:
+ * Mason/workspace/group-maint.html.in:
+ * Mason/workspace/kill-cookie.html.in:
+ * Mason/workspace/noauth-autohandler.in:
+ * Mason/workspace/query.html.in:
+ * Mason/workspace/sample-insert.html.in:
+ * Mason/workspace/user-insert.html.in:
+ * Mason/workspace/workspace.html.in:
+ added GENEX_EXTRALIBS
+
+ * apache/genex-2.conf.in (Message):
+ seperated out the MasonCompRoot and MasonDataDir from the
+ substitution
+ added the handler.pl
+ removed the importing of modules, hopefully having it in the
+ handler script will work better for Apache
+
+ * apache/genex-2-handler.pl.in:
+ A first shot at using a handler.pl file to run Mason
+
+ 2003-04-23 Jason E. Stewart <ja...@op...>
+
+ * Mason/workspace/parameter-value-insert.html (Repository):
+ replaced repetitive code with new components
+
+ * Mason/workspace/comps/ro_rw_group.mason (Repository):
+ added the ability to set default groups for each menu
+
+ * Mason/workspace/protocol-application-insert.html (Repository):
+ Added a better introduction message
+
+ 2003-04-21 Jason E. Stewart <ja...@op...>
+
+ * Mason/workspace/sample-insert.html.in (Repository):
+ * Mason/workspace/protocol-step-insert.html (Repository):
+ * Mason/workspace/protocol-insert.html (Repository):
+ * Mason/workspace/procedure-insert.html (Repository):
+ * Mason/workspace/parameter-insert.html (Repository):
+ * Mason/workspace/group-create.html.in (Repository):
+ * Mason/workspace/data-loader.html.in (Repository):
+ * Mason/workspace/array-design.html.in (Repository):
+ all command line args are quoted
+
+ 2003-04-20 Jason E. Stewart <ja...@op...>
+
+ * Mason/workspace/index.html (Repository):
+ reorganized
+
2003-04-19 Jason E. Stewart <ja...@op...>
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