genex-dev — GeneX developers

Re: [GeneX-dev] removing files from etc/MANIFEST.in

[Harry M. <hj...@ta...>]

Corrected this & will keep this in mind for later stirring of the docs pot.

hjm


Jason E. Stewart wrote:
> Hey Harry,
> 
> the docs/Array-model.txt file was being used in the documentation tab
> for the Mason GUI. Any file that is listed in the MANIFEST
> (etc/MANIFEST.in) is being installed during a 'make install_files'.
> 
> So if you remove something from SVN, check the MANIFEST, otherwise
> next time you do a 'make install' the user gets an error.
> 
> In this case, a bunch of files have to be changed because it was
> listed in one of the navbar menus for the Mason GUI:
> * Mason/nologin/docs/comps/nav-doc.mason
> * etc/MANIFEST.in
> 
> I'll let you change them - if you have questions let me know.

-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
             <<plain text preferred>>

Re: [GeneX-dev] removing files from etc/MANIFEST.in

[Harry M. <hj...@ta...>]

Jason - I can see how files are copied via the MANIFEST.in -> MANIFEST, but I'm 
not clear on how files make their way from ...nologin/docs/templates (where the 
Array-model file was referenced) to ...nologin/docs/ which is where the URL is 
pointing to.  Obviously my deletion of it in the doc/ dir caused the failure of 
the URL, but I don't follow the process, as I didn't touch the reference to it 
in the .../nologin/docs stanza in the MANIFEST.in file.

Is there a 'copy-on-installation' that is triggered when you run the make install?

Aha!  I see - you've wrapped the plain text file with <pre> tags, that why it's 
called a template.  this is sort of cool, but it also makes changing docs a 
multi-stage gymnastic.  Don't most browsers return text as plain text anyway? 
Mozilla and Konqueror do.

hjm



Jason E. Stewart wrote:
> Hey Harry,
> 
> the docs/Array-model.txt file was being used in the documentation tab
> for the Mason GUI. Any file that is listed in the MANIFEST
> (etc/MANIFEST.in) is being installed during a 'make install_files'.
> 
> So if you remove something from SVN, check the MANIFEST, otherwise
> next time you do a 'make install' the user gets an error.
> 
> In this case, a bunch of files have to be changed because it was
> listed in one of the navbar menus for the Mason GUI:
> * Mason/nologin/docs/comps/nav-doc.mason
> * etc/MANIFEST.in
> 
> I'll let you change them - if you have questions let me know.


-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
             <<plain text preferred>>

[GeneX-dev] ctid and oid now in views

[<ja...@op...>]

Hey Harry,

As of r1253 ctid and oid are selectable from security views.

Please try hooking up OO.o and ensure that it actually works.

Cheers,
jas.

[GeneX-dev] removing files from etc/MANIFEST.in

[<ja...@op...>]

Hey Harry,

the docs/Array-model.txt file was being used in the documentation tab
for the Mason GUI. Any file that is listed in the MANIFEST
(etc/MANIFEST.in) is being installed during a 'make install_files'.

So if you remove something from SVN, check the MANIFEST, otherwise
next time you do a 'make install' the user gets an error.

In this case, a bunch of files have to be changed because it was
listed in one of the navbar menus for the Mason GUI:
* Mason/nologin/docs/comps/nav-doc.mason
* etc/MANIFEST.in

I'll let you change them - if you have questions let me know.

Cheers,
jas.

Re: [GeneX-dev] Brandon King's howto-new_genex2_file_format.txt

[<ja...@op...>]

Harry J Mangalam <hj...@ta...> writes:

> I've reviewed Brandon's doc included here - it looks like it should
> really be merged into Jason's DataLoading-HOWTO.html.
>
> Is there a reason not to do this?  Is anyone busy updating that file 
> (DataLoading-HOWTO.html)?  If not, I'll do this part at any rate.

Brandon's file is very useful, but it's a bit old. So whenever he
mentions some command line tool, that tool still exists, but it has a
much easier to use Mason GUI that can (in most cases 'should') be used
instead.

>
> In order to be able to upload a new type of expression data, you have
> to submit 3 entries into the database first:
>
> 1. FeatureExtractionSoftware
> 2. ArrayDesign
> 3. ExperimentSet

ExperimentSet => Experiment (This was changed to match MAGE)

It has a few extra steps now and is current in my data loading howto.


> I will cover how to prepare these entries.
>
> ------------------------------
> -1. FeatureExtractionSoftware-
> ------------------------------
> The FeatureExtractionSoftware is defined as a
> QuantitationTypeDimension in MAGE-ML. 

Bio-MAGE is now included with genex.

> Make a copy of qtdim-quantarray.pl or qtdim-genepix.pl and open it
> into your favorite text editor. These files should be located in
> /lib/Perl/script/ from your cvs checkout.

we could include these files with genex if needed.

> Step 1: Choose a name and identifier for your QTDimension
> Step 2: Define your quantitation types
> Step 3: Create your QuantitationTypeDimension (QTD) MAGE-ML file

These are all really useful and should be in the QT Dim Creation HOWTO.

> Step 4: Upload your QTD (a.k.a FeatureExtractionSoftware to Genex 2.x
> ---------------------------------------------------------------------
> Next you add the FeatureExtractionSoftware to the database. Run
> /usr/local/genex/bin/qtdim-insert.pl --help for the list of parameters
> you need to provide.
>
>     Note: --feature_identifier_string=string allows you to define
>     which columns uniquely identify a particular row of data. In a GPR
>     file the "Block", "Column", "Row" columns would uniquely identify
>     a row of data. These happen to be Columns 1, 2, and 3 from the GPR
>     file. To use these as the feature_identifier_string you would type
>     --feature_identifier_string="0.1.2". Notice that the first column
>     = 0, the 2nd = 1, 3rd = 2, etc.
>
>     WARNING: Currently the only way to get this feature to work
>     correctly as of Dec 3rd, 2002, is to define 4 columns
>     "#.#.#.#". Since GPR files only use 3, you can code it as follows
>     --feature_identifier_string="0.0.1.2". This will be fixed in
>     future versions of qtdim-insert.pl

Huh. If this is still an issue we should file a bug report.

>     Note: --data_start_regex1=regex is a regular expression which will
>     define the row just above the header row defining the names of the
>     columns of data. (This is two rows above where the row that
>     expression data begins.)
>     
>     Note: --data_start_regex2=regex is a regular expression which defines
>     the header row that defines the names of the columns of data (This
>     is the row just before the expression data begins).

This information is already in the data loading howto.

> ------------------------------
> -2. ArrayDesign              -
> ------------------------------

This is good info and should go in the ArrayDesign creation howto.  

Loading ArrayDesign's is done with the Mason GUI.

> ------------------------------
> -3. ExperimentSet            -
> ------------------------------

Experiment's are created using the Mason GUI

> ------------------------------
> -4. Upload Your Data File    -
> ------------------------------
>
> Step 1:
>  Copy your data file to '/usr/local/genex/uploads/'. Make sure the
>  file has '.txt' at the end of the file name.

that is now /usr/local/genex/uploads/<user-name>/

and files do *not* need any special suffix.

> Step 2:
>  Load up the Mason data-loader.html from a web browser (Located at
>  http://YOUR_SERVER/genex/mason/workspace/)

the correct name is mbad-load.html and the URL is in the data loading HOWTO

> Step 3:
>  Set the read only & read/write groups
>  Select your ArrayDesign for your particular data file
>  Select your FeatureExtractionSoftware
>  Select your ExperimentSet
>  Select the data file you want to upload

this is slightly old. The correct steps are in the HOWTO.

> Step 4:
>  Click Upload and hope...!
>
>    Note: You can also upload your file using the
>    /usr/local/genex/bin/mbad-insert.pl script. (mbad = Measured
>    BioAssay Data)

This is correct, and it will be useful to include a more detailed
dicussion of this tool for curators that want to upload hundreds of
data files at the same time.

Cheers,
jas.

Re: [GeneX-dev] Big Scratch table float => int trouble

[<ja...@op...>]

ja...@op... (Jason E. Stewart) writes:

> My simple-minded approach to converting float => int in the scratch
> table broke.

FYI

This is now fixed. 

Based on Harry's idea, all data tables in the DB now store floats as
ints. 

When MBA data is loaded, the perl script converts the floating point
numbers into ints before running the INSERT on the DB.

All columns that are storing floats as ints are prefixed with 'i_' to
mark them as special.

I'm working on a mechanism to make the actually floating point numbers
available in the views along side the integer columns.

Cheers,
jas.

Re: [GeneX-dev] scatch tables and filters

[<ja...@op...>]

Harry J Mangalam <hj...@ta...> writes:

> This doc is synthesized form a GAIM chat that Jason and I had a while back.
> Please read though it and see if it reflects your vison of reality and if
> not, let me know.

Hey Harry,

Thanks for this. I'm thinking that maybe we want to have part of this
as some kind of an overview document for people deciding whether to
use genex or not - like 'Genex advantages' or something and list it on
the front page of the SF WWW site.

The rest wants to be used as a technical HOWTO for curators who need
to add processing tools to the DB.

I'll comment on technical bits later.

Cheers,
jas.

Re: [GeneX-dev] review and update of the docs dir.

[<ja...@op...>]

Harry J Mangalam <hj...@ta...> writes:

> 2004-05.10 Harry Mangalam <hj...@ta...>
>    * del doc/Array-model.txt (merged into glossary)

fine

>    * updated GeneX-ODBC.HOWTO
>    * added scratch.tables.and.filters.txt (from GAIM convers)

interesting name...

>    * updated glossary
>    * rec merging Brandon's howto-new_genex2_file_format.txt into
>       Jason's DataLoading-HOWTO.html or perhaps better into 
>       ArrayDesignCreation-HOWTO.html, which itself should be a part of 
>       the DataLoading-HOWTO.html.  These xml-derived files need to be edited 
>       in XML to retain xml->html congruence, so wait til jason responds about
>       how best to do this

I think keeping the ArrayDesign creation guide seperate is best - most
people will want to load data, only a handful will need to create
their own ArrayDesign's.

>    * delete the old Adding_New_GeneX-Apps.txt as it's now being re-done via 
>       protocols (and thus will be described in what will be the expanded 
>       version started in 'scratch.tables.and.filters.txt'

fine

>    * codingGuideline.txt will remain as is.

I can update this, but since it's a developer's doc, it's got low priority.

>    * Contributing is slightloy dated and mostly refers to providing patches to
>       the .in files which Jason has indicated are no longer going to be used
>       very much  - this file should probably be retired.

Likewise, this has low priority

>    * Cutting_a_Release.notes refers entirely to CVS which we no longer use and
>       dates back to the NCGR days.  I think we'll be using svn to tag releases
>       and release straight from svn rather than go back to the way we used to 
>       do releases at NCGR, no?  THis file should be removed.

byebye

>    * Darwin_HOWTO_Template.xml - this looks to be the XML template for the 
>       Apple Darwin HOWTO's.. Interesting, but not really relevant to GeneX 
>       docs, I think - this should be removed form the svn repo.

This was one of the template's I used to create the genex HOWTO's - it
can safely be removed, and we can create our own template if we decide
to continue using docbook

>    * docbook2html.pl - ditto this.  This is more a doc tool and users 
> shouldn't
>       really see this.  Maybe we should start a useful_tools directory where 
>       we can stash these kinds of tools that we want carried along with the
>       genex code, but more out of sight?

It can be moved to the Perl/scripts directory.

>    * genex-ents.xml has nothing to do with Tolkien characters, but seems to 
>       be a fragment of XML dealing with maillists.  Should be
>       removed.

This is needed for the XML files. If we decide to keep using docbook,
we can create an 'xml' subdirectory and all the XML files can go
their. 

>    * HOWTO_Load_QuantArray_Data.txt is my old HOWTO, but I'm not sure it has
>       anything to do with the current state of reality.  Jason?  Can this 
>       even be updated or is it completely out-of-sync?

Mostly out of sync.

>    * Porting.txt - extremely old, short description of how to port GeneX.  
>       So old and worn that it's not worth keeping.  No special info in 
>       it anyway.

byebye

>    * Security.txt looks to be an older doc that talks about the security 
>       model in GeneX.  There's no date on it, so I don't know how old it is, 
>       so Jason should take a look at it and see if it's still valid.

This is current and up-to-date. 

A good way to tell is check the docs that I have linked in the docs
tab in the Mason interface.

Cheers,
jas.

Re: [GeneX-dev] how to handle html/xml doc files

[<ja...@op...>]

ja...@op... (Jason E. Stewart) writes:

> Norm Walsh, one of the co-authors of Docbook, is a long-time open
> source supporter, and his written lots and lots of tools and
> documentation for how to use Docbook. For example, his O'Reilly is a
> debian package 'docbook-defguide'.

Sorry, that didn't get finished properly. 

Norm wrote a book for O'Reilly called 'Docbook: The Definative Guide',
and since the book was written *in* Docbook it is available as a bunch
of HTML files (or PDF) and it is availble as a seperate package in
debian. These are the packages I have installed:

  ii  docbook
  ii  docbook-defguide
  ii  docbook-xml
  ii  docbook-xsl-stylesheets

There are others but they are either optional translators, like
docbook2texi, or they are for SGML, like docbook-dsssl.

I'm used to editing XML docs, so it doesn't phase me at all, but I can
understand that it is very foreign to other people. I started them in
Docbook because I thought it was a good idea - but if it doesn't work
out because it's too wierd for everyone else, then I'm fine with
however others want to do it.

Cheers,
jas.

Re: [GeneX-dev] how to handle html/xml doc files

[<ja...@op...>]

Harry J Mangalam <hj...@ta...> writes:

> Before I get further into this, there are some docs that have both html and 
> xml sources.  I just realized that the html is probably generated from the 
> XML, so how do we handle this?  There ar a zillion HTML editors, fewer XML 
> editors; and I'm not familiar with authoring in XML. 
>
> How do you want this to occur?  If I'm going to edit, I need to know what the 
> outputs are.

The XML docs are in docbook. The HTML is generated using
docs/docbook2html.pl.

Docbook is now the standard documentation format on Linux, all the
tools and templates are being set up to handle it. I think we would be
wise to use it also. The main issue with docbook is that it is an XML
or SGML based format and to many people editing raw markup language
files is like brushing your teeth with a chainsaw.

Most people who use it use the incredible emacs tool psgml-mode for
editing XML/SGML, but for people who are emacs-allergic that doesn't
really help.

I just downloaded and tested a spiffy XML editor that has a free trial
version:

  http://www.oxygenxml.com/

It's java and even runs on my powerpc linux box.

Norm Walsh, one of the co-authors of Docbook, is a long-time open
source supporter, and his written lots and lots of tools and
documentation for how to use Docbook. For example, his O'Reilly is a
debian package 'docbook-defguide'.

Cheers,
jas.

[GeneX-dev] how to handle html/xml doc files

[Harry J M. <hj...@ta...>]

Before I get further into this, there are some docs that have both html and 
xml sources.  I just realized that the html is probably generated from the 
XML, so how do we handle this?  There ar a zillion HTML editors, fewer XML 
editors; and I'm not familiar with authoring in XML. 

How do you want this to occur?  If I'm going to edit, I need to know what the 
outputs are.
-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta... 
            <<plain text preferred>>

Re: [GeneX-dev] Scratch float => int conversion working

[Harry M. <hj...@ta...>]

OK - I'll start testing this today if I can finish off the docs that are still 
hanging.  And then once things look good, install on matrix and finish off the 
DataLoading HOWTO with JWW.

hjm


Jason E. Stewart wrote:
> Hey Harry,
> 
> as of r1245, the data tables store all float values as ints, and as
> far as my minimal testing shows, it all works, including security.
> 
> I did it very simplistically, so that whenever a user requests to
> create a float column called 'foo' in the DB, I actually create an
> 'int' column called 'i_foo', but I store the QT Dimension in the DB as
> 'foo' => float so that all applications that want to access the data
> can first check the QT Dimension for the data table, and know how to
> properly get the data out.
> 
> Also the multiplication factor is a system wide configuration
> variable, GENEX_FLOAT_MULT. We can add it to GeneX.conf at some point
> to allow users to set it.
> 
> For the near future...
> 
> I plan on creating a view on top of each of the data tables so that
> the original column 'foo' appears as a float, alongside the 'i_foo'
> which appears as an int. That will make it simpler for users to get
> back the original float. But I'd like to do a little testing to see
> how much it slows down the query.
> 
> Cheers,
> jas.
> 
> 
> -------------------------------------------------------
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-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
             <<plain text preferred>>

[GeneX-dev] [ genex-Bugs-952381 ] mbad-load.pl must convert floats => ints

[SourceForge.net <no...@so...>]

Bugs item #952381, was opened at 2004-05-12 00:38
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=952381&group_id=16453

Category: Administrative Apps
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: mbad-load.pl must convert floats => ints

Initial Comment:
The decision was made that all data tables would store
floats as ints.

Therefore, it is now the job of mbad-load.pl to do the
converion before inserting the data into the MBA Data
tables.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=952381&group_id=16453

[GeneX-dev] [ genex-Bugs-952386 ] All data tables must store floats as ints

[SourceForge.net <no...@so...>]

Bugs item #952386, was opened at 2004-05-12 00:44
Message generated for change (Comment added) made by jason_e_stewart
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=952386&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: All data tables must store floats as ints

Initial Comment:
We need to track which columns are intended to hold
floating point values.

Step 1) make all floating point columns be float
columns with an 'i_' as prefix, e.g. column 'foo'
becomes 'i_foo'.

Step 2) make a view on top of this that provides the
original column, 'foo', as 'i_foo / 1000'. 

The issue with Step 2 is how to do it in such a way
that genex_admin users don't create problems.

----------------------------------------------------------------------

>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-12 03:08

Message:
Logged In: YES 
user_id=85550

stage 1) is complete. 

Modified qtdim-insert.pl to rename columns to 'i_foo' and
create_scratch_view_sql() to remove the old multiplication
attempt. 

Made system wide config variable GENEX_FLOAT_MULT

----------------------------------------------------------------------

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[GeneX-dev] Scratch float => int conversion working

[<ja...@op...>]

Hey Harry,

as of r1245, the data tables store all float values as ints, and as
far as my minimal testing shows, it all works, including security.

I did it very simplistically, so that whenever a user requests to
create a float column called 'foo' in the DB, I actually create an
'int' column called 'i_foo', but I store the QT Dimension in the DB as
'foo' => float so that all applications that want to access the data
can first check the QT Dimension for the data table, and know how to
properly get the data out.

Also the multiplication factor is a system wide configuration
variable, GENEX_FLOAT_MULT. We can add it to GeneX.conf at some point
to allow users to set it.

For the near future...

I plan on creating a view on top of each of the data tables so that
the original column 'foo' appears as a float, alongside the 'i_foo'
which appears as an int. That will make it simpler for users to get
back the original float. But I'd like to do a little testing to see
how much it slows down the query.

Cheers,
jas.

[GeneX-dev] [ genex-Bugs-952386 ] All data tables must store floats as ints

[SourceForge.net <no...@so...>]

Bugs item #952386, was opened at 2004-05-12 00:44
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=952386&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: All data tables must store floats as ints

Initial Comment:
We need to track which columns are intended to hold
floating point values.

Step 1) make all floating point columns be float
columns with an 'i_' as prefix, e.g. column 'foo'
becomes 'i_foo'.

Step 2) make a view on top of this that provides the
original column, 'foo', as 'i_foo / 1000'. 

The issue with Step 2 is how to do it in such a way
that genex_admin users don't create problems.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=952386&group_id=16453

[GeneX-dev] [ genex-Bugs-952381 ] mbad-load.pl must convert floats => ints

[SourceForge.net <no...@so...>]

Bugs item #952381, was opened at 2004-05-12 00:38
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=952381&group_id=16453

Category: Administrative Apps
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: mbad-load.pl must convert floats => ints

Initial Comment:
The decision was made that all data tables would store
floats as ints.

Therefore, it is now the job of mbad-load.pl to do the
converion before inserting the data into the MBA Data
tables.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=952381&group_id=16453

[GeneX-dev] [ genex-Bugs-848045 ] create default Scratch view with two (data) columns

[SourceForge.net <no...@so...>]

Bugs item #848045, was opened at 2003-11-24 00:26
Message generated for change (Comment added) made by jason_e_stewart
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=116453&aid=848045&group_id=16453

Category: DB Schema
Group: Genex-2
Status: Closed
Resolution: Fixed
Priority: 5
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: create default Scratch view with two (data) columns

Initial Comment:
create default Scratch view with two (data) columns - Ch1Intensity  and Ch2Intensity

----------------------------------------------------------------------

>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-11 23:08

Message:
Logged In: YES 
user_id=85550

Changed my mind. It's now part of the default test data at
install

----------------------------------------------------------------------

Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-02-02 06:10

Message:
Logged In: YES 
user_id=85550

"Bad idea."

----------------------------------------------------------------------

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[GeneX-dev] [ genex-Bugs-848044 ] create default Scratch view with one (data) column

[SourceForge.net <no...@so...>]

Bugs item #848044, 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=848044&group_id=16453

Category: DB Schema
Group: Genex-2
>Status: Closed
>Resolution: Fixed
Priority: 7
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: create default Scratch view with one (data) column

Initial Comment:
create default Scratch view with one (data) column - Intensity

----------------------------------------------------------------------

Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-04-30 10:36

Message:
Logged In: YES 
user_id=85550

This should be done as part of the installer when the test
data set is being created.

And it should be populated with a DBA.

Bumped priority so that it's fixed pre-beta

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[GeneX-dev] [ genex-Bugs-945446 ] Insert -> FactorValues for PBA -> ERROR

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Bugs item #945446, was opened at 2004-04-30 11:04
Message generated for change (Comment added) made by jason_e_stewart
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Category: Mason GUI
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 8
Submitted By: Harry Mangalam (mangalam)
Assigned to: Jason E. Stewart (jason_e_stewart)
Summary: Insert -> FactorValues for PBA -> ERROR

Initial Comment:
From:
http://bodi.tacgi.com/genex/mason/login/annotate/annotate.html
hitting the Insert -> FactorValues for PBA
I get:
ERROR: Page: edit/pba-factorvalue-insert.html not found
on top of a table that shows the experiments that I've
entered.

did this work..?

hjm

----------------------------------------------------------------------

>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-11 22:59

Message:
Logged In: YES 
user_id=85550

fixed the URL, and updated the code to ensure it works.

Committed to r1221

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[GeneX-dev] Progress

[<ja...@op...>]

Hey All,

I fixed what is the last permissions hole registered on SF - it was a
bug that enabled anyone to modify any data in the scratch table,
whether it belonged to them or not.

Fixed in my local copy.

Cheers,
jas.

Re: [GeneX-dev] HOw to finish docs?

[<ja...@op...>]

Harry Mangalam <hj...@ta...> writes:

> I'm not following your dissatisfaction.  It seem that lyx supports
> SGML (tho thru some installation gymnastics are called for, tho maybe
> not - the debian description includes:

You cannot *import* a DocBook file.

So if you exporto to DocBook, it's a one way game. I don't use LyX, I
use emacs. So if a user creates some document, and exports it to
DocBook, and then I go and make changes, the user has no way of
re-loading my changes because LyX only supports DocBook export.

It's internal format is meant to support LaTeX.

> OOo does support DocBook, tho in a very grotty and alpha-stage way.
> However, from my previous experience in trying to use Docbook from
> within OOo (possible but quite ugly), I'm not sure that we should be
> trying to use DocBook (at least yet).  If we're not trying to use
> DocBook, maybe we should just use the native OOo format and convert to
> HTML and PDF using its native export abilities.  This allows mere
> humans to contribute to the doc support and still supports the formats
> we desire - and when DocBook support stabilizes, we can use it's
> DocBook support to convert our docs to DocBook.
>
> I like LyX quite a bit, but it only exists on Linux - OOo works quite
> well on Lin&Win and even MacOSX, so why don't we just use it for now
> and export to HTML/PDF as needed?

I don't want to spend a lot more time thinking about it, but I was
really hoping for many reasons to use a text based format.

Give me a day to think about it.

Cheers,
jas.

[GeneX-dev] [ genex-Bugs-952015 ] admin users cannot see data in views if not in ro_gs_fk

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Bugs item #952015, was opened at 2004-05-11 10:36
Message generated for change (Tracker Item Submitted) made by Item Submitter
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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: admin users cannot see data in views if not in ro_gs_fk

Initial Comment:
admin users should be able to see all data, even when
looking through a view - this is probably important for
using scratch views.

There should be a function is_admin() that returns true
if the user is in the genex_admin group. Then we can
make the sec view sql where clause be:

   WHERE is_genex_admin() or ...



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[GeneX-dev] [ genex-Bugs-848007 ] fix scratch views with lookup table security permissions

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Bugs item #848007, was opened at 2003-11-23 23:06
Message generated for change (Comment added) made by jason_e_stewart
You can respond by visiting: 
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Category: Installer
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: fix scratch views with lookup table security  permissions

Initial Comment:
need mechanism to create scratch views with lookup table security  permissions based on dba_fk. 

----------------------------------------------------------------------

>Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-11 10:33

Message:
Logged In: YES 
user_id=85550

Ah.... The scratch table was not flagged as securable, and
the dba_fk was not flagged as an lt_fkey. Once these were
fixed it works.

However, the permissions now exclude genex_admin users from
seeing the data - they can see it through the genex_scratch
table, but not through the views. But this is a general problem

----------------------------------------------------------------------

Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-05-10 07:54

Message:
Logged In: YES 
user_id=85550

The scratch views are now being created use
genex_scratch_view, but genex_scratch_view does not have the
proper WHERE clause to use dba_fk as a lookup table fkey.

----------------------------------------------------------------------

Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-04-30 10:54

Message:
Logged In: YES 
user_id=85550

This is true, the proper GRANT's are not being run, but even
with permission, users not in the security group are allowed
to edit data.

This is a bad security hole, bump priority to max.

----------------------------------------------------------------------

Comment By: Jason E. Stewart (jason_e_stewart)
Date: 2004-04-30 10:44

Message:
Logged In: YES 
user_id=85550

The mechanism exists, but views are not being given the
proper GRANT, so members of genex_user are beig refused.

Bumped priority to get fixed pre-beta

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Re: [GeneX-dev] HOw to finish docs?

[Harry M. <hj...@ta...>]

Hi Jason,

I'm not following your dissatisfaction.  It seem that lyx supports SGML (tho 
thru some installation gymnastics are called for, tho maybe not - the debian 
description includes:


Description: High Level Word Processor
  LyX is an almost WYSIWYG-frontend for LaTeX that runs under the X Window
  System. It makes the power and typesetting quality of LaTeX available for
  people who are used to word processors. Since LyX supports LaTeX's concept
  of general mark-ups, it is even easier and faster to create professional
  quality documents with it than with usual word processors. It is also
  possible to use LaTeX-commands within LyX, so nothing of LaTeX's power is
  lost.
  .
  This meta-package installs LyX common files, the frontend (Qt or XForms)
  and other packages needed by LyX.
  .
  This package can be safely removed after install.
  .
  You can extend the functionality of LyX by installing these packages:
   * ispell or aspell: an interactive spelling corrector
   * kdeprint or lpr: a printing tool
   * konqueror or www-browser: allows to view HTML documents
   * kghostview or postscript-viewer: allows to view PostScript documents
   * kghostview or pdf-viewer: allows to view PDF documents
   * sgmltools-lite: allows to export SGML DocBook documents
   * linuxdoc-tools: allows to export SGML LinuxDoc documents
   * rcs: allows to use versioning feature
   * tex4ht or hevea or tth or latex2html: allows to export HTML documents
   * gnuhtml2latex: allows to import HTML documents
   * wv: allows to import Word documents
Origin: debian
Task: tex


Actually I just installed the bits via debian which involved a total of about 17 
sec of my time, and it does seem to support docbook templates just fine - very 
slick.  However while Lyx is a very cool app, it's not really familiar in 
appearance or operation to most users.  (I happen to think that LyX does it the 
RIGHT way and that OOo and MSW do it the wrong way, but that's an argument for 
another time.)

OOo does support DocBook, tho in a very grotty and alpha-stage way.  However, 
from my previous experience in trying to use Docbook from within OOo (possible 
but quite ugly), I'm not sure that we should be trying to use DocBook (at least 
yet).  If we're not trying to use DocBook, maybe we should just use the native 
OOo format and convert to HTML and PDF using its native export abilities.  This 
allows mere humans to contribute to the doc support and still supports the 
formats we desire - and when DocBook support stabilizes, we can use it's DocBook 
support to convert our docs to DocBook.

I like LyX quite a bit, but it only exists on Linux - OOo works quite well on 
Lin&Win and even MacOSX, so why don't we just use it for now and export to 
HTML/PDF as needed?

hjm

Jason E. Stewart wrote:
> ja...@op... (Jason E. Stewart) writes:
> 
> 
>>According to the following, LyX supports Docbook SGML:
>>
>>  http://bgu.chez.tiscali.fr/doc/db4lyx/
>>
>>And the output is well-formed XML with an SGML header - so my little
>>XML => HTML processing script could be modified to remove the SGML
>>header and add an XML header before it transforms it to HTML.
>>
>>I'm installing it
> 
> 
> Unfortunately, it is export only. This means that the files would have
> to be versioned using the LaTeX or LyX format, and then exported to
> Docbook when we wanted to publish them in HTML or PDF.
> 
> Only half the battle. LyX is an OK editor for the WYSIWYG crowd, and I
> certainly know LaTeX inside and out, but I'm still not really
> thrilled.
> 
> Cheers,
> jas.
> 
> 
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-- 
Cheers, Harry
Harry J Mangalam - 949 856 2847 (v&f) - hj...@ta...
             <<plain text preferred>>