genex-dev — GeneX developers

Re: [GeneX-dev] Linux version of curation tool

[Michael P. <mic...@ho...>]

I added the following line to our httpd.conf file:

AddType application/xar xar

I think bringing it in as "text/plain" may result in
some problems.

Regards,

Michael Pear
----- Original Message -----
From: "Jiaye Zhou" <ze...@in...>
To: <gen...@li...>; "Todd Peterson" <tf...@nc...>
Cc: <gen...@li...>; <and...@ah...>
Sent: Monday, March 26, 2001 2:27 PM
Subject: Re: [GeneX-dev] Linux version of curation tool


Seems the webserver is not feeding it to the user response session correctly,
and try to send the file as type text/plain type. Take a look at the mine
setting on the server side, should be in /etc/mime.types ( and this is where
apache looks) or httpd.conf. Try setting it to application/curationtool.
(should be able to get a save option). I don't have access to genex, so can't
look myself.

Jiaye

Quoting Todd Peterson <tf...@nc...>:

> Lonny and web guys
>
> I tried saving screen gibberish with Netscape 4.75 and 4.51 and get an
> exception in the Curation Tool when reading the resulting control-bundle
> .xar file. It seems that Netscape saves the control bundle incorrectly.
>
> A good control-bundle (using Explorer) is 48,697 bytes for all species.
> Saved with Netscape, the file is 48,875 bytes. Messed with
> preferences/applications and MIME types etc. until I was blue in the
> face.
> Netscape would not recognize the control bundle as a file to save to
> disk.
>
> Web guys, this used to work. What happened?
>
> Todd
>
> ----- Original Message -----
> From: "Lonny Montoya" <lon...@st...>
> To: <and...@ah...>
> Cc: <gen...@nc...>; <gen...@li...>
> Sent: Monday, March 26, 2001 1:59 PM
> Subject: [GeneX-dev] Linux version of curation tool
>
>
> > Hi Erik,
> >
> > Here is what I think is going on with this:
> >
> > >---------- Forwarded message ----------
> > >Date: Mon, 26 Mar 2001 08:47:36 -0700
> > >From: Erik Andries <and...@ah...>
> > >To: Lonny Montoya <lx...@nc...>
> > >Subject: Re: Linux version of GeneX
> > >
> > >Lonnie Montoya,
> > >
> > >I download the latest version of the Linux Curation tool and
> > >I got the following errors.  See the attachment for the
> > >session re-enactment.
> > >
> > >Erik Andries
> > >
> > >
> > >These are the following messages when I type "go.sh"
> > >
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >
> >
> > These messages are because the jvm can't find a font it is looking
> for.
> It
> > is possible that this was caused by using a copy of the curation tool
> > created with another JDK besides Sun's.  This shouldn't present a
> problem
> in
> > the operation of the curation tool, however, it should just use the
> default
> > font instead.  The fact that you can read the buttons and labels in
> the
> tool
> > suggest that it is using the default font and these messages can be
> ignored
> > as they are not causing a problem.  You can test whether this is the
> problem
> > by downloading Version 1.0 of the Curation Tool at:
> >
> > http://genex.ncgr.org/genex/download/curation_tool/linux/
> >
> > This shouldn't happen with this version as it was created with the Sun
> JDK.
> > If you are still getting these messages with Version 1.0, there may be
> > something else going on.  Let me know what the result is when you try
> it.
> >
> > >
> > >Then the main window pops.  I hit the CREATE NEW EXPERIMENT SET icon
> and
> I
> > enter new experiment set window.
> > >I hit the READ CONTROL FILES icon and enter the window where I enter
> my
> > login name and password.
> > >Suppose I do the test c·³ase (where I highlight all the
> > >species for my control bundle).
> > >I hit the SUBMIT REQUEST icon and then I get
> > >
> > >for a few seconds...
> > >
> > >  "Curation Tool Download Generation Status Y
> > >  our Curation Tool download bundle is now being created.
> > >  Current run time is 0 seconds.
> > >  Output of the xml-write program:"
> > >
> > >and then...
> > >
> > >sÁ?(åXt?Ë?K?P®øA??åt¦avÙþA~ sC¬aCI_}¸WYÆ×;Ý?µ»þCà¡íúf5Ó»¿MÜ
> > ><¤fõ]uµ¯aËÁ§â,ÞÛç&Vë«ks25ÔÅ*"Ù§²s"..1÷¿Ú:
> 3<SSõà,ÐÐ2..Ì?E3.õÔµÉ
> > i.Ç" UTdð ìÅórÒY¶}±Ô.¼7(ë
> > >ÅXvR mHºW"y¯õ0öY«
> > >ځ:,tq3~ï.R&ï:³"¦?^§W[#Y"{°ÛVÐ_<
> > "¯(N¹Îßì2,ê\3"Pknðv??UL)?8?^¶a%f)3)í1Y[*-ä|x)+
> > ¢ÿþ®U'F¤åxN.-ã[+µJýYbo\OOÀäC<çU?>0ñ\ꬱ??Õ\?HIóZWÈJ.
> > >êÁlÂØ®2PäÚæºÈr?ë³-;<h?Ûê6èd¥??çÊ­??µiw?ÚfÈŶ«2¾¨&0
ék ñ
> bÝ-Q,ÜgÎÛZ
> ß°
> > 'Ç.i /J==-"`ÁðÕL¡j9ã9ø_4g~6sJîn2È·Pô!Üb+5?!>?
> > >Êh~?&ÓAìC"f<'m"3fZP+Áe©(â YÌzI#(;·ðLå?,so¨º)­EO´ÄUi± Xl
> > >ËJ_«sP
> > >qtkL[wl'
> > ¡êTãX½÷,?dVÄ·P@bÊ<
> p=^ק¸¯Võ^ÒS.¸Q´¬·A5-Ð.öÌÉ7.7[ªàyòÓjY't½cdSÁ<qBìò
> > d¡Ú-­@¤!ô*
> > >TP*¥åY³v$·-Óȸ&H$ÐXÂ1^iF²74?H°ù"
)C
> > >¶ÔP°í-Q)ÙyT¿ë܍j-fÜF"Ç-
> > >¥Á"?%Y{òÒå-D-qì
> > ,ß~3õ
> ÞXÂ-lWá>~Áõý>@"íÚ6Q?ð$èáÀ»ª¶Ú.d?uÒÁO:ûP>æíÐf<d-A¶C¯ÜÈ^Ã-¸è~²à
> > eáC<T?>ITäxÒ:Ö÷Q>rÑa,¨QÊGúAQxt²}s³ß6¶ÌIµÚâ#YÊ&^LKر0µ¥g>ÇBU
> > ?¿\Ã×xF"»öQ÷7¦îâ<o²^
> >
> >£P½º/TbèT©?~wU"®?«?òÊ2¶?Oò"0sç_ȶÜntB`×F@¿Zý1Ò§=:àcodk«N®Þ?»
> > ãû¨I¶F3Èr;üÝ1pPän3 >d¤ãØÖU".«µÎ68TûpIÚzV[ø"E|úµ6B9f
¿£q
> > >,bÐ­hsa4(bGxÐV¡8xÖªÍcL©RçxÜB
;Q©¨jßNð,=²J w
> çB£¦WhÉs%L`ÛÈ
-Æ?fg/`R
> > >àðW.·EóP"¨ö¬¬kUFª5Ù,UoV»ììZT1(±³ÎZ\-²¿iÍ
> > ½ñiÎ2¶×2±G³ÕäNËHòèê¡(äH.8Àâg¥Ô±;`ÆÛ
> >Dyù_¿¼½ÁxùìûÿíÓó_Þf/¼ÿ×>Õ¿½ÿC0çûÿ/
> >
> 2>>ÝøRYÒYÚYÖYÞYqyüø,5õ)ý©ýiýéý9kòò?ÛóÓO-ß~ùæ«ËËå?_C,üÊÇÉÿYÿö6{|)>ÿñÆòùï
> > |æÿ/1>üîo
> >
> >÷-x'útùðûG4)ï/¾~D?SßèFß×u¼ô7ï}YÕ¥?x?a°Ìn"^?k`VòTY@r°?y¹KÔLÐàtü;äó¥?p:
> > *q?!ÛÆ?<%=!wo+?%5Ôv?Èø*ý?0w+ö>D?Ò)>ɹö½oMa7Î#{â?? È Öç}X¼¢Åo?Ýñ?tÊãSPK
> > >#=õùÃ?Á´Æ0ÏÚ)J?,Û¤jÃÄ?V¶j?Õ;Yi$^?WäaÑÕI?o¹ñ·\¢?Üó%°kÔª¤ "]ÀëS¶Ï°»
> > >
> > >That's as far as I get the with the Linux version of the curation
> tool.
> Is
> > there
> > >a relationship between the messages I get when I type "go.sh" and the
> > >crazy output when I SUBMIT REQUEST the control bundle?
> > >
> >
> > This crazy output is what a binary file looks like in the browser
> window.
> > It isn't related to the font error messages.  Netscape on Linux and
> Unix
> > often downloads a binary file to the browser window like this.  I'm
> not
> sure
> > why Nescape does this by default, but it is usually the source of some
> > confusion.  What you should do is wait for the file to finish
> downloading
> > and then click on "Save Page As" in the File menu to save the file.
> Save
> > the file to the proper subdirectory (i.e.
> > /home/lxm/ct100_usrlnx/data/control-bundle-downloaded) and then go
> back to
> > the curation tool to continue.  Even though the binary file is
> displayed
> in
> > the browser window like that, it still should save ok.  Note that you
> may
> > have to create the control-bundle-downloaded subdirectory yourself.
> >
> > I hope this helps out.
> >
> >
> > Lonny
> >
> >
> >
> > _______________________________________________
> > Genex-dev mailing list
> > Gen...@li...
> > http://lists.sourceforge.net/lists/listinfo/genex-dev
> >
>
>
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
>

_______________________________________________
Genex-dev mailing list
Gen...@li...
http://lists.sourceforge.net/lists/listinfo/genex-dev

[GeneX-dev] Re: Some Installation Problems

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

I figured this was generally useful, so I forwarded it to the list.

jas.

Re: [GeneX-dev] Linux version of curation tool

[Todd P. <tf...@nc...>]

hmmm...got this when I did a dos2unix on garbled version and re-read it on
Windows version of curation tool.

Tried again just now and did indeed get a save dialog (cool!). Read Control
Bundle button worked fine. Looked around at data and there are a lot of
'box' characters (the little squares). Looks like we have some problems with
character encoding for the XML.

Looked some more...found that good control-bundle for Windows version of
curation tool has dos eol's where the current download bundle uses Unix
style. The XML encoding 'said' UTF-8 on both. But, in my experience, what it
says and what it is could be different.

Todd

----- Original Message -----
From: "Harry J. Mangalam" <hj...@nc...>
To: <gen...@li...>
Cc: "Todd Peterson" <tf...@nc...>; <and...@ah...>
Sent: Monday, March 26, 2001 5:29 PM
Subject: Re: [GeneX-dev] Linux version of curation tool


> Hi ALl,
>
> OK - I added that to the /etc/mime.types adn in fact Jiaye wins a Kewpie
> doll as it does force a download dialog, and does download the file, but
the
> Curation Tool does not recognize it as such - unix unzip processes it
> correctly:
> 42 % unzip control-bundle.xar
> Archive:  control-bundle.xar
>   inflating: META-INF/MANIFEST.MF
>   inflating: control-bundle/control-bundle.xml
>   inflating: control-bundle/control-bundle_ALS_01.ext
>   inflating: control-bundle/control-bundle_CSF_01.ext
>   inflating: control-bundle/control-bundle_USF_01.ext
>
> but the curation tool cannot read it via the 'Read Control Files' button,
> failing with:
>
> 40 % org.xml.sax.SAXParseException: The markup in the document preceding
the
> root element must be well-formed.
>         at java.lang.Throwable.<init>(Throwable.java:96)
>         at java.lang.Exception.<init>(Exception.java:44)
>         at org.xml.sax.SAXException.<init>(SAXException.java:45)
>         at org.xml.sax.SAXParseException.<init>(SAXParseException.java:56)
>         at
> org.apache.xerces.framework.XMLParser.reportError(XMLParser.java:1016)
>         at

blah, blah, etc

>         at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:99)
>         at java.awt.EventDispatchThread.run(EventDispatchThread.java:90)
>
> implying...?
>
>

rest of msg excluded...see previous msg in thread.

Re: [GeneX-dev] Linux version of curation tool

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

But were you able to read it in with the Curation Tool?

hjm


On Mon, 26 Mar 2001, Jiaye Zhou wrote:

> Hey Todd,
>  
>  I added xar extension under Zip Compressed Data association, with mime type
> application/x-zip-compressed. And I was able to get the save to disk option 
> with netscape. I still think we should do this on the server side though, 
> instead of having the each user do it.
> 

[hey - don't forget to trim old cruft - this is being archived]

Re: [GeneX-dev] Linux version of curation tool

[Jiaye Z. <ze...@in...>]

Hey Todd,
=20
 I added xar extension under Zip Compressed Data association, with mime t=
ype
application/x-zip-compressed. And I was able to get the save to disk opti=
on=20
with netscape. I still think we should do this on the server side though,=
=20
instead of having the each user do it.

Jiaye

Quoting Todd Peterson <tf...@nc...>:

> Lonny and web guys
>=20
> I tried saving screen gibberish with Netscape 4.75 and 4.51 and get an
> exception in the Curation Tool when reading the resulting control-bundl=
e
> .xar file. It seems that Netscape saves the control bundle incorrectly.
>=20
> A good control-bundle (using Explorer) is 48,697 bytes for all species.
> Saved with Netscape, the file is 48,875 bytes. Messed with
> preferences/applications and MIME types etc. until I was blue in the
> face.
> Netscape would not recognize the control bundle as a file to save to
> disk.
>=20
> Web guys, this used to work. What happened?
>=20
> Todd
>=20
> ----- Original Message -----
> From: "Lonny Montoya" <lon...@st...>
> To: <and...@ah...>
> Cc: <gen...@nc...>; <gen...@li...>
> Sent: Monday, March 26, 2001 1:59 PM
> Subject: [GeneX-dev] Linux version of curation tool
>=20
>=20
> > Hi Erik,
> >
> > Here is what I think is going on with this:
> >
> > >---------- Forwarded message ----------
> > >Date: Mon, 26 Mar 2001 08:47:36 -0700
> > >From: Erik Andries <and...@ah...>
> > >To: Lonny Montoya <lx...@nc...>
> > >Subject: Re: Linux version of GeneX
> > >
> > >Lonnie Montoya,
> > >
> > >I download the latest version of the Linux Curation tool and
> > >I got the following errors.  See the attachment for the
> > >session re-enactment.
> > >
> > >Erik Andries
> > >
> > >
> > >These are the following messages when I type "go.sh"
> > >
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >
> >
> > These messages are because the jvm can't find a font it is looking
> for.
> It
> > is possible that this was caused by using a copy of the curation tool
> > created with another JDK besides Sun's.  This shouldn't present a
> problem
> in
> > the operation of the curation tool, however, it should just use the
> default
> > font instead.  The fact that you can read the buttons and labels in
> the
> tool
> > suggest that it is using the default font and these messages can be
> ignored
> > as they are not causing a problem.  You can test whether this is the
> problem
> > by downloading Version 1.0 of the Curation Tool at:
> >
> > http://genex.ncgr.org/genex/download/curation_tool/linux/
> >
> > This shouldn't happen with this version as it was created with the Su=
n
> JDK.
> > If you are still getting these messages with Version 1.0, there may b=
e
> > something else going on.  Let me know what the result is when you try
> it.
> >
> > >
> > >Then the main window pops.  I hit the CREATE NEW EXPERIMENT SET icon
> and
> I
> > enter new experiment set window.
> > >I hit the READ CONTROL FILES icon and enter the window where I enter
> my
> > login name and password.
> > >Suppose I do the test c=B7=B3ase (where I highlight all the
> > >species for my control bundle).
> > >I hit the SUBMIT REQUEST icon and then I get
> > >
> > >for a few seconds...
> > >
> > >  "Curation Tool Download Generation Status Y
> > >  our Curation Tool download bundle is now being created.
> > >  Current run time is 0 seconds.
> > >  Output of the xml-write program:"
> > >
> > >and then...
> > >
> > >s=C1?(=E5Xt?=CB?K?P=AE=F8A??=E5t=A6av=D9=FEA~ sC=ACaCI_}=B8WY=C6=D7;=
=DD?=B5=BB=FEC=E0=A1=ED=FAf5=D3=BB=BFM=DC
> > >=1F<=08=A4f=06=11=F5]u=C2=13=B5=AFa=CB=C1=A7=E2,=DE=DB=E7&V=EB=ABks2=
5=D4=C5*"=D9=A7=B2=15s"..1=F7=03=BF=DA:
> 3<SS=16=11=F5=E0,=D0=14=D02..=CC?E3.=F5=D4=B5=C9
> > i.=C7" U=12T=14d=F0 =EC=C5=F3r=17=D2Y=B6}=B1=D4.=BC7(=EB
> > >=C5XvR=1F=04=8F mH=BAW"y=AF=F50=F6Y=AB
> > >=DA=81:,tq3=9D~=EF=12.R&=EF:=B3"=A6?^=A7W[#=19Y"{=B0=1A=DBV=D0_<=19
> > "=AF(N=B9=CE=DF=EC2,=EA\3"=07Pkn=F0v??UL)?8?^=B6a%f)3)=ED1Y[*-=C3=A4|=
x)+
> > =A2=FF=FE=AEU'F=A4=E5xN.-=E3[+=B5J=FDYbo\OO=C0=E4C<=E7U?>0=F1\=EA=AC=B1=
??=D5\?HI=F3ZW=C8J.
> > >=EA=C1l=C2=D8=AE2P=E4=DA=E6=BA=C8r?=EB=B3-;<h?=DB=EA6=E8d=A5??=E7=CA=
=AD??=B5iw?=DAf=C8=C5=B6=AB2=BE=A8&0=01=E9k =F1
> b=13=07=DD=1E-Q,=DC=1Bg=CE=DBZ
> =DF=06=B0=08
> > '=C7.i=14 /J=3D=3D-"`=C1=1D=F0=D5L=A1=12j9=E39=F8_4g~6sJ=EEn2=C8=B7P=F4=
!=DCb+5?!>?
> > >=CAh~=10?&=D3=15A=ECC=06"f<=19'm"3=17fZP+=C1e=A9(=E2 Y=14=CCzI#=9D(;=
=B7=F0L=E5=16?,so=A8=BA)=ADEO=B4=C4Ui=B1 Xl
> > >=CBJ_=ABsP
> > >=8D=18=16qtkL[wl=1B'
> > =A1=07=EAT=13=E3X=BD=10=F7,?dV=C4=B7P@b=CA<
> p=3D^=D7=A7=B8=AFV=F5^=D2=0FS.=B8Q=B4=AC=B7A5-=D0.=10=F6=CC=C97.7[=AA=E0=
y=F2=D3=04j=19Y't=BDcd=8DS=C1<qB=EC=F2
> > =19=12d=A1=DA-=05=8F=AD@=04=A4!=F4*
> > >T=12P*=A5=E5=05Y=B3v=08$=19=B7-=D3=C8=B8&H$=D0X=C21^i=1DF=B274?H=B0=F9=
=08"=01)C=07
> > >=B6=19=D4P=B0=ED-Q)=D9yT=BF=EB=DC=8Dj-f=DCF=8D"=C7-=02
> > >=A5=C1"?=06%Y{=F2=1C=D2=E5-=06D=1A-=13q=EC=0E
> > ,=DF~3=F5
> =DEX=C2-=1BlW=E1>~=81=C1=04=F5=FD>@"=ED=DA=066=15Q?=1E=F0$=E8=E1=C0=BB=90=
=AA=B6=DA.d?u=D2=C1O:=FBP>=90=E6=ED=D0=1Bf<d-A=B6C=AF=DC=C8^=C3-=B8=E8~=B2=
=E0
> > e=E1C<T?>IT=E4x=D2:=D6=06=F7=19Q>r=D1a,=A8Q=CAG=FAAQxt=11=B2}s=19=B3=DF=
6=B6=13=19=CC=1BI=B5=DA=E2=10#Y=CA&^LK=D8=B10=B5=05=0E=A5g>=C7BU
> > ?=BF\=C3=D7xF"=BB=F6Q=F7=187=A6=EE=81=E2<o=19=B2^=18
> >
> >=A3P=BD=1A=BA/Tb=E8T=A9=1C?~wU"=AE?=AB?=02=F2=CA2=B6?O=F2"0s=E7_=15=C8=
=B6=04=DCntB`=D7F=14@=BFZ=FD=901=D2=A7=3D=08:=E0co=04dk=AB=02N=AE=DE=11?=BB=
=1A
> > =81=E3=03=FB=A8=02I=B6F3=C8r;=FC=02=16=C3=9D1pP=E4n3 >d=A4=E3=17=D8=0E=
=D6U".=AB=B5=CE68T=FBpI=DAzV[=F8"E=08|=FA=8F=B56B9f=01=BF=A3q
> > >=1B,b=14=8D=D0=ADhsa4(bGx=D0V=A1=9D8x=D6=AA=CDcL=A9R=0E=E7x=DC=1EB=01=
;Q=A9=A8j=DFN=F0,=3D=B2J w
> =E7B=A3=A6Wh=C9s%L`=DB=C8=01-=17=C6?fg=04/`=11R
> > >=E0=F0W.=B7E=F3P"=A8=F6=04=AC=ACkUF=90=AA5=D9,UoV=19=BB=EC=ECZ=03T1(=
=B1=B3=1F=CEZ\-=B2=BFi=CD
> > =BD=F1i=CE2=B6=D72=B1G=B3=D5=19=E4=1CN=CBH=F2=E8=EA=A1(=E4H.=178=C0=1E=
=E2g=A5=D4=B1;`=C6=DB
> >Dy=F9_=BF=BC=BD=C1x=F9=EC=FB=FF=ED=D3=F3_=DEf=8F/=BC=FF=D7>=D5=BF=BD=FF=
C0=E7=FB=FF/
> >
> 2=1E>>=DD=F8RY=D2Y=DAY=D6Y=DEYqy=FC=F8,5=F5)=FD=A9=FDi=FD=E9=FD9k=F2=F2=
?=DB=F3=D3O-=DF~=7F=F9=E6=AB=CB=CB=E5?_C,=FC=CA=C7=7F=C9=FF=1FY=FF=F66{|)=
>=FF=F1=C6=F2=1F=F9=EF
> > |=E6=FF/1>=FC=EE=11o
> >
> >=F7-=0F=0F=0Fx'=FAt=F9=F0=FBG4)=EF/=1F=BE~D?S=DF=0F=E8F=DF=D7u=BC=05=F4=
7=EF}Y=D5=A5?x?a=B0=CCn"^?k`V=F2TY@r=B0?y=B9K=D4L=D0=E0t=FC;=E4=F3=A5?p:
> > *q?!=DB=C6?<%=3D!wo+?%5=D4v?=C8=F8*=FD?0w+=F6>D?=D2)>=C9=B9=F6=BDoMa7=
=CE#{=E2?? =C8 =D6=E7}X=BC=A2=C5o?=DD=F1?t=CA=E3SPK
> > >#=3D=F5=F9=C3?=C1=B4=C60=CF=DA)J?,=DB=A4j=C3=C4?V=B6j?=D5;Yi$^?W=E4a=
=D1=D5I?o=B9=F1=B7\=A2?=DC=F3%=B0k=D4=AA=A4 "]=C0=EBS=B6=CF=B0=BB
> > >
> > >That's as far as I get the with the Linux version of the curation
> tool.
> Is
> > there
> > >a relationship between the messages I get when I type "go.sh" and th=
e
> > >crazy output when I SUBMIT REQUEST the control bundle?
> > >
> >
> > This crazy output is what a binary file looks like in the browser
> window.
> > It isn't related to the font error messages.  Netscape on Linux and
> Unix
> > often downloads a binary file to the browser window like this.  I'm
> not
> sure
> > why Nescape does this by default, but it is usually the source of som=
e
> > confusion.  What you should do is wait for the file to finish
> downloading
> > and then click on "Save Page As" in the File menu to save the file.=20
> Save
> > the file to the proper subdirectory (i.e.
> > /home/lxm/ct100_usrlnx/data/control-bundle-downloaded) and then go
> back to
> > the curation tool to continue.  Even though the binary file is
> displayed
> in
> > the browser window like that, it still should save ok.  Note that you
> may
> > have to create the control-bundle-downloaded subdirectory yourself.
> >
> > I hope this helps out.
> >
> >
> > Lonny
> >
> >
> >
> > _______________________________________________
> > Genex-dev mailing list
> > Gen...@li...
> > http://lists.sourceforge.net/lists/listinfo/genex-dev
> >
>=20
>=20
>=20
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
>=20

Re: [GeneX-dev] Linux version of curation tool

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

Hi ALl,

OK - I added that to the /etc/mime.types adn in fact Jiaye wins a Kewpie
doll as it does force a download dialog, and does download the file, but th=
e
Curation Tool does not recognize it as such - unix unzip processes it
correctly:
42 % unzip control-bundle.xar
Archive:  control-bundle.xar
  inflating: META-INF/MANIFEST.MF
  inflating: control-bundle/control-bundle.xml
  inflating: control-bundle/control-bundle_ALS_01.ext
  inflating: control-bundle/control-bundle_CSF_01.ext
  inflating: control-bundle/control-bundle_USF_01.ext

but the curation tool cannot read it via the 'Read Control Files' button,
failing with:

40 % org.xml.sax.SAXParseException: The markup in the document preceding th=
e
root element must be well-formed.
        at java.lang.Throwable.<init>(Throwable.java:96)
        at java.lang.Exception.<init>(Exception.java:44)
        at org.xml.sax.SAXException.<init>(SAXException.java:45)
        at org.xml.sax.SAXParseException.<init>(SAXParseException.java:56)
        at
org.apache.xerces.framework.XMLParser.reportError(XMLParser.java:1016)
        at
org.apache.xerces.framework.XMLDocumentScanner.reportFatalXMLError(XMLDocum=
entScanner.java:625)
        at
org.apache.xerces.framework.XMLDocumentScanner$XMLDeclDispatcher.dispatch(X=
MLDocumentScanner.java:804)
        at
org.apache.xerces.framework.XMLDocumentScanner.parseSome(XMLDocumentScanner=
=2Ejava:380)
        at org.apache.xerces.framework.XMLParser.parse(XMLParser.java:908)
        at
org.ncgr.genex.model.XMLToDataManager.parseFile(XMLToDataManager.java:54)
        at
org.ncgr.genex.curator.NewExperimentSet.readControlFilesEvent(NewExperiment=
Set.java:180)
        at
org.ncgr.genex.curator.NewExperimentSet.actionPerformed(NewExperimentSet.ja=
va:80)
        at
javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:14
50)
        at
javax.swing.AbstractButton$ForwardActionEvents.actionPerformed(AbstractButt=
on.java:1504)
        at
javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:=
384)
        at
javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:256)
        at
javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListene=
r.java:216)
        at
java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:236)
        at java.awt.Component.processMouseEvent(Component.java:3753)
        at java.awt.Component.processEvent(Component.java(Compiled Code))
        at java.awt.Container.processEvent(Container.java(Compiled Code))
        at java.awt.Component.dispatchEventImpl(Component.java(Compiled
Code))
        at java.awt.Container.dispatchEventImpl(Container.java(Compiled
Code))
        at java.awt.Component.dispatchEvent(Component.java(Compiled Code))
        at
java.awt.LightweightDispatcher.retargetMouseEvent(Container.java(Compiled
Code))
        at
java.awt.LightweightDispatcher.processMouseEvent(Container.java(Compiled
Code))
        at java.awt.LightweightDispatcher.dispatchEvent(Container.java:2139=
)
        at java.awt.Window.dispatchEventImpl(Window.java(Compiled Code))
          at java.awt.Window.dispatchEventImpl(Window.java(Compiled Code))
        at java.awt.Component.dispatchEvent(Component.java(Compiled Code))
        at java.awt.EventQueue.dispatchEvent(EventQueue.java(Compiled Code)=
)
        at
java.awt.EventDispatchThread.pumpOneEvent(EventDispatchThread.java(Compiled
Code))
        at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:99)
        at java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

implying...?


On Mon, 26 Mar 2001, Jiaye Zhou wrote:

> Seems the webserver is not feeding it to the user response session correc=
tly,=20
> and try to send the file as type text/plain type. Take a look at the mine=
=20
> setting on the server side, should be in /etc/mime.types ( and this is wh=
ere=20
> apache looks) or httpd.conf. Try setting it to application/curationtool.=
=20
> (should be able to get a save option). I don't have access to genex, so c=
an't=20
> look myself.
>=20
> Jiaye =20
>=20
> Quoting Todd Peterson <tf...@nc...>:
>=20
> > Lonny and web guys
> >=20
> > I tried saving screen gibberish with Netscape 4.75 and 4.51 and get an
> > exception in the Curation Tool when reading the resulting control-bundl=
e
> > .xar file. It seems that Netscape saves the control bundle incorrectly.
> >=20
> > A good control-bundle (using Explorer) is 48,697 bytes for all species.
> > Saved with Netscape, the file is 48,875 bytes. Messed with
> > preferences/applications and MIME types etc. until I was blue in the
> > face.
> > Netscape would not recognize the control bundle as a file to save to
> > disk.
> >=20
> > Web guys, this used to work. What happened?
> >=20
> > Todd
> >=20
> > ----- Original Message -----
> > From: "Lonny Montoya" <lon...@st...>
> > To: <and...@ah...>
> > Cc: <gen...@nc...>; <gen...@li...>
> > Sent: Monday, March 26, 2001 1:59 PM
> > Subject: [GeneX-dev] Linux version of curation tool
> >=20
> >=20
> > > Hi Erik,
> > >
> > > Here is what I think is going on with this:
> > >
> > > >---------- Forwarded message ----------
> > > >Date: Mon, 26 Mar 2001 08:47:36 -0700
> > > >From: Erik Andries <and...@ah...>
> > > >To: Lonny Montoya <lx...@nc...>
> > > >Subject: Re: Linux version of GeneX
> > > >
> > > >Lonnie Montoya,
> > > >
> > > >I download the latest version of the Linux Curation tool and
> > > >I got the following errors.  See the attachment for the
> > > >session re-enactment.
> > > >
> > > >Erik Andries
> > > >
> > > >
> > > >These are the following messages when I type "go.sh"
> > > >
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >Font specified in font.properties not found
> > > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > > >
> > >
> > > These messages are because the jvm can't find a font it is looking
> > for.
> > It
> > > is possible that this was caused by using a copy of the curation tool
> > > created with another JDK besides Sun's.  This shouldn't present a
> > problem
> > in
> > > the operation of the curation tool, however, it should just use the
> > default
> > > font instead.  The fact that you can read the buttons and labels in
> > the
> > tool
> > > suggest that it is using the default font and these messages can be
> > ignored
> > > as they are not causing a problem.  You can test whether this is the
> > problem
> > > by downloading Version 1.0 of the Curation Tool at:
> > >
> > > http://genex.ncgr.org/genex/download/curation_tool/linux/
> > >
> > > This shouldn't happen with this version as it was created with the Su=
n
> > JDK.
> > > If you are still getting these messages with Version 1.0, there may b=
e
> > > something else going on.  Let me know what the result is when you try
> > it.
> > >
> > > >
> > > >Then the main window pops.  I hit the CREATE NEW EXPERIMENT SET icon
> > and
> > I
> > > enter new experiment set window.
> > > >I hit the READ CONTROL FILES icon and enter the window where I enter
> > my
> > > login name and password.
> > > >Suppose I do the test c=B7=B3ase (where I highlight all the
> > > >species for my control bundle).
> > > >I hit the SUBMIT REQUEST icon and then I get
> > > >
> > > >for a few seconds...
> > > >
> > > >  "Curation Tool Download Generation Status Y
> > > >  our Curation Tool download bundle is now being created.
> > > >  Current run time is 0 seconds.
> > > >  Output of the xml-write program:"
> > > >
> > > >and then...
> > > >
> > > >s=C1?(=E5Xt?=CB?K?P=AE=F8A??=E5t=A6av=D9=FEA~ sC=ACaCI_}=B8WY=C6=D7;=
=DD?=B5=BB=FEC=E0=A1=ED=FAf5=D3=BB=BFM=DC
> > > >=1F<=08=A4f=06=11=F5]u=C2=13=B5=AFa=CB=C1=A7=E2,=DE=DB=E7&V=EB=ABks2=
5=D4=C5*"=D9=A7=B2=15s"..1=F7=03=BF=DA:
> > 3<SS=16=11=F5=E0,=D0=14=D02..=CC?E3.=F5=D4=B5=C9
> > > i.=C7" U=12T=14d=F0 =EC=C5=F3r=17=D2Y=B6}=B1=D4.=BC7(=EB
> > > >=C5XvR=1F=04=8F mH=BAW"y=AF=F50=F6Y=AB
> > > >=DA=81:,tq3=9D~=EF=12.R&=EF:=B3"=A6?^=A7W[#=19Y"{=B0=1A=DBV=D0_<=19
> > > "=AF(N=B9=CE=DF=EC2,=EA\3"=07Pkn=F0v??UL)?8?^=B6a%f)3)=ED1Y[*-=C3=A4|=
x)+
> > > =A2=FF=FE=AEU'F=A4=E5xN.-=E3[+=B5J=FDYbo\OO=C0=E4C<=E7U?>0=F1\=EA=AC=
=B1??=D5\?HI=F3ZW=C8J.
> > > >=EA=C1l=C2=D8=AE2P=E4=DA=E6=BA=C8r?=EB=B3-;<h?=DB=EA6=E8d=A5??=E7=CA=
=AD??=B5iw?=DAf=C8=C5=B6=AB2=BE=A8&0=01=E9k =F1
> > b=13=07=DD=1E-Q,=DC=1Bg=CE=DBZ
> > =DF=06=B0=08
> > > '=C7.i=14 /J=3D=3D-"`=C1=1D=F0=D5L=A1=12j9=E39=F8_4g~6sJ=EEn2=C8=B7P=
=F4!=DCb+5?!>?
> > > >=CAh~=10?&=D3=15A=ECC=06"f<=19'm"3=17fZP+=C1e=A9(=E2 Y=14=CCzI#=9D(;=
=B7=F0L=E5=16?,so=A8=BA)=ADEO=B4=C4Ui=B1 Xl
> > > >=CBJ_=ABsP
> > > >=8D=18=16qtkL[wl=1B'
> > > =A1=07=EAT=13=E3X=BD=10=F7,?dV=C4=B7P@b=CA<
> > p=3D^=D7=A7=B8=AFV=F5^=D2=0FS.=B8Q=B4=AC=B7A5-=D0.=10=F6=CC=C97.7[=AA=
=E0y=F2=D3=04j=19Y't=BDcd=8DS=C1<qB=EC=F2
> > > =19=12d=A1=DA-=05=8F=AD@=04=A4!=F4*
> > > >T=12P*=A5=E5=05Y=B3v=08$=19=B7-=D3=C8=B8&H$=D0X=C21^i=1DF=B274?H=B0=
=F9=08"=01)C=07
> > > >=B6=19=D4P=B0=ED-Q)=D9yT=BF=EB=DC=8Dj-f=DCF=8D"=C7-=02
> > > >=A5=C1"?=06%Y{=F2=1C=D2=E5-=06D=1A-=13q=EC=0E
> > > ,=DF~3=F5
> > =DEX=C2-=1BlW=E1>~=81=C1=04=F5=FD>@"=ED=DA=066=15Q?=1E=F0$=E8=E1=C0=BB=
=90=AA=B6=DA.d?u=D2=C1O:=FBP>=90=E6=ED=D0=1Bf<d-A=B6C=AF=DC=C8^=C3-=B8=E8~=
=B2=E0
> > > e=E1C<T?>IT=E4x=D2:=D6=06=F7=19Q>r=D1a,=A8Q=CAG=FAAQxt=11=B2}s=19=B3=
=DF6=B6=13=19=CC=1BI=B5=DA=E2=10#Y=CA&^LK=D8=B10=B5=05=0E=A5g>=C7BU
> > > ?=BF\=C3=D7xF"=BB=F6Q=F7=187=A6=EE=81=E2<o=19=B2^=18
> > >
> > >=A3P=BD=1A=BA/Tb=E8T=A9=1C?~wU"=AE?=AB?=02=F2=CA2=B6?O=F2"0s=E7_=15=C8=
=B6=04=DCntB`=D7F=14@=BFZ=FD=901=D2=A7=3D=08:=E0co=04dk=AB=02N=AE=DE=11?=BB=
=1A
> > > =81=E3=03=FB=A8=02I=B6F3=C8r;=FC=02=16=C3=9D1pP=E4n3 >d=A4=E3=17=D8=
=0E=D6U".=AB=B5=CE68T=FBpI=DAzV[=F8"E=08|=FA=8F=B56B9f=01=BF=A3q
> > > >=1B,b=14=8D=D0=ADhsa4(bGx=D0V=A1=9D8x=D6=AA=CDcL=A9R=0E=E7x=DC=1EB=
=01;Q=A9=A8j=DFN=F0,=3D=B2J w
> > =E7B=A3=A6Wh=C9s%L`=DB=C8=01-=17=C6?fg=04/`=11R
> > > >=E0=F0W.=B7E=F3P"=A8=F6=04=AC=ACkUF=90=AA5=D9,UoV=19=BB=EC=ECZ=03T1(=
=B1=B3=1F=CEZ\-=B2=BFi=CD
> > > =BD=F1i=CE2=B6=D72=B1G=B3=D5=19=E4=1CN=CBH=F2=E8=EA=A1(=E4H.=178=C0=
=1E=E2g=A5=D4=B1;`=C6=DB
> > >Dy=F9_=BF=BC=BD=C1x=F9=EC=FB=FF=ED=D3=F3_=DEf=8F/=BC=FF=D7>=D5=BF=BD=
=FFC0=E7=FB=FF/
> > >
> > 2=1E>>=DD=F8RY=D2Y=DAY=D6Y=DEYqy=FC=F8,5=F5)=FD=A9=FDi=FD=E9=FD9k=F2=F2=
?=DB=F3=D3O-=DF~=7F=F9=E6=AB=CB=CB=E5?_C,=FC=CA=C7=7F=C9=FF=1FY=FF=F66{|)>=
=FF=F1=C6=F2=1F=F9=EF
> > > |=E6=FF/1>=FC=EE=11o
> > >
> > >=F7-=0F=0F=0Fx'=FAt=F9=F0=FBG4)=EF/=1F=BE~D?S=DF=0F=E8F=DF=D7u=BC=05=
=F47=EF}Y=D5=A5?x?a=B0=CCn"^?k`V=F2TY@r=B0?y=B9K=D4L=D0=E0t=FC;=E4=F3=A5?p:
> > > *q?!=DB=C6?<%=3D!wo+?%5=D4v?=C8=F8*=FD?0w+=F6>D?=D2)>=C9=B9=F6=BDoMa7=
=CE#{=E2?? =C8 =D6=E7}X=BC=A2=C5o?=DD=F1?t=CA=E3SPK
> > > >#=3D=F5=F9=C3?=C1=B4=C60=CF=DA)J?,=DB=A4j=C3=C4?V=B6j?=D5;Yi$^?W=E4a=
=D1=D5I?o=B9=F1=B7\=A2?=DC=F3%=B0k=D4=AA=A4 "]=C0=EBS=B6=CF=B0=BB
> > > >
> > > >That's as far as I get the with the Linux version of the curation
> > tool.
> > Is
> > > there
> > > >a relationship between the messages I get when I type "go.sh" and th=
e
> > > >crazy output when I SUBMIT REQUEST the control bundle?
> > > >
> > >
> > > This crazy output is what a binary file looks like in the browser
> > window.
> > > It isn't related to the font error messages.  Netscape on Linux and
> > Unix
> > > often downloads a binary file to the browser window like this.  I'm
> > not
> > sure
> > > why Nescape does this by default, but it is usually the source of som=
e
> > > confusion.  What you should do is wait for the file to finish
> > downloading
> > > and then click on "Save Page As" in the File menu to save the file.=
=20
> > Save
> > > the file to the proper subdirectory (i.e.
> > > /home/lxm/ct100_usrlnx/data/control-bundle-downloaded) and then go
> > back to
> > > the curation tool to continue.  Even though the binary file is
> > displayed
> > in
> > > the browser window like that, it still should save ok.  Note that you
> > may
> > > have to create the control-bundle-downloaded subdirectory yourself.
> > >
> > > I hope this helps out.
> > >
> > >
> > > Lonny
> > >
> > >
> > >
> > > _______________________________________________
> > > Genex-dev mailing list
> > > Gen...@li...
> > > http://lists.sourceforge.net/lists/listinfo/genex-dev
> > >
> >=20
> >=20
> >=20
> > _______________________________________________
> > Genex-dev mailing list
> > Gen...@li...
> > http://lists.sourceforge.net/lists/listinfo/genex-dev
> >=20
>=20
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
>=20

Re: [GeneX-dev] Linux version of curation tool

[Jiaye Z. <ze...@in...>]

Seems the webserver is not feeding it to the user response session correc=
tly,=20
and try to send the file as type text/plain type. Take a look at the mine=
=20
setting on the server side, should be in /etc/mime.types ( and this is wh=
ere=20
apache looks) or httpd.conf. Try setting it to application/curationtool.=20
(should be able to get a save option). I don't have access to genex, so c=
an't=20
look myself.

Jiaye =20

Quoting Todd Peterson <tf...@nc...>:

> Lonny and web guys
>=20
> I tried saving screen gibberish with Netscape 4.75 and 4.51 and get an
> exception in the Curation Tool when reading the resulting control-bundl=
e
> .xar file. It seems that Netscape saves the control bundle incorrectly.
>=20
> A good control-bundle (using Explorer) is 48,697 bytes for all species.
> Saved with Netscape, the file is 48,875 bytes. Messed with
> preferences/applications and MIME types etc. until I was blue in the
> face.
> Netscape would not recognize the control bundle as a file to save to
> disk.
>=20
> Web guys, this used to work. What happened?
>=20
> Todd
>=20
> ----- Original Message -----
> From: "Lonny Montoya" <lon...@st...>
> To: <and...@ah...>
> Cc: <gen...@nc...>; <gen...@li...>
> Sent: Monday, March 26, 2001 1:59 PM
> Subject: [GeneX-dev] Linux version of curation tool
>=20
>=20
> > Hi Erik,
> >
> > Here is what I think is going on with this:
> >
> > >---------- Forwarded message ----------
> > >Date: Mon, 26 Mar 2001 08:47:36 -0700
> > >From: Erik Andries <and...@ah...>
> > >To: Lonny Montoya <lx...@nc...>
> > >Subject: Re: Linux version of GeneX
> > >
> > >Lonnie Montoya,
> > >
> > >I download the latest version of the Linux Curation tool and
> > >I got the following errors.  See the attachment for the
> > >session re-enactment.
> > >
> > >Erik Andries
> > >
> > >
> > >These are the following messages when I type "go.sh"
> > >
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >Font specified in font.properties not found
> > [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> > >
> >
> > These messages are because the jvm can't find a font it is looking
> for.
> It
> > is possible that this was caused by using a copy of the curation tool
> > created with another JDK besides Sun's.  This shouldn't present a
> problem
> in
> > the operation of the curation tool, however, it should just use the
> default
> > font instead.  The fact that you can read the buttons and labels in
> the
> tool
> > suggest that it is using the default font and these messages can be
> ignored
> > as they are not causing a problem.  You can test whether this is the
> problem
> > by downloading Version 1.0 of the Curation Tool at:
> >
> > http://genex.ncgr.org/genex/download/curation_tool/linux/
> >
> > This shouldn't happen with this version as it was created with the Su=
n
> JDK.
> > If you are still getting these messages with Version 1.0, there may b=
e
> > something else going on.  Let me know what the result is when you try
> it.
> >
> > >
> > >Then the main window pops.  I hit the CREATE NEW EXPERIMENT SET icon
> and
> I
> > enter new experiment set window.
> > >I hit the READ CONTROL FILES icon and enter the window where I enter
> my
> > login name and password.
> > >Suppose I do the test c=B7=B3ase (where I highlight all the
> > >species for my control bundle).
> > >I hit the SUBMIT REQUEST icon and then I get
> > >
> > >for a few seconds...
> > >
> > >  "Curation Tool Download Generation Status Y
> > >  our Curation Tool download bundle is now being created.
> > >  Current run time is 0 seconds.
> > >  Output of the xml-write program:"
> > >
> > >and then...
> > >
> > >s=C1?(=E5Xt?=CB?K?P=AE=F8A??=E5t=A6av=D9=FEA~ sC=ACaCI_}=B8WY=C6=D7;=
=DD?=B5=BB=FEC=E0=A1=ED=FAf5=D3=BB=BFM=DC
> > >=1F<=08=A4f=06=11=F5]u=C2=13=B5=AFa=CB=C1=A7=E2,=DE=DB=E7&V=EB=ABks2=
5=D4=C5*"=D9=A7=B2=15s"..1=F7=03=BF=DA:
> 3<SS=16=11=F5=E0,=D0=14=D02..=CC?E3.=F5=D4=B5=C9
> > i.=C7" U=12T=14d=F0 =EC=C5=F3r=17=D2Y=B6}=B1=D4.=BC7(=EB
> > >=C5XvR=1F=04=8F mH=BAW"y=AF=F50=F6Y=AB
> > >=DA=81:,tq3=9D~=EF=12.R&=EF:=B3"=A6?^=A7W[#=19Y"{=B0=1A=DBV=D0_<=19
> > "=AF(N=B9=CE=DF=EC2,=EA\3"=07Pkn=F0v??UL)?8?^=B6a%f)3)=ED1Y[*-=C3=A4|=
x)+
> > =A2=FF=FE=AEU'F=A4=E5xN.-=E3[+=B5J=FDYbo\OO=C0=E4C<=E7U?>0=F1\=EA=AC=B1=
??=D5\?HI=F3ZW=C8J.
> > >=EA=C1l=C2=D8=AE2P=E4=DA=E6=BA=C8r?=EB=B3-;<h?=DB=EA6=E8d=A5??=E7=CA=
=AD??=B5iw?=DAf=C8=C5=B6=AB2=BE=A8&0=01=E9k =F1
> b=13=07=DD=1E-Q,=DC=1Bg=CE=DBZ
> =DF=06=B0=08
> > '=C7.i=14 /J=3D=3D-"`=C1=1D=F0=D5L=A1=12j9=E39=F8_4g~6sJ=EEn2=C8=B7P=F4=
!=DCb+5?!>?
> > >=CAh~=10?&=D3=15A=ECC=06"f<=19'm"3=17fZP+=C1e=A9(=E2 Y=14=CCzI#=9D(;=
=B7=F0L=E5=16?,so=A8=BA)=ADEO=B4=C4Ui=B1 Xl
> > >=CBJ_=ABsP
> > >=8D=18=16qtkL[wl=1B'
> > =A1=07=EAT=13=E3X=BD=10=F7,?dV=C4=B7P@b=CA<
> p=3D^=D7=A7=B8=AFV=F5^=D2=0FS.=B8Q=B4=AC=B7A5-=D0.=10=F6=CC=C97.7[=AA=E0=
y=F2=D3=04j=19Y't=BDcd=8DS=C1<qB=EC=F2
> > =19=12d=A1=DA-=05=8F=AD@=04=A4!=F4*
> > >T=12P*=A5=E5=05Y=B3v=08$=19=B7-=D3=C8=B8&H$=D0X=C21^i=1DF=B274?H=B0=F9=
=08"=01)C=07
> > >=B6=19=D4P=B0=ED-Q)=D9yT=BF=EB=DC=8Dj-f=DCF=8D"=C7-=02
> > >=A5=C1"?=06%Y{=F2=1C=D2=E5-=06D=1A-=13q=EC=0E
> > ,=DF~3=F5
> =DEX=C2-=1BlW=E1>~=81=C1=04=F5=FD>@"=ED=DA=066=15Q?=1E=F0$=E8=E1=C0=BB=90=
=AA=B6=DA.d?u=D2=C1O:=FBP>=90=E6=ED=D0=1Bf<d-A=B6C=AF=DC=C8^=C3-=B8=E8~=B2=
=E0
> > e=E1C<T?>IT=E4x=D2:=D6=06=F7=19Q>r=D1a,=A8Q=CAG=FAAQxt=11=B2}s=19=B3=DF=
6=B6=13=19=CC=1BI=B5=DA=E2=10#Y=CA&^LK=D8=B10=B5=05=0E=A5g>=C7BU
> > ?=BF\=C3=D7xF"=BB=F6Q=F7=187=A6=EE=81=E2<o=19=B2^=18
> >
> >=A3P=BD=1A=BA/Tb=E8T=A9=1C?~wU"=AE?=AB?=02=F2=CA2=B6?O=F2"0s=E7_=15=C8=
=B6=04=DCntB`=D7F=14@=BFZ=FD=901=D2=A7=3D=08:=E0co=04dk=AB=02N=AE=DE=11?=BB=
=1A
> > =81=E3=03=FB=A8=02I=B6F3=C8r;=FC=02=16=C3=9D1pP=E4n3 >d=A4=E3=17=D8=0E=
=D6U".=AB=B5=CE68T=FBpI=DAzV[=F8"E=08|=FA=8F=B56B9f=01=BF=A3q
> > >=1B,b=14=8D=D0=ADhsa4(bGx=D0V=A1=9D8x=D6=AA=CDcL=A9R=0E=E7x=DC=1EB=01=
;Q=A9=A8j=DFN=F0,=3D=B2J w
> =E7B=A3=A6Wh=C9s%L`=DB=C8=01-=17=C6?fg=04/`=11R
> > >=E0=F0W.=B7E=F3P"=A8=F6=04=AC=ACkUF=90=AA5=D9,UoV=19=BB=EC=ECZ=03T1(=
=B1=B3=1F=CEZ\-=B2=BFi=CD
> > =BD=F1i=CE2=B6=D72=B1G=B3=D5=19=E4=1CN=CBH=F2=E8=EA=A1(=E4H.=178=C0=1E=
=E2g=A5=D4=B1;`=C6=DB
> >Dy=F9_=BF=BC=BD=C1x=F9=EC=FB=FF=ED=D3=F3_=DEf=8F/=BC=FF=D7>=D5=BF=BD=FF=
C0=E7=FB=FF/
> >
> 2=1E>>=DD=F8RY=D2Y=DAY=D6Y=DEYqy=FC=F8,5=F5)=FD=A9=FDi=FD=E9=FD9k=F2=F2=
?=DB=F3=D3O-=DF~=7F=F9=E6=AB=CB=CB=E5?_C,=FC=CA=C7=7F=C9=FF=1FY=FF=F66{|)=
>=FF=F1=C6=F2=1F=F9=EF
> > |=E6=FF/1>=FC=EE=11o
> >
> >=F7-=0F=0F=0Fx'=FAt=F9=F0=FBG4)=EF/=1F=BE~D?S=DF=0F=E8F=DF=D7u=BC=05=F4=
7=EF}Y=D5=A5?x?a=B0=CCn"^?k`V=F2TY@r=B0?y=B9K=D4L=D0=E0t=FC;=E4=F3=A5?p:
> > *q?!=DB=C6?<%=3D!wo+?%5=D4v?=C8=F8*=FD?0w+=F6>D?=D2)>=C9=B9=F6=BDoMa7=
=CE#{=E2?? =C8 =D6=E7}X=BC=A2=C5o?=DD=F1?t=CA=E3SPK
> > >#=3D=F5=F9=C3?=C1=B4=C60=CF=DA)J?,=DB=A4j=C3=C4?V=B6j?=D5;Yi$^?W=E4a=
=D1=D5I?o=B9=F1=B7\=A2?=DC=F3%=B0k=D4=AA=A4 "]=C0=EBS=B6=CF=B0=BB
> > >
> > >That's as far as I get the with the Linux version of the curation
> tool.
> Is
> > there
> > >a relationship between the messages I get when I type "go.sh" and th=
e
> > >crazy output when I SUBMIT REQUEST the control bundle?
> > >
> >
> > This crazy output is what a binary file looks like in the browser
> window.
> > It isn't related to the font error messages.  Netscape on Linux and
> Unix
> > often downloads a binary file to the browser window like this.  I'm
> not
> sure
> > why Nescape does this by default, but it is usually the source of som=
e
> > confusion.  What you should do is wait for the file to finish
> downloading
> > and then click on "Save Page As" in the File menu to save the file.=20
> Save
> > the file to the proper subdirectory (i.e.
> > /home/lxm/ct100_usrlnx/data/control-bundle-downloaded) and then go
> back to
> > the curation tool to continue.  Even though the binary file is
> displayed
> in
> > the browser window like that, it still should save ok.  Note that you
> may
> > have to create the control-bundle-downloaded subdirectory yourself.
> >
> > I hope this helps out.
> >
> >
> > Lonny
> >
> >
> >
> > _______________________________________________
> > Genex-dev mailing list
> > Gen...@li...
> > http://lists.sourceforge.net/lists/listinfo/genex-dev
> >
>=20
>=20
>=20
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
>=20

[GeneX-dev] All users on genex now part of 'genex' group

[Harry M. <man...@ho...>]

Only of concern to the NCGR & associated users:

All youse guys are now by default part of the 'genex' group so when you write CVS info back into the tree, others don't get blocked by bad permissions.

Your original groups are available, but you'll have to set them explicitly if you want them applied to anything.

This should not be a problem for anyone, but if so, you know who to complain to.
-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

[GeneX-dev] Re: Linux version of curation tool

[Todd P. <tf...@nc...>]

Erik,

I have attached a good control bundle. This is a binary file which is really
just a Java Jar file.

Todd Peterson
GeneX Developer
NCGR

----- Original Message -----
From: "Lonny Montoya" <lon...@st...>
To: <and...@ah...>
Cc: <gen...@nc...>; <gen...@li...>
Sent: Monday, March 26, 2001 1:59 PM
Subject: Linux version of curation tool


> Hi Erik,
>
etc., etc.

Re: [GeneX-dev] Linux version of curation tool

[Todd P. <tf...@nc...>]

Lonny and web guys

I tried saving screen gibberish with Netscape 4.75 and 4.51 and get an
exception in the Curation Tool when reading the resulting control-bundle
.xar file. It seems that Netscape saves the control bundle incorrectly.

A good control-bundle (using Explorer) is 48,697 bytes for all species.
Saved with Netscape, the file is 48,875 bytes. Messed with
preferences/applications and MIME types etc. until I was blue in the face.
Netscape would not recognize the control bundle as a file to save to disk.

Web guys, this used to work. What happened?

Todd

----- Original Message -----
From: "Lonny Montoya" <lon...@st...>
To: <and...@ah...>
Cc: <gen...@nc...>; <gen...@li...>
Sent: Monday, March 26, 2001 1:59 PM
Subject: [GeneX-dev] Linux version of curation tool


> Hi Erik,
>
> Here is what I think is going on with this:
>
> >---------- Forwarded message ----------
> >Date: Mon, 26 Mar 2001 08:47:36 -0700
> >From: Erik Andries <and...@ah...>
> >To: Lonny Montoya <lx...@nc...>
> >Subject: Re: Linux version of GeneX
> >
> >Lonnie Montoya,
> >
> >I download the latest version of the Linux Curation tool and
> >I got the following errors.  See the attachment for the
> >session re-enactment.
> >
> >Erik Andries
> >
> >
> >These are the following messages when I type "go.sh"
> >
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >Font specified in font.properties not found
> [--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
> >
>
> These messages are because the jvm can't find a font it is looking for.
It
> is possible that this was caused by using a copy of the curation tool
> created with another JDK besides Sun's.  This shouldn't present a probl=
em
in
> the operation of the curation tool, however, it should just use the
default
> font instead.  The fact that you can read the buttons and labels in the
tool
> suggest that it is using the default font and these messages can be
ignored
> as they are not causing a problem.  You can test whether this is the
problem
> by downloading Version 1.0 of the Curation Tool at:
>
> http://genex.ncgr.org/genex/download/curation_tool/linux/
>
> This shouldn't happen with this version as it was created with the Sun
JDK.
> If you are still getting these messages with Version 1.0, there may be
> something else going on.  Let me know what the result is when you try i=
t.
>
> >
> >Then the main window pops.  I hit the CREATE NEW EXPERIMENT SET icon a=
nd
I
> enter new experiment set window.
> >I hit the READ CONTROL FILES icon and enter the window where I enter m=
y
> login name and password.
> >Suppose I do the test c=B7=B3ase (where I highlight all the
> >species for my control bundle).
> >I hit the SUBMIT REQUEST icon and then I get
> >
> >for a few seconds...
> >
> >  "Curation Tool Download Generation Status Y
> >  our Curation Tool download bundle is now being created.
> >  Current run time is 0 seconds.
> >  Output of the xml-write program:"
> >
> >and then...
> >
> >s=C1?(=E5Xt?=CB?K?P=AE=F8A??=E5t=A6av=D9=FEA~ sC=ACaCI_}=B8WY=C6=D7;=DD=
?=B5=BB=FEC=E0=A1=ED=FAf5=D3=BB=BFM=DC
> >=1F<=08=A4f=06=11=F5]u=C2=13=B5=AFa=CB=C1=A7=E2,=DE=DB=E7&V=EB=ABks25=D4=
=C5*"=D9=A7=B2=15s"..1=F7=03=BF=DA:
3<SS=16=11=F5=E0,=D0=14=D02..=CC?E3.=F5=D4=B5=C9
> i.=C7" U=12T=14d=F0 =EC=C5=F3r=17=D2Y=B6}=B1=D4.=BC7(=EB
> >=C5XvR=1F=04=8F mH=BAW"y=AF=F50=F6Y=AB
> >=DA=81:,tq3=9D~=EF=12.R&=EF:=B3"=A6?^=A7W[#=19Y"{=B0=1A=DBV=D0_<=19
> "=AF(N=B9=CE=DF=EC2,=EA\3"=07Pkn=F0v??UL)?8?^=B6a%f)3)=ED1Y[*-=C3=A4|x)=
+
> =A2=FF=FE=AEU'F=A4=E5xN.-=E3[+=B5J=FDYbo\OO=C0=E4C<=E7U?>0=F1\=EA=AC=B1=
??=D5\?HI=F3ZW=C8J.
> >=EA=C1l=C2=D8=AE2P=E4=DA=E6=BA=C8r?=EB=B3-;<h?=DB=EA6=E8d=A5??=E7=CA=AD=
??=B5iw?=DAf=C8=C5=B6=AB2=BE=A8&0=01=E9k =F1 b=13=07=DD=1E-Q,=DC=1Bg=CE=DB=
Z
=DF=06=B0=08
> '=C7.i=14 /J=3D=3D-"`=C1=1D=F0=D5L=A1=12j9=E39=F8_4g~6sJ=EEn2=C8=B7P=F4=
!=DCb+5?!>?
> >=CAh~=10?&=D3=15A=ECC=06"f<=19'm"3=17fZP+=C1e=A9(=E2 Y=14=CCzI#=9D(;=B7=
=F0L=E5=16?,so=A8=BA)=ADEO=B4=C4Ui=B1 Xl
> >=CBJ_=ABsP
> >=8D=18=16qtkL[wl=1B'
> =A1=07=EAT=13=E3X=BD=10=F7,?dV=C4=B7P@b=CA<
p=3D^=D7=A7=B8=AFV=F5^=D2=0FS.=B8Q=B4=AC=B7A5-=D0.=10=F6=CC=C97.7[=AA=E0y=
=F2=D3=04j=19Y't=BDcd=8DS=C1<qB=EC=F2
> =19=12d=A1=DA-=05=8F=AD@=04=A4!=F4*
> >T=12P*=A5=E5=05Y=B3v=08$=19=B7-=D3=C8=B8&H$=D0X=C21^i=1DF=B274?H=B0=F9=
=08"=01)C=07
> >=B6=19=D4P=B0=ED-Q)=D9yT=BF=EB=DC=8Dj-f=DCF=8D"=C7-=02
> >=A5=C1"?=06%Y{=F2=1C=D2=E5-=06D=1A-=13q=EC=0E
> ,=DF~3=F5
=DEX=C2-=1BlW=E1>~=81=C1=04=F5=FD>@"=ED=DA=066=15Q?=1E=F0$=E8=E1=C0=BB=90=
=AA=B6=DA.d?u=D2=C1O:=FBP>=90=E6=ED=D0=1Bf<d-A=B6C=AF=DC=C8^=C3-=B8=E8~=B2=
=E0
> e=E1C<T?>IT=E4x=D2:=D6=06=F7=19Q>r=D1a,=A8Q=CAG=FAAQxt=11=B2}s=19=B3=DF=
6=B6=13=19=CC=1BI=B5=DA=E2=10#Y=CA&^LK=D8=B10=B5=05=0E=A5g>=C7BU
> ?=BF\=C3=D7xF"=BB=F6Q=F7=187=A6=EE=81=E2<o=19=B2^=18
> >=A3P=BD=1A=BA/Tb=E8T=A9=1C?~wU"=AE?=AB?=02=F2=CA2=B6?O=F2"0s=E7_=15=C8=
=B6=04=DCntB`=D7F=14@=BFZ=FD=901=D2=A7=3D=08:=E0co=04dk=AB=02N=AE=DE=11?=BB=
=1A
> =81=E3=03=FB=A8=02I=B6F3=C8r;=FC=02=16=C3=9D1pP=E4n3 >d=A4=E3=17=D8=0E=D6=
U".=AB=B5=CE68T=FBpI=DAzV[=F8"E=08|=FA=8F=B56B9f=01=BF=A3q
> >=1B,b=14=8D=D0=ADhsa4(bGx=D0V=A1=9D8x=D6=AA=CDcL=A9R=0E=E7x=DC=1EB=01;=
Q=A9=A8j=DFN=F0,=3D=B2J w
=E7B=A3=A6Wh=C9s%L`=DB=C8=01-=17=C6?fg=04/`=11R
> >=E0=F0W.=B7E=F3P"=A8=F6=04=AC=ACkUF=90=AA5=D9,UoV=19=BB=EC=ECZ=03T1(=B1=
=B3=1F=CEZ\-=B2=BFi=CD
> =BD=F1i=CE2=B6=D72=B1G=B3=D5=19=E4=1CN=CBH=F2=E8=EA=A1(=E4H.=178=C0=1E=E2=
g=A5=D4=B1;`=C6=DB
>Dy=F9_=BF=BC=BD=C1x=F9=EC=FB=FF=ED=D3=F3_=DEf=8F/=BC=FF=D7>=D5=BF=BD=FFC=
0=E7=FB=FF/
>
2=1E>>=DD=F8RY=D2Y=DAY=D6Y=DEYqy=FC=F8,5=F5)=FD=A9=FDi=FD=E9=FD9k=F2=F2?=DB=
=F3=D3O-=DF~=7F=F9=E6=AB=CB=CB=E5?_C,=FC=CA=C7=7F=C9=FF=1FY=FF=F66{|)>=FF=
=F1=C6=F2=1F=F9=EF
> |=E6=FF/1>=FC=EE=11o
>
>=F7-=0F=0F=0Fx'=FAt=F9=F0=FBG4)=EF/=1F=BE~D?S=DF=0F=E8F=DF=D7u=BC=05=F47=
=EF}Y=D5=A5?x?a=B0=CCn"^?k`V=F2TY@r=B0?y=B9K=D4L=D0=E0t=FC;=E4=F3=A5?p:
> *q?!=DB=C6?<%=3D!wo+?%5=D4v?=C8=F8*=FD?0w+=F6>D?=D2)>=C9=B9=F6=BDoMa7=CE=
#{=E2?? =C8 =D6=E7}X=BC=A2=C5o?=DD=F1?t=CA=E3SPK
> >#=3D=F5=F9=C3?=C1=B4=C60=CF=DA)J?,=DB=A4j=C3=C4?V=B6j?=D5;Yi$^?W=E4a=D1=
=D5I?o=B9=F1=B7\=A2?=DC=F3%=B0k=D4=AA=A4 "]=C0=EBS=B6=CF=B0=BB
> >
> >That's as far as I get the with the Linux version of the curation tool.
Is
> there
> >a relationship between the messages I get when I type "go.sh" and the
> >crazy output when I SUBMIT REQUEST the control bundle?
> >
>
> This crazy output is what a binary file looks like in the browser windo=
w.
> It isn't related to the font error messages.  Netscape on Linux and Uni=
x
> often downloads a binary file to the browser window like this.  I'm not
sure
> why Nescape does this by default, but it is usually the source of some
> confusion.  What you should do is wait for the file to finish downloadi=
ng
> and then click on "Save Page As" in the File menu to save the file.  Sa=
ve
> the file to the proper subdirectory (i.e.
> /home/lxm/ct100_usrlnx/data/control-bundle-downloaded) and then go back=
 to
> the curation tool to continue.  Even though the binary file is displaye=
d
in
> the browser window like that, it still should save ok.  Note that you m=
ay
> have to create the control-bundle-downloaded subdirectory yourself.
>
> I hope this helps out.
>
>
> Lonny
>
>
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
>

[GeneX-dev] Re: Linux version of curation tool

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

Hi Lonnie and Erik,

I concur with Lonnie.  You should be able to set your Netscape application
preferences to deal with this type by file extension if this behavior
bothers you (but that said, I tried to set it in my Netscape but while the
preference seemed to be set, it stil exhibited the same behavior).  Anyone
else know how to map this file type to a behavior under Netscape/Linux?

Is there some hidden trick to getting Netscape to actually pat attention to
user settings?

hjm

[GeneX-dev] Linux version of curation tool

[Lonny M. <lon...@st...>]

Hi Erik,

Here is what I think is going on with this:

>---------- Forwarded message ----------
>Date: Mon, 26 Mar 2001 08:47:36 -0700
>From: Erik Andries <and...@ah...>
>To: Lonny Montoya <lx...@nc...>
>Subject: Re: Linux version of GeneX
>
>Lonnie Montoya,
>
>I download the latest version of the Linux Curation tool and
>I got the following errors.  See the attachment for the
>session re-enactment.
>
>Erik Andries
>
>
>These are the following messages when I type "go.sh"
>
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>Font specified in font.properties not found
[--symbol-medium-r-normal--*-%d-*-*-p-*-adobe-fontspecific]
>

These messages are because the jvm can't find a font it is looking for.  =
It
is possible that this was caused by using a copy of the curation tool
created with another JDK besides Sun's.  This shouldn't present a problem=
 in
the operation of the curation tool, however, it should just use the defau=
lt
font instead.  The fact that you can read the buttons and labels in the t=
ool
suggest that it is using the default font and these messages can be ignor=
ed
as they are not causing a problem.  You can test whether this is the prob=
lem
by downloading Version 1.0 of the Curation Tool at:

http://genex.ncgr.org/genex/download/curation_tool/linux/

This shouldn't happen with this version as it was created with the Sun JD=
K.
If you are still getting these messages with Version 1.0, there may be
something else going on.  Let me know what the result is when you try it.

>
>Then the main window pops.  I hit the CREATE NEW EXPERIMENT SET icon and=
 I
enter new experiment set window.
>I hit the READ CONTROL FILES icon and enter the window where I enter my
login name and password.
>Suppose I do the test c=B7=B3ase (where I highlight all the
>species for my control bundle).
>I hit the SUBMIT REQUEST icon and then I get
>
>for a few seconds...
>
>  "Curation Tool Download Generation Status Y
>  our Curation Tool download bundle is now being created.
>  Current run time is 0 seconds.
>  Output of the xml-write program:"
>
>and then...
>
>s=C1?(=E5Xt?=CB?K?P=AE=F8A??=E5t=A6av=D9=FEA~ sC=ACaCI_}=B8WY=C6=D7;=DD?=
=B5=BB=FEC=E0=A1=ED=FAf5=D3=BB=BFM=DC
>=1F<=08=A4f=06=11=F5]u=C2=13=B5=AFa=CB=C1=A7=E2,=DE=DB=E7&V=EB=ABks25=D4=
=C5*"=D9=A7=B2=15s"..1=F7=03=BF=DA: 3<SS=16=11=F5=E0,=D0=14=D02..=CC?E3.=F5=
=D4=B5=C9
i.=C7" U=12T=14d=F0 =EC=C5=F3r=17=D2Y=B6}=B1=D4.=BC7(=EB
>=C5XvR=1F=04=8F mH=BAW"y=AF=F50=F6Y=AB
>=DA=81:,tq3=9D~=EF=12.R&=EF:=B3"=A6?^=A7W[#=19Y"{=B0=1A=DBV=D0_<=19
"=AF(N=B9=CE=DF=EC2,=EA\3"=07Pkn=F0v??UL)?8?^=B6a%f)3)=ED1Y[*-=C3=A4|x)+
=A2=FF=FE=AEU'F=A4=E5xN.-=E3[+=B5J=FDYbo\OO=C0=E4C<=E7U?>0=F1\=EA=AC=B1??=
=D5\?HI=F3ZW=C8J.
>=EA=C1l=C2=D8=AE2P=E4=DA=E6=BA=C8r?=EB=B3-;<h?=DB=EA6=E8d=A5??=E7=CA=AD?=
?=B5iw?=DAf=C8=C5=B6=AB2=BE=A8&0=01=E9k=0C=F1 b=13=07=DD=1E-Q,=DC=1Bg=CE=DB=
Z =DF=06=B0=08
'=C7.i=14 /J=3D=3D-"`=C1=1D=F0=D5L=A1=12j9=E39=F8_4g~6sJ=EEn2=C8=B7P=F4!=DC=
b+5?!>?
>=CAh~=10?&=D3=15A=ECC=06"f<=19'm"3=17fZP+=C1e=A9(=E2 Y=14=CCzI#=9D(;=B7=F0=
L=E5=16?,so=A8=BA)=ADEO=B4=C4Ui=B1 Xl
>=CBJ_=ABsP
>=8D=18=16qtkL[wl=1B'
=A1=07=EAT=13=E3X=BD=10=F7,?dV=C4=B7P@b=CA<=0Bp=3D^=D7=A7=B8=AFV=F5^=D2=0F=
S.=B8Q=B4=AC=B7A5-=D0.=10=F6=CC=C97.7[=AA=E0y=F2=D3=04j=19Y't=BDcd=8DS=C1=
<qB=EC=F2
=19=12d=A1=DA-=05=8F=AD@=04=A4!=F4*
>T=12P*=A5=E5=05Y=B3v=08$=19=B7-=D3=C8=B8&H$=D0X=C21^i=1DF=B274?H=B0=F9=08=
"=01)C=07
>=B6=19=D4P=B0=ED-Q)=D9yT=BF=EB=DC=8Dj-f=DCF=8D"=C7-=02
>=A5=C1"?=06%Y{=F2=1C=D2=E5-=06D=1A-=13q=EC=0E
,=DF~3=F5=0C=DEX=C2-=1BlW=E1>~=81=C1=04=F5=FD>@"=ED=DA=066=15Q?=1E=F0$=E8=
=E1=C0=BB=90=AA=B6=DA.d?u=D2=C1O:=FBP>=90=E6=ED=D0=1Bf<d-A=B6C=AF=DC=C8^=C3=
-=B8=E8~=B2=E0
e=E1C<T?>IT=E4x=D2:=D6=06=F7=19Q>r=D1a,=A8Q=CAG=FAAQxt=11=B2}s=19=B3=DF6=B6=
=13=19=CC=1BI=B5=DA=E2=10#Y=CA&^LK=D8=B10=B5=05=0E=A5g>=C7BU
?=BF\=C3=D7xF"=BB=F6Q=F7=187=A6=EE=81=E2<o=19=B2^=18
>=A3P=BD=1A=BA/Tb=E8T=A9=1C?~wU"=AE?=AB?=02=F2=CA2=B6?O=F2"0s=E7_=15=C8=B6=
=04=DCntB`=D7F=14@=BFZ=FD=901=D2=A7=3D=08:=E0co=04dk=AB=02N=AE=DE=11?=BB=1A
=81=E3=03=FB=A8=02I=B6F3=C8r;=FC=02=16=C3=9D1pP=E4n3=0C>d=A4=E3=17=D8=0E=D6=
U".=AB=B5=CE68T=FBpI=DAzV[=F8"E=08|=FA=8F=B56B9f=01=BF=A3q
>=1B,b=14=8D=D0=ADhsa4(bGx=D0V=A1=9D8x=D6=AA=CDcL=A9R=0E=E7x=DC=1EB=01;Q=A9=
=A8j=DFN=F0,=3D=B2J w =E7B=A3=A6Wh=C9s%L`=DB=C8=01-=17=C6?fg=04/`=11R
>=E0=F0W.=B7E=F3P"=A8=F6=04=AC=ACkUF=90=AA5=D9,UoV=19=BB=EC=ECZ=03T1(=B1=B3=
=1F=CEZ\-=B2=BFi=CD
=BD=F1i=CE2=B6=D72=B1G=B3=D5=19=E4=1CN=CBH=F2=E8=EA=A1(=E4H.=178=C0=1E=E2=
g=A5=D4=B1;`=C6=DB=0C>Dy=F9_=BF=BC=BD=C1x=F9=EC=FB=FF=ED=D3=F3_=DEf=8F/=BC=
=FF=D7>=D5=BF=BD=FFC0=E7=FB=FF/
2=1E>>=DD=F8RY=D2Y=DAY=D6Y=DEYqy=FC=F8,5=F5)=FD=A9=FDi=FD=E9=FD9k=F2=F2?=DB=
=F3=D3O-=DF~=7F=F9=E6=AB=CB=CB=E5?_C,=FC=CA=C7=7F=C9=FF=1FY=FF=F66{|)>=FF=
=F1=C6=F2=1F=F9=EF
|=E6=FF/1>=FC=EE=11o
>=F7-=0F=0F=0Fx'=FAt=F9=F0=FBG4)=EF/=1F=BE~D?S=DF=0F=E8F=DF=D7u=BC=05=F47=
=EF}Y=D5=A5?x?a=B0=CCn"^?k`V=F2TY@r=B0?y=B9K=D4L=D0=E0t=FC;=E4=F3=A5?p:
*q?!=DB=C6?<%=3D!wo+?%5=D4v?=C8=F8*=FD?0w+=F6>D?=D2)>=C9=B9=F6=BDoMa7=CE#=
{=E2?? =C8 =D6=E7}X=BC=A2=C5o?=DD=F1?t=CA=E3SPK
>#=3D=F5=F9=C3?=C1=B4=C60=CF=DA)J?,=DB=A4j=C3=C4?V=B6j?=D5;Yi$^?W=E4a=D1=D5=
I?o=B9=F1=B7\=A2?=DC=F3%=B0k=D4=AA=A4 "]=C0=EBS=B6=CF=B0=BB
>
>That's as far as I get the with the Linux version of the curation tool. =
 Is
there
>a relationship between the messages I get when I type "go.sh" and the
>crazy output when I SUBMIT REQUEST the control bundle?
>

This crazy output is what a binary file looks like in the browser window.
It isn't related to the font error messages.  Netscape on Linux and Unix
often downloads a binary file to the browser window like this.  I'm not s=
ure
why Nescape does this by default, but it is usually the source of some
confusion.  What you should do is wait for the file to finish downloading
and then click on "Save Page As" in the File menu to save the file.  Save
the file to the proper subdirectory (i.e.
/home/lxm/ct100_usrlnx/data/control-bundle-downloaded) and then go back t=
o
the curation tool to continue.  Even though the binary file is displayed =
in
the browser window like that, it still should save ok.  Note that you may
have to create the control-bundle-downloaded subdirectory yourself.

I hope this helps out.


Lonny

[GeneX-dev] Size of data in CyberT, etc

[Harry M. <man...@ho...>]

Hi Again, Erik,

just another data point - you should be able to run 1000 genes x 20 ratios (or 20 control & 20 experimental values) fine with the current settings - just did it on both my machine and genex without a
problem)  but let me know if you have problems.
-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

[GeneX-dev] (no subject)

[Jiaye Z. <ze...@in...>]

Hey Harry, 
sorry, left the ! out...here's the corrected version:

In httpd.conf (/etc/httpd/conf/httpd.conf maybe?)
replace the line: 
  CustomLog /var/log/httpd/access_log common
with:
  SetEnvIf Request_URI \.gif$ images 
  SetEnvIf Request_URI \.jpg$ images
  CustomLog /var/log/httpd/access_log common env!=images  #use !=
  #if you would like to keep track of requests for images
  CustomLog /var/log/httpd/image.log common env=images  


Jiaye

  

Re: [GeneX-dev] Logging hits..

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

> Excellent!! Analog was a really good idea. I noticed this:
> 
>    Failure Report
>    
>    Listing the top 30 files by the number of failed requests, sorted by
>    the number of failed requests.
>    
>    reqs: file
>    ----: ----
>      34: /genex/RCluster-Demo/%%GENEX_GRAPHICS_DIR%%/genexlittlelogo.jpg
>      34: /genex/RCluster-Demo/%%GENEX_GRAPHICS_DIR%%/ncgr_red.gif
>      34: /genex/RCluster-Demo/%%GENEX_GRAPHICS_DIR%%/rcluster.jpg
>  
> There must be an unsubstituted link in one of the rcluster demo html
> pages, can you check it out harry?

Already fixed; the logger is still filetering the old log files
 
>   13: /cgi-bin/images/html2.gif
>   13: /cgi-bin/images/barb16.gif
>   13: /cgi-bin/images/analogo.gif
>   13: /cgi-bin/images/barb8.gif
>   13: /cgi-bin/images/barb4.gif
>   13: /cgi-bin/images/barb32.gif
>   13: /cgi-bin/images/barb2.gif
>   13: /cgi-bin/images/barb1.gif
> 
> This looks like one of the CGI scripts is looking for an images
> directory that probably exists in the htdocs directory instead?


I'll look at this one.

> 
> Then there's this:
> 
>    Host Report
>    
>    Listing hosts with at least 100 requests, sorted alphabetically.
>    
>    reqs: %bytes: host
>    ----: ------: ----
>     387: 17.65%: 24.1.175.29
>     100:  0.27%: 63.227.107.74
> 
> Looks like amadeus is falling sharply behind harwin :-( 
> It's probably just Harry downloading the server a bunch of times just
> to inflate the hit-rate ;-)

Jah, you betcha..

Harry 'mr download' 

Re: [GeneX-dev] [Fwd: Re: Problems using CyberT software]

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

"Harry Mangalam" <man...@ho...> writes:

> FYI, we're starting to get complaints!  (which is good - means some
> one is trying..)

Ohmygod USERS!!!!! Aahhhhhhhhhhhh what do we do?????

;-)

jas.

[GeneX-dev] [Fwd: Re: Problems using CyberT software]

[Harry M. <man...@ho...>]

FYI, we're starting to get complaints!  (which is good - means some one is trying..)

-------- Original Message --------
Subject: Re: Problems using CyberT software
Date: Fri, 23 Mar 2001 09:51:03 -0800
From: Harry Mangalam <man...@ho...>
To: Rifat Hamoudi <ri...@ic...>
CC: genexdev at SF <gen...@li...>
References: <SIM...@su...>

Hi Rifat,

Thanks for trying CyberT.  Could you tell me which machine you're running it on?  T There are a number of installations now and not all of them are up to date.

That said, there is a sample data set that should be included with all of them (I've attached one to this note as well).

At the URL:
http://genex.ncgr.org/cgi-bin/genex/cybert/CyberT-6.2.paired.form.pl
at the upper right hand corner there is a link labeled 'Example Paired Data Set'
which is linked to a dataset that should work with this analysis.

In the Demo page:
http://genex.ncgr.org/genex/CyberT-Demo/Basic_CyberT_Demo.shtml

there is a version which is set up to use this dataset with all the parameters pre-set.


There should also be a description of the acceptable format link to the page just after the "Data File to Upload: (Format expected, Data Coding) which describes the data format:

=====
File Format Expected

The format expected is essentially the output of a spreadsheet file in ASCII or plain text with the values delimited by tabs, commas, or spaces. Comments can be inserted anywhere in the text as long
as the comment lines are prefixed by a '#'. 

Missing values are coded as 'NA' (not 'na' - case matters) and values below background are coded as zero ("0")  
=====

If you're still having trouble, please send me the file you're trying to analyze and I'll see what's wrong with it.


Best wishes and thanks agin for trying it.

Harry

Rifat Hamoudi wrote:
> 
> Dear Sir/Madam,
>                 I am having problems with using the CyberT
> software. I am testing it using your example data file for the
> Gene Expression Array Analysis for Ratio (Paired) Data and
> finding it difficult to get example output. I have used your
> data set but it keeps coming up with errors like the followings :
> 
> ALL Messages, including errors (fatal and not) from R follow
> below...
> 
> Many errors are not fatal and deal only with some aspects of the
> postscript generation, but check your output carefully. Please
> check the Cyber-T FAQ for a more detailed explanation
> 
> Warning messages:
> 1: "^" not meaningful for factors in: Ops.factor((h[, end + 4]),
> 2) 2: no genes pass the Bonferroni test in: doitall.pair(ss, 5,
> 4, 4, 0.25, 2)
> 
> And then in the results the Mean value is NA which and Observed
> number is 1.
> 
> I think the problem lies in the parser and how it works. What
> would be helpful if you could tell me how the Label Column and
> Ratio Data should be. I was using #3 4 8 but it gives error. I
> would be grateful if you could explain to me how the parser
> expect the data to be in Label Column, Ratio Data and Minimum
> Non-Zero Replicate Required fields.

what you should be using is 

3 4 8

not 

#3 4 8

I'll include an example of that in the help file.

> Alternatively if you could send me a file that works I would
> appreciated it.

It should be attached.

> Thanks
> 
> ======================================
> 
> Rifat Hamoudi,
> Haddow Laboratories,
> Institute of Cancer Research,
> 15, Cotswold Road,
> Sutton,
> SM2 5NG.
> Tel   : 0208-643 8901 ext. 4658
> Fax   : 0208-770 7290
> Pager : 07669 801 509
> Email : ri...@ic...
> 
> =======================================

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

Re: [GeneX-dev] [genex2] data in DB

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

"Michael Pear" <mic...@ho...> writes:

> Is it worth setting up the extra structure for Group ownership?  

Oops. I think you are correct and it was a mistaken effort on my part.

> 3) the group is owned by whomever set it up and they alone can add or delete
> members.

This was actually my original intent. I just wanted to record the
'owner' of the group. And because of my (poor) choice of name for the
ContactOwner table, I thought that was what it is intended to do. I
now realize that all that is necessary, is just an 'owner_us_fk' in
the GroupSec table.

> Before deciding on this, we should discuss how groups are intended
> tob e used, how someone is added to a group or removed from a group
> and when.  

This seems fairly more clear to me now. Here are the groups I see in
common use:
* public (all users in DB)
* superuser (only the superuser(s))
* lab-centric (only members of my lab)
* NULL (only the owner can read/write) -- currently the ro_gs_fk and
  rw_gs_fk have NOT NULL constraints, but having NULL groups makes
  sense when interpreted this way.

so read access would be:

   SELECT * FROM SomeTable,Security WHERE sec_fk=sec_pk AND 
     (owner_us_fk='me' OR ro_gs_fk IN (my_group_list));

where 'my_group_list' is:

   SELECT gs_fk FROM GroupSec WHERE us_fk='me';

which could be cached for perfomance...

UPDATE is the same except with rw_gs_fk

> I think this security portion can suck up time, and will
> have to be supported by the applications, so I'd suggest drawing the
> line before it gets too complicated.

Agreed, thanks for catching me from going to far. I was attempting to
store who had created the group, and there was no field to do it in. I
thought the GroupOwner table was the simplest way, and I'm glad you
caught it.

jas.

Re: [GeneX-dev] [genex2] data in DB

[Michael P. <mic...@ho...>]

Hi Jason,

 Is it worth setting up the extra structure for Group ownership?
I'd suggest adopting one of the following policies be allowed in the system
that could avoid building the extra schema and supporting
UI/API/etc.

1) Allow designation of one or more users (in UserSec) as "administrators"
who would have the priveleges to change group infomation for groups they 
are members of. Maybe have a "superuser" who could change anything.

2) Allow any user who is member of a group to make changes to a group they
are members of.

3) the group is owned by whomever set it up and they alone can add or delete
members.

Before deciding on this, we should discuss how groups are intended tob e used,
how someone is added to a group or removed from a group and when.
I think this security portion can suck up time, and will have to be supported
by the applications, so I'd suggest drawing the line before it gets too complicated.

Regards,

Michael Pear

----- Original Message ----- 
From: "Jason E. Stewart" <ja...@op...>
To: <gen...@li...>
Sent: Thursday, March 22, 2001 12:15 AM
Subject: [GeneX-dev] [genex2] data in DB


> Hey All,
> 
> Thought I'd pass on another success note. I've made the generic 
> xml2db API for the following classes:
> * Contact
> * ContactType
> * ContactOwner
> * GroupSec
> * UserSec
> * GroupLink
> * Security
> 
> I created a test GeneXML file with 2 contacts, 2 groups, 2 security
> entries, and 2 users, and using a perl script successfully entered all
> the info into the DB.
> 
> Alright!!! 
> 
> Now there is enough info in the DB to begin to use the DataLoader.
> 
> BTW, I realized that we are missing some information. Groups need to
> have security information as well, we need to know who has permission
> to modify a group. This leads me to believe we need a GroupOwner table
> as a linking table between Security and GroupSec, analagous to
> ContactOwner between Contact and Security.
> 
> I've included a UML diagram that I made in ArgoUML that shows what I
> mean. 
> 
> jas.
> 
> 


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

[GeneX-dev] [genex2] data in DB

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

Hey All,

Thought I'd pass on another success note. I've made the generic 
xml2db API for the following classes:
* Contact
* ContactType
* ContactOwner
* GroupSec
* UserSec
* GroupLink
* Security

I created a test GeneXML file with 2 contacts, 2 groups, 2 security
entries, and 2 users, and using a perl script successfully entered all
the info into the DB.

Alright!!! 

Now there is enough info in the DB to begin to use the DataLoader.

BTW, I realized that we are missing some information. Groups need to
have security information as well, we need to know who has permission
to modify a group. This leads me to believe we need a GroupOwner table
as a linking table between Security and GroupSec, analagous to
ContactOwner between Contact and Security.

I've included a UML diagram that I made in ArgoUML that shows what I
mean. 

jas.

[GeneX-dev] Re: Even More on J-Express <=> GeneX]

[Harry M. <man...@ho...>]

Hi Bjarte and Inge,

You've probably seen the GeneX release announcement, but probably not yet seen the latest issue of Genome Technology which contains an assessment of microarray software by Nat Goodman.  In it,
J-Express comes off pretty well, the best of the 'nearly commercial' tools.  It is also misrepresented as being part of the 'GeneX Suite'.  We do make many (nice) references to it, but we've never
referred to it as part of the suite or implied ownership to my knowledge.

I'm going to send the clarification to Nat.  If you have any additions or corrections, please let me know.

Cheers
harry
==================

Hi Nat,

Of course, it would happen - the afternoon of the day we announce the full release of GeneX, I get your article on "Sampling the Menu of Microarray Software".  It's a nice survey, but a couple of
issues:

1) While I strongly agree with your assessment of J-Express as the best of
  breed, it's not actually part of the GeneX suite.  We support an output
  format that allows you to import data directly into J-Express and we are
  working with the authors to add direct GeneX connectivity to it which will
  make it even more effective, but it's not ours.  Bjarte Dysvik and Inge 
  Jonassen alone get the credit.


2) While GeneX is mostly a database product, it also has a few analytical
  tools incorporated into it that make it more attractive:   

  a) CyberT, a web interface to an R library developed by Tony Long and
    Pierre Baldi at UC Irvine that tests significance between data sets
    via  a t-test (with Bonferonni correction for repetition) and a
    Bayesian  estimate of variance that can be applied to small samples. 
    It passes  the data it generates to xgobi, a free Xwindows analytical &
    visualization program that supports linked data windows, PCA, etc.

  b) Rcluster, a Web interface to many of the R cluster libraries that 
    provides several clustering approaches, using multiple metrics.
  
  c) Xcluster, Gavin Sherlock's much improved, speedy, and memory efficient
    port of Eisen's orignal clustering apprach to unix (also includes
    Kmeans and Self Organizing Maps).  NCGR provides the web interface; users
    must license the code directly from Stanford / Eisen.

All the above tools can take data either from a database query or by direct
upload of simple datasets.  Try them at: http://genex.ncgr.org/genex
    
GeneX is not a full-featured commercial system (as you pointed out, normalization is a key area and one which we have not addressed yet), but it is functional and
comes with source code to encourage the kind of exploratory approach that 
will have to be applied to large-scale gene expression analysis.

If you want a platform to demo it or teach with at the Camebridge HealthTech, let us know and we can probably get you a system with a demo GeneX DB pre-loaded.  
Bjarte and Inge would probably be willing to provide their latest version as well.
-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

[GeneX-dev] ANNOUNCE: GeneX, an Open Source gene expression database

[Harry M. <man...@ho...>]

                 The GeneX Gene Expression Database 
                             from the 
                National Center for Genome Resources 
                      [http://genex.ncgr.org]

The GeneX team is happy (well, relieved anyway ;) ) to announce a public
release of NCGR's GeneX Gene Expression Database system.

The GeneX project is an Open Source endeavor to provide the gene expression
community a way of designing a system that best meets their needs.  The
system can be downloaded from Sourceforge (http://genex.sourceforge.net) or
from NCGR's GeneX web site (http://genex.ncgr.org) and is licensed under the
GNU LGPL.  

We hope this provides a partial outlet for those labs that have experience
with expression analysis, some coding ability, and the desire to contribute
to project that can, with a little effort, add the feaures that they want 
but doesn't require a build-from-scratch effort.

It provides a basic working system including:

- installation scripts
- a small amount of example data
- the Genex.pm Perl wrapper API to the database
- utilities to manipulate the XML transport format
- analytical tools which can be used with data from the database or with data
  uploaded directly.  They include apps for significance & permutation 
  testing as well as several kinds of clustering.
  * CyberT - a significance testing tool which uses repeated t-tests (with
    Bonferonni correction) and an optional Bayesian estimation of variance.
    CyberT also uses xgobi (an XWindows app) to perform 3D
    visualizations of the results, Principle Component Analysis, and linked
    maps.
  * Rcluster - an interface to the R cluster libs (several clustering
    approaches, using several metrics)
  * xcluster - Gavin Sherlock's speedy and memory-efficient clustering app
    which also includes KMeans clustering and Self-Organizing Maps (we
    provide the interface - you have to license the xcluster code directly 
    from Stanford:  http://genome-www.stanford.edu/~sherlock/cluster.html)
- an interactive tool to load & annotate data (& a scriptable one is under
    development to load multiple experiments in bulk, albeit with less
    annotation). 

Its advantages are that it:
- is freely available in source code (tarball and anonymous CVS).
- has relatively small hardware requirements.
- requires no proprietary software to run.
- is relatively simple to install .. operative word 'relatively' ;) .
- supports multiple kinds of array data (Affy, Cy3,Cy5, radiolabeled blot).
- can incorporate commandline analytical routines very easily as CGIs.
- can share data via an XML for which there are free tools available.
- it has been developed using a number of R (aka GNU S) libs:
    (http://cran.r-project.org/) and will continue to add more support for 
    this Open Source Software approach.
- can export data in a variety of formats for use with other tools.
  * J-Express (http://www.ii.uib.no/~bjarted/jexpress) can directly import
    one std format.
  * with a local installation, you can export the data in xgobi format and
    with minimal scripting in R, you could export in a number of other 
    formats as well.  Use the source, Luke!
- it has a fairly active development community. 

Its disadvantages (hey! it's free; there ARE disadvantages!) are:
- the user interface is crude.
- the query interface is crude and simple (but pretty easy to customize).
- we do not yet provide for easy normalization, altho such an interface is
    under development (contributed by an external user) and more input would
    be most welcome.
- it uses a heterogeneous (albeit standard) mix of software components.
- it requires some knowledge of Linux and Postgres (or whatever RDBMS in
    which you want to implement it) to make it work.  It is definitely *NOT* 
    Plug and Play.
- it is a relatively young project and therefore will probably not support 
    some critical operations.
- the current data loader is functional, but sub-optimal (and is being
    re-written from scratch with the input of several labs).
- there are some known security issues (and certainly more unknown ones)
- its scalability is largely untested.

We're hoping that with enough interested, engaged users, each contributing
what they can (suggestions, bug descriptions, & especially code), useful
features can be suggested and implemented, bugs can be killed quickly, ports
to additional RDBMS can be completed, useful applications can be added, the
Data Model and XML feature set improved and contributed back to make the
MGED MAML XML as robust as it needs to be. 

We welcome your feedback (really!) [ge...@nc...]

The GeneX Team

  * Bill Beavis                        > William Anderson
  * Greg Colello                       > Andrew Dalke
  * Harry Mangalam                     > Carol Harger
  * Lonny Montoya                      > Peter Hraber
  * Michael Pear (honorary)            > Karen Schlauch
  * Todd Peterson                      > Mark Waugh
  * Jason Stewart                      > Jennifer Weller
  * Jiaye Zhou

  * current                            > alumni (thanks guys!)

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

Re: [GeneX-dev] Harry & harwin may be incommunicado

[Todd P. <tf...@nc...>]

better get one of them fancy generators like ncgr has.

----- Original Message -----
From: "Harry Mangalam" <man...@ho...>
To: "genexdev at SF" <gen...@li...>
Sent: Monday, March 19, 2001 4:08 PM
Subject: [GeneX-dev] Harry & harwin may be incommunicado


> ...due to rolling power outages thru SCal today and maybe tomorrow.  Now
at Stage 3 alert (< 1.5% to max capacity).
>
> --
> Cheers,
> Harry
>
> Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... ||
man...@ho...
>
> _______________________________________________
> Genex-dev mailing list
> Gen...@li...
> http://lists.sourceforge.net/lists/listinfo/genex-dev
>

[GeneX-dev] Harry & harwin may be incommunicado

[Harry M. <man...@ho...>]

...due to rolling power outages thru SCal today and maybe tomorrow.  Now at Stage 3 alert (< 1.5% to max capacity).

-- 
Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || man...@ho...

[GeneX-dev] [genex2]: more good news

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

Hey All,

So it turns out I had some trigger problems. Which are now
straightened out.

Most tables now have 4 update columns:
creation_date
created_by
modification_date
modified_by

And there is also now the TableAdmin table that tracks the last
modification time of every table (so that automated diffs can be
created of the DB state).

Any table with update columns has a trigger on INSERT to automatically
set the update columns and the TableAdmin entry, and on UPDATE to
ajust the modification_date and the TableAdmin entry. It now all
works.

genex2=# select con_pk,creation_date,modification_date from contact;
 con_pk |     creation_date      |   modification_date    
--------+------------------------+------------------------
      1 | 2001-03-19 13:59:37-07 | 2001-03-19 13:59:37-07
      2 | 2001-03-19 13:59:37-07 | 2001-03-19 13:59:37-07
(2 rows)

genex2=# select * from contacttype;
 con_fk | type  
--------+-------
      1 | login
      2 | login
(2 rows)

genex2=# insert into contacttype (con_fk,type) values (1,'test');
INSERT 15272640 1
genex2=# select con_pk,creation_date,modification_date from contact;
 con_pk |     creation_date      |   modification_date    
--------+------------------------+------------------------
      2 | 2001-03-19 13:59:37-07 | 2001-03-19 13:59:37-07
      1 | 2001-03-19 13:59:37-07 | 2001-03-19 14:00:17-07
(2 rows)


Yeah!!!! New modification time!!!!


genex2=# select * from tableadmin;
    table_name     |   modification_date    
-------------------+------------------------
 GenexAdmin        | 2001-03-19 13:58:31-07

[snip]

 Contact           | 2001-03-19 14:00:17-07
(35 rows)

Yeah!!!! The modification time is propagated to tableadmin!!!!

Ok, now to enter security information...

jas.