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Re: FW: [Miamexpress-installation] MIAMEXPRESS experiment_mageml.pl troubles
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From: Niran A. <ni...@eb...> - 2004-05-19 15:51:49
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Hi Razvan, We haven't really tested MIAMExpress in Mac's Safari browser and I guess there might be some problems... Yes, MIAMExpress is grabbing public protocols from ArrayExpress...hence, the reason that you might get "Error getting arrays from database" message if ArrayExpress is down. You will also get this error message on the Create Hybridizations page. To get a restrictly locally version of MIAMExpress, you might have to comment out those specific APIs that call ArrayExpress. Since ArrayExpress doesn't currently have a web service api for this, we are parsing html documents returned from ArrayExpress. We are also planning on having access to public protocols in MIAMExpress as well in release 2.0. After release 2.0, we plan to freeze this version of MIAMExpress except for minor version releases which will contain control vocabulary migrations and bug fixes. We have plans to start work on a new MIAMExpress from scratch (might be called MIAMExpress NG...Next Generation) and it will include the ability to import MAGE-ML files as well....though this won't be ready for quite some time. Cheers, Niran. Razvan Lapadat wrote: > Hello Niran, > > Regarding the Array::Compare module- I realized that it was a Perl module 5 > minutes after sending the email... sorry :-( > Thanks for the other tips as well. > I found out something rather strange yesterday on the 'Browse existing > array designs page'; on a Apple Powerbook using OsX and Safari (browser) > selecting one of the existing array designs and pressing 'Return' leads to > an 'Error 500' message- this happened on both our local install and on the > EBI insatll, around 2.00 PM. I know that the list of arrays is generated > from both the local TARDESIN table and your repository- two weeks ago your > servers were under maintenance (it was a Saturday) and trying to select the > 'Browse existing array designs' page led to a "Error getting arrays from > database message". I don't know if the above mentioned is related to the > later. Which prompts me to another question about the possibility to mirror > locally the whole TARDESIN table- and which modules need to be modified if > one would want to have a strictly local install to avoid these kind of > problems. Running a grep on the cgi-bin directory for possible ebi.ac.uk > calls returns: > > ++++++++++++++++++++++++++++++++++++BEGIN > BLOCK++++++++++++++++++++++++++++++++++++++++++++ > > ./db/MX_dbapi4.pm:191: $rc = > READ_HTTP("http://www.ebi.ac.uk/arrayexpress/query/report?cmd=featurelist&array=".$accno,\$content); > -- > ./db/MX_dbapi4.pm:266: $rc = > READ_HTTP("http://www.ebi.ac.uk/arrayexpress/query/report?cmd=arraydesignlist",\$content); > -- > ./gui/MX_GUI_array_design_submission.pm-834- print $page->start_Tr(); > ./gui/MX_GUI_array_design_submission.pm:835: > MX_GUI_prepare_restrict_label2($page, "Array description file (ADF):", > "http://www.ebi.ac.uk/miamexpress/help/adf/ArrayIntroduction.htm"); > ./gui/MX_GUI_array_design_submission.pm-836- print > $page->start_td({-valign =>"top"}); > -- > ./gui/MX_GUI_browse_array_design.pm-309- > $page->b($page->a( > ./gui/MX_GUI_browse_array_design.pm:310: > {-href=>"http://www.ebi.ac.uk/arrayexpress/query/result?queryFor=array&orderBy2=identifier&aAccession=&aDesignName=&aProvider=", > ./gui/MX_GUI_browse_array_design.pm-311- -target =>"ae > window"}, > -- > ./gui/MX_GUI_common.pm-310- print $page->start_td(); > ./gui/MX_GUI_common.pm:311: print > $page->a({-href =>"http://www.ebi.ac.uk/miamexpress/", > ./gui/MX_GUI_common.pm-312- -target =>"view window"}, > -- > ./gui/MX_GUI_common.pm-342- MX_GUI_put_spaces(1); > ./gui/MX_GUI_common.pm:343: print > $page->a({-href =>"http://www.ebi.ac.uk/miamexpress/help/", > ./gui/MX_GUI_common.pm-344- -target =>"view window", > -class=>"big", -style=>"cursor:help;"}, "Help Pages"); > -- > ./gui/MX_GUI_login.pm:191: print > $page->a({-href =>"http://www.ebi.ac.uk/", > ./gui/MX_GUI_login.pm-192- -target =>"view window"}, > -- > ./gui/MX_GUI_login.pm-236- {-color=>"blue", > ./gui/MX_GUI_login.pm:237: -size > =>-1},$page->a({-href=>"http://www.ebi.ac.uk/arrayexpress/"} > ./gui/MX_GUI_login.pm-238- ,$page->i("ArrayExpress"))); > -- > ./gui/MX_GUI_login.pm-243- {-color=>"blue", > ./gui/MX_GUI_login.pm:244: -size > =>-1},$page->a({-href=>"http://www.ebi.ac.uk/miamexpress/help/"} > ./gui/MX_GUI_login.pm-245- ,$page->i("MIAMExpress Help > Documentation"))); > -- > ./gui/MX_GUI_login.pm-358- print $page->a({-href > =>"mailto:".$MX_system_options->main_email."?subject=Accession Number > Query"}, "curation team."); > ./gui/MX_GUI_login.pm:359: print "<br><br>Arrays, Protocols and > Experiments will be finally released into the <a > href='http://www.ebi.ac.uk/arrayexpress/'>ArrayExpress</a> public domain on > publication of the paper."; > ./gui/MX_GUI_login.pm-360- print "<br><br>If you have used <b>Affymetrix > arrays</b>, please see "; > ./gui/MX_GUI_login.pm-361- print $page->a( > ./gui/MX_GUI_login.pm:362: {-href > =>"http://www.ebi.ac.uk/miamexpress/help/affymetrix.html", > ./gui/MX_GUI_login.pm-363- -title =>"Help topic", > -- > ./gui/MX_GUI_login.pm-368- print $page->a( > ./gui/MX_GUI_login.pm:369: {-href > =>"http://www.ebi.ac.uk/miamexpress/help/faq.html", > ./gui/MX_GUI_login.pm-370- -title =>"Help topic", > ++++++++++++++++++++++++++++++++++++END > BLOCK++++++++++++++++++++++++++++++++++++++++++++++ > > I suspect that the most likely candidates are: > ./db/MX_dbapi4.pm > ./gui/MX_GUI_browse_array_design.pm > > Thanks again, > Razvan Lapadat > |