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View Code? Open in Web Editor NEWthings behind nectarmutation.org
Home Page: http://nectarmutation.org/main
things behind nectarmutation.org
Home Page: http://nectarmutation.org/main
############################################################ # Nectar-WebV3.00 is served from # http://www.nectarmutation.org # ########################################################## # rsync sudo rsync -a /BiO/Serve/mysql/NECTAR_DEVEL/ /BiO/Serve/mysql/NECTAR Run script/nectar_webv2_server.pl to test the application. #Stub $catalyst.pl Nectar::Web #Controller [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl controller Browser::Mutation [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl controller Browser::Run [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl controller Browser::Disease [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl controller Browser::Gene [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl controller Browser::Patient [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl controller Util::Downloader [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl controller Util::Messenger [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl controller Util::Service [sung@cmr000018 Nectar-WebDev]$ ./script/nectar_webv2_create.pl controller User [sung@cmr000018 Nectar-WebDev]$ ./script/nectar_webv2_create.pl controller Captcha [sung@cardiodb Nectar-WebV2.99]$ ./script/nectar_webv2_create.pl controller Parser::VCF #Model [sung@cmr000018 Nectar-WebDev]$ cpanm DBIx::Class::TimeStamp [sung@cmr000018 Nectar-WebDev]$ cpanm DBIx::Class::PassphraseColumn [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl model CARDIODB DBIC::Schema Nectar::Schema::CARDIODB create=static dbi:mysql:dbname=CARDIODB_DEVEL\;host=fs01 sung snrnsk [sung@cmr000018 Nectar-WebDev]$ ./script/nectar_webv2_create.pl model NECTAR DBIC::Schema Nectar::Schema::NECTAR create=static components=TimeStamp,PassphraseColumn dbi:mysql:dbname=NECTAR\;host=fs01 sung snrnsk [sung@cmr000018 Nectar-WebDev]$ ./script/nectar_webv2_create.pl model UNIPROT DBIC::Schema Nectar::Schema::UNIPROT create=static dbi:mysql:dbname=UNIPROT\;host=fs01 sung snrnsk [sung@cmr000018 Nectar-WebV2.99]$ ./script/nectar_webv2_create.pl model COSMIC DBIC::Schema Nectar::Schema::COSMIC create=static dbi:mysql:dbname=COSMIC\;host=fs01 sung snrnsk [sung@cardiodb Nectar-WebV2.99]$ ./script/nectar_webv2_create.pl model VCF add following at 'lib/Nectar/Schema/CARDIODB/Result/TargetGene.pm' as this is a view: __PACKAGE__->set_primary_key("id"); #View [sung@cmr000018 Nectar-WebV2]$ ./script/nectar_webv2_create.pl view TT TTSite [sung@beomaster01 Nectar-WebV2]$ ./script/nectar_webv2_create.pl view JSON JSON ./script/nectar_web_create.pl view Download ./script/nectar_web_create.pl view XML::Feed ./script/nectar_web_create.pl view Excel Excel::Template::Plus # JavaScript [sung@beomaster01 Web]$ cp /data/Install/JavaScript/coda-slider/javascripts/* Cardiodb.org/Nectar-WebV2/root/static/js/ # CSS [sung@beomaster01 Web]$ cp /data/Install/JavaScript/coda-slider/stylesheets/coda-slider-2.0.css Cardiodb.org/Nectar-WebV2/root/static/css/ # relative/absolute URL link 1. nectar.js 2. static/mutation_profile.html (look at img src) # HTML::FormHandler [sung@cmr000018 Nectar-WebDev]$ form_generator.pl --rs_name=User --schema_name=Nectar::Schema::NECTAR --db_dsn=dbi:mysql:database=NECTAR;host=fs01 ## Before Publishing Nectar (pribaly via Apache) check the proper URL shown below: 1. root/static/site/reg_warning.html <form method='post' action='/main/register/tnc' id='reg_agree'> <!-- /register/tnc to set a session argument--> 2. root/static/js/nectar.js boxy_content +="<a style=\"font-size: 9px; text-align: right;\" title=\"create account\" href=\"/main/register\">need an account?</a><br/>"; $.post("/main/sendmail", { subject: c.find("input[name='subject']").val(), sender: c.find("input[name='sender']").val(), comment: c.find("#comment").val()}, $.post("/main/login", { username: c.find("input[name='username']").val(), password: c.find("input[name='password']").val()}, loginBoxy.hideAndUnload(window.location = "/"); 3. lib/Nectar/Form/Captcha.pm and lib/Nectar/Form/Register.pm sub captcha_image_url { return '/main/captcha/image' } 4. root/static/site/not_logged_in.html <form id="login" method='post' action="/main/login"> <a href="/main/register" title="create your account">need an account?</a> 5. root/lib/js/login_ready.tt2 boxy_content +="<a style=\"font-size: 10px; text-align: right;\" title=\"create account\" href=\"/main/register\">need an account?</a><br/>"; 6. root/src/Form/login.tt2 <form id="login" method='post' action="[%c.uri_for('/main/login')%]"> <a href="[%c.uri_for('/main/register')%]" title="create your account">need an account?</a> ### Sitemap ### mysql NECTAR --skip-column-names < script/SQL/sitemap_gene.sql > root/static/site/sitemap_genes.txt mysql NECTAR --skip-column-names < script/SQL/sitemap_disease.sql > root/static/site/sitemap_diseases.txt mysql NECTAR --skip-column-names < script/SQL/sitemap_remove_disease.sql > root/static/site/sitemap_remove_diseases.txt mysql NECTAR --skip-column-names < script/SQL/sitemap_gbrowse_ensp.sql > root/static/site/sitemap_gbrowse_ensp.txt mysql NECTAR --skip-column-names < script/SQL/sitemap_das_para.sql > root/static/site/sitemap_das_para.txt ### NEW SQL for 'get_colocated_mutations' SELECT me.*, _UnifiedCalls.chr, _UnifiedCalls.v_start, _UnifiedCalls.v_end, _UnifiedCalls.reference, _UnifiedCalls.genotype FROM V2Ensembls me JOIN _UnifiedCalls _UnifiedCalls ON _UnifiedCalls.id = me.uid WHERE me.ensp = 'ENSP00000279022' AND me.p_start = '19' AND me.is_canonical = 1
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