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/** \file
\brief Contains the EIpanel functions for NCBI
*/
#include "ExternalInterface.h"
void EIpanel::init_ncbi()
{
RETMAX = 25 ;
t1 = new wxTextCtrl ( up , ID_T1 , _T("") , wxDefaultPosition , wxDefaultSize , wxTE_PROCESS_ENTER ) ;
b1 = new wxButton ( up , ID_B1 , txt("b_find") , wxDefaultPosition ) ;
b2 = new wxButton ( up , ID_B2 , txt("t_open") , wxDefaultPosition ) ;
b3 = new wxButton ( up , ID_B3 , txt("b_open_link") , wxDefaultPosition ) ;
c1 = new wxChoice ( up , ID_C1 ) ;
c1->Append ( _T("Nucleotide") ) ;
c1->Append ( _T("Protein") ) ;
c1->Append ( _T("PubMed") ) ;
b_last = new wxButton ( up , ID_B_LAST , txt("b_last") , wxDefaultPosition ) ;
b_next = new wxButton ( up , ID_B_NEXT , txt("b_next") , wxDefaultPosition ) ;
b_last->Disable () ;
b_next->Disable () ;
b3->Disable () ;
/*
structure, genome, pmc, omim, taxonomy, books, probeset, domains, unists, cdd, snp, journals, unigene, popset
c1->Append ( "" ) ;
*/
v1 = new wxBoxSizer ( wxVERTICAL ) ;
h0 = new wxBoxSizer ( wxHORIZONTAL ) ;
h0->Add ( c1 , 0 , wxEXPAND , 5 ) ;
h0->Add ( t1 , 1 , wxEXPAND , 5 ) ;
h0->Add ( b1 , 0 , wxEXPAND , 5 ) ;
h0->Add ( b2 , 0 , wxEXPAND , 5 ) ;
h0->Add ( b3 , 0 , wxEXPAND , 5 ) ;
h0->Add ( b_last , 0 , wxEXPAND , 5 ) ;
h0->Add ( b_next , 0 , wxEXPAND , 5 ) ;
// PubMed-specific
wxString off = _T(" ") ;
h1 = new wxBoxSizer ( wxHORIZONTAL ) ;
t2 = new wxTextCtrl ( up , ID_T2 , _T("") , wxDefaultPosition , wxDefaultSize , wxTE_PROCESS_ENTER ) ;
t3 = new wxTextCtrl ( up , ID_T3 , _T("") , wxDefaultPosition , wxDefaultSize , wxTE_PROCESS_ENTER ) ;
t4 = new wxTextCtrl ( up , ID_T4 , _T("") , wxDefaultPosition , wxDefaultSize , wxTE_PROCESS_ENTER ) ;
c2 = new wxChoice ( up , ID_C2 ) ;
c2->Append ( _T("Author") ) ;
c2->Append ( _T("Journal") ) ;
c2->Append ( _T("Pub date") ) ;
h1->Add ( new wxStaticText ( up , -1 , txt("author(s)") ) , 0 , wxEXPAND , 5 ) ;
h1->Add ( t2 , 1 , wxEXPAND , 5 ) ;
h1->Add ( new wxStaticText ( up , -1 , off + txt("from") ) , 0 , wxEXPAND , 5 ) ;
h1->Add ( t3 , 1 , wxEXPAND , 5 ) ;
h1->Add ( new wxStaticText ( up , -1 , off + txt("to") ) , 0 , wxEXPAND , 5 ) ;
h1->Add ( t4 , 1 , wxEXPAND , 5 ) ;
h1->Add ( new wxStaticText ( up , -1 , off + txt("sort") ) , 0 , wxEXPAND , 5 ) ;
h1->Add ( c2 , 1 , wxEXPAND , 5 ) ;
st_msg = new wxStaticText ( up , -1 , _T("") ) ;
v1->Add ( h0 , 0 , wxEXPAND , 0 ) ;
v1->Add ( h1 , 0 , wxEXPAND|wxTOP|wxBOTTOM , 3 ) ;
v1->Add ( st_msg , 0 , wxEXPAND|wxTOP|wxBOTTOM , 3 ) ;
up->SetSizer ( v1 ) ;
v1->Fit ( up ) ;
v1->Show ( h1 , false ) ; // Hide PubMed specifics
v1->Show ( st_msg , false ) ; // Hide message
c1->SetSelection ( 0 ) ;
c2->SetSelection ( 2 ) ;
t1->SetFocus() ;
t1->SetSelection ( -1 , -1 ) ;
}
void EIpanel::process_ncbi()
{
myExternal ex ;
wxString database = c1->GetStringSelection() ;
database = database.Lower() ;
wxString search = t1->GetValue() ;
wxString authors = t2->GetValue() ;
wxString from = t3->GetValue() ;
wxString to = t4->GetValue() ;
wxString sort = c2->GetStringSelection().Lower() ;
sort.Replace ( _T(" ") , _T("+") ) ;
if ( database == _T("pubmed") && !authors.IsEmpty() )
{
while ( !authors.IsEmpty() )
{
search = authors.BeforeFirst ( ',' ) + _T(" [au] ") + search ;
authors = authors.AfterFirst ( ',' ) ;
}
}
search.Replace ( _T(" ") , _T("+") ) ;
// Invoking ESearch
wxString query = _T("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?") ;
query += _T("db=") + database ;
query += _T("&retstart=") + wxString::Format ( _T("%d") , res_start ) ;
query += _T("&retmax=") + wxString::Format ( _T("%d") , RETMAX ) ;
query += _T("&tool=GENtle") ;
query += _T("&retmode=xml") ;
if ( database == _T("pubmed") )
{
if ( !from.IsEmpty() ) query += _T("&mindate=") + from ;
if ( !to.IsEmpty() ) query += _T("&maxdate=") + to ;
query += _T("&sort=") + sort ;
}
query += _T("&term=") + search ;
// query = wxURL::ConvertToValidURI ( query ) ;//!!!!!!!!!!!!!
// wxURI uri ( query ) ;
// query = uri.BuildUnescapedURI () ;
wxString res ;
res = ex.getText ( query ) ; // The XML is now in res
TiXmlDocument doc ;
doc.Parse ( res.mb_str() ) ;
if ( res == _T("") || doc.Error() )
{
showMessage ( txt("t_error") ) ;
return ;
}
// Extracting items from XML
res_count = 0 ;
wxArrayString ids ;
TiXmlNode *x = doc.FirstChild ( "eSearchResult" ) ;
if ( x )
{
TiXmlNode *y ;
y = x->FirstChild ( "Count" ) ;
if ( y ) valFC(y).ToLong ( &res_count ) ;
y = x->FirstChild ( "ResStart" ) ;
if ( y ) valFC(y).ToLong ( &res_start ) ;
x = x->FirstChild ( "IdList" ) ;
if ( x )
{
for ( x = x->FirstChild ( "Id" ) ; x ; x = x->NextSibling ( "Id" ) )
ids.Add ( valFC ( x ) ) ;
}
}
// wxMessageBox ( wxString::Format ( _T("%d of %d") , res_count , res_start ) ) ;
if ( ids.IsEmpty() )
{
showMessage ( _T("The search returned no results.") ) ;
return ;
}
int a ;
res = _T("") ;
for ( a = 0 ; a < ids.GetCount() ; a++ )
{
if ( !res.IsEmpty() ) res += _T(",") ;
res += ids[a] ;
}
// Invoking ESummary
query = _T("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?") ;
query += _T("db=") + database ;
query += _T("&tool=GENtle&") ;
query += _T("id=") + res ;
query += _T("&retmode=xml") ;
query += _T("&retmax=") + wxString::Format ( _T("%d") , RETMAX ) ;
res = ex.getText ( query ) ; // The XML is now in res
//cout << res.mb_str() << endl ;
// wxTheClipboard->Open(); wxTheClipboard->SetData( new wxTextDataObject(res) ); wxTheClipboard->Close();
if ( res != _T("") ) doc.Parse ( res.mb_str() ) ;
x = doc.FirstChild ( "eSummaryResult" ) ;
if ( res == _T("") || doc.Error() || !x )
{
showMessage ( txt("t_error") ) ;
return ;
}
// Parsing ESummary XML
a = 0 ;
for ( x = x->FirstChild ( "DocSum" ) ; x ; x = x->NextSibling ( "DocSum" ) )
{
TiXmlNode *y = x ;
wxString title , authors , source , pubdate , id , caption ;
id = valFC ( x->FirstChild ( "Id" ) ) ;
for ( y = x->FirstChild ( "Item" ) ; y ; y = y->NextSibling ( "Item" ) )
{
wxString at ( y->ToElement()->Attribute ( "Name" ) , wxConvUTF8 ) ;
at = at.Upper() ;
if ( at == _T("TITLE") ) title = valFC ( y ) ;
else if ( at == _T("PUBDATE") ) pubdate = valFC ( y ) ;
else if ( at == _T("SOURCE") ) source = valFC ( y ) ;
else if ( at == _T("CAPTION") ) caption = valFC ( y ) ;
else if ( at == _T("AUTHORLIST") )
{
TiXmlNode *z ;
for ( z = y->FirstChild ( "Item" ) ; z ; z = z->NextSibling ( "Item" ) )
{
if ( wxString(z->ToElement()->Attribute ( "Name" ),wxConvUTF8).Upper() != _T("AUTHOR") ) continue ;
if ( !authors.IsEmpty() ) authors += _T(", ") ;
authors += valFC ( z ) ;
}
}
}
wxString s ;
if ( database == _T("nucleotide") || database == _T("protein") )
{
s = _T("<table width='100%'><tr>") ;
s += _T("<td align=right valign=center width='50px'>") ;
s += wxString::Format ( _T("%d") , a + res_start + 1 ) ;
s += _T("</td>") ;
s += _T("<td width='10%'>") + caption + _T("</td>") ;
s += _T("<td>") + title + _T("</td>") ;
s += _T("</tr></table>") ;
}
else if ( database == _T("pubmed") )
{
s = _T("<table width='100%'><tr>") ;
s += _T("<td rowspan=2 align=right valign=top width='50px'>") ;
s += wxString::Format ( _T("%d") , a + res_start + 1 ) ;
s += _T("</td>") ;
s += _T("<td colspan=3><b>") + title + _T("</b></td>") ; // !!!!!!!!!!!!!!!!!!!!
s += _T("</tr><tr>") ;
s += _T("<td valign=top width='10%'>") + pubdate + _T("</td>") ;
s += _T("<td valign=top width='10%'>") + source + _T("</td>") ;
s += _T("<td valign=top>") + authors + _T("</td>") ;
s += _T("</tr></table>") ;
}
hlb->Set ( a++ , s , id ) ;
}
int res_to = res_start + RETMAX ;
if ( res_to > res_count ) res_to = res_count ;
wxString msg = wxString::Format ( txt("t_ext_show_res") , res_start + 1 , res_to , res_count ) ;
msg += _T(" (") + wxString ( txt("t_data_by_ncbi") ) + _T(")") ;
showMessage ( msg ) ;
b_next->Enable ( res_start + RETMAX <= res_count ) ;
b_last->Enable ( res_start > 0 ) ;
b3->Enable ( true ) ;
t1->SetFocus() ;
}
void EIpanel::execute_ncbi()
{
wxString database = c1->GetStringSelection() ;
execute_ncbi_load ( database ) ;
}
void EIpanel::execute_ncbi_load ( wxString database )
{
// Opening selected items
int a ;
wxString ids ;
for ( a = 0 ; a < hlb->was.GetCount() ; a++ )
{
if ( !hlb->IsSelected ( a ) ) continue ;
if ( hlb->data[a] == _T("") ) continue ;
if ( !ids.IsEmpty() ) ids += _T(",") ;
ids += hlb->data[a] ;
}
database = database.Lower() ;
if ( database == _T("nucleotide") || database == _T("protein") ) // Requesting sequence
{
wxString query = _T("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?") ;
query += _T("db=") + database ;
query += _T("&tool=GENtle") ;
// query += "&retmax=" + wxString::Format ( "%d" , RETMAX ) ;
query += _T("&id=") + ids ;
if ( database == _T("nucleotide") ) query += _T("&retmode=xml&rettype=gb") ;
else query += _T("&retmode=text&rettype=gp") ;
myExternal ex ;
wxString res = ex.getText ( query ) ;
// wxTheClipboard->Open(); wxTheClipboard->SetData( new wxTextDataObject(res) ); wxTheClipboard->Close();
if ( database == _T("nucleotide") )
{
if ( res.Left ( 5 ) == _T("LOCUS") )
{
TGenBank gb ;
gb.paste ( res ) ;
// wxMessageBox ( "GB" , wxString::Format ( "%d" , gb.success ) ) ;
if ( gb.success ) myapp()->frame->newGB ( gb ) ;
}
else
{
TXMLfile xml ;
xml.parse ( res ) ;
// wxMessageBox ( res , wxString::Format ( "%d" , xml.success() ) ) ;
if ( xml.success() ) myapp()->frame->newXML ( xml ) ;
}
}
else
{
TGenBank gb ;
gb.paste ( res ) ;
if ( gb.success )
myapp()->frame->newGB ( gb , _T("") ) ;
}
}
else if ( database == _T("pubmed") ) // Requesting paper
{
wxString query = _T("http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?") ;
query += _T("db=") + database ;
query += _T("&cmd=retrieve") ;
query += _T("&list_uids=") + ids ;
query += _T("&dopt=abstract") ;
wxExecute ( myapp()->getHTMLCommand ( query ) ) ;
}
}
void EIpanel::execute_ncbi_b3()
{
wxString script , database = c1->GetStringSelection().Lower() ;
if ( database == _T("pubmed") )
{
database += _T("&dopt=Abstract&cmd=Retrieve") ;
script = _T("query") ;
}
else script = _T("viewer") ;
for ( int i = 0 ; i < hlb->data.GetCount() ; i++ )
{
if ( !hlb->IsSelected ( i ) ) continue ;
wxString s = hlb->data[i] ;
s = s.BeforeFirst ( '|' ) ;
s = _T("http://www.ncbi.nlm.nih.gov/entrez/") + script + _T(".fcgi?db=") + database + _T("&list_uids=") + s ;
s = myapp()->getHTMLCommand ( s ) ;
wxExecute ( s ) ;
}
}
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