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revision 1.110, Tue Apr 29 20:54:51 2008 UTC revision 1.114, Wed Sep 3 20:59:57 2008 UTC
# Line 15  Line 15 
15      use CustomAttributes;      use CustomAttributes;
16      use RemoteCustomAttributes;      use RemoteCustomAttributes;
17      use CGI;      use CGI;
18        use WikiTools;
19      use base qw(ERDB);      use base qw(ERDB);
20    
21  =head1 Sprout Database Manipulation Object  =head1 Sprout Database Manipulation Object
# Line 147  Line 148 
148          my $user = ($FIG_Config::arch eq 'win' ? 'self' : scalar(getpwent()));          my $user = ($FIG_Config::arch eq 'win' ? 'self' : scalar(getpwent()));
149          $retVal->{_ca} = CustomAttributes->new(user => $user);          $retVal->{_ca} = CustomAttributes->new(user => $user);
150      }      }
151        # Insure we have access to the stem module.
152        WikiUse('Lingua::Stem');
153        $retVal->{stemmer} = Lingua::Stem->new();
154        $retVal->{stemmer}->stem_caching({ -level => 2 });
155      # Return it.      # Return it.
156      return $retVal;      return $retVal;
157  }  }
# Line 531  Line 536 
536      # Get the parameters.      # Get the parameters.
537      my ($self, %options) = @_;      my ($self, %options) = @_;
538      # Get the control's name and ID.      # Get the control's name and ID.
539      my $menuName = $options{name} || 'myGenomeControl';      my $menuName = $options{name} || $options{id} || 'myGenomeControl';
540      my $menuID = $options{id} || $menuName;      my $menuID = $options{id} || $menuName;
541        Trace("Genome menu name = $menuName with ID $menuID.") if T(3);
542      # Compute the IDs for the status display.      # Compute the IDs for the status display.
543      my $divID = "${menuID}_status";      my $divID = "${menuID}_status";
544      my $urlID = "${menuID}_url";      my $urlID = "${menuID}_url";
# Line 547  Line 553 
553      if (ref $selections ne 'ARRAY') {      if (ref $selections ne 'ARRAY') {
554          $selections = [ split /\s*,\s*/, $selections ];          $selections = [ split /\s*,\s*/, $selections ];
555      }      }
556      my %selected = map { $_ => } @{$selections};      my %selected = map { $_ => 1 } @{$selections};
557      # Extract the filter information. The default is no filtering. It can be passed as a tab-delimited      # Extract the filter information. The default is no filtering. It can be passed as a tab-delimited
558      # string or a list reference.      # string or a list reference.
559      my $filterParms = $options{filter} || "";      my $filterParms = $options{filter} || "";
# Line 623  Line 629 
629      # Set up the style class.      # Set up the style class.
630      my $classTag = ($class ? " class=\"$class\"" : "" );      my $classTag = ($class ? " class=\"$class\"" : "" );
631      # Create the SELECT tag and stuff it into the output array.      # Create the SELECT tag and stuff it into the output array.
632      my @lines = ("<SELECT name=\"$menuID\" id=\"$menuID\" $onChangeTag$multipleTag$classTag size=\"$rows\">");      my @lines = ("<SELECT name=\"$menuName\" id=\"$menuID\" $onChangeTag$multipleTag$classTag size=\"$rows\">");
633      # Loop through the groups.      # Loop through the groups.
634      for my $group (@groups) {      for my $group (@groups) {
635          # Get the genomes in the group.          # Get the genomes in the group.
# Line 659  Line 665 
665          my $searchThingLabel = ($multiSelect ? "<INPUT type=\"button\" name=\"MacroSearch\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectShowing('$menuID', '$searchThingName'); $showSelect;\" />"          my $searchThingLabel = ($multiSelect ? "<INPUT type=\"button\" name=\"MacroSearch\" class=\"button\" value=\"Select genomes containing\" onClick=\"selectShowing('$menuID', '$searchThingName'); $showSelect;\" />"
666                                               : "Show genomes containing");                                               : "Show genomes containing");
667          push @lines, "<br />$searchThingLabel&nbsp;" .          push @lines, "<br />$searchThingLabel&nbsp;" .
668                       "<INPUT type=\"text\" id=\"$searchThingName\" name=\"$searchThingName\" size=\"30\" onKeyup=\"showTyped('$menuID', '$searchThingName');\" />";                       "<INPUT type=\"text\" id=\"$searchThingName\" name=\"$searchThingName\" size=\"30\" onKeyup=\"showTyped('$menuID', '$searchThingName');\" />" .
669                         Hint("GenomeControl", "Type here to filter the genomes displayed.") . "<br />";
670          # For multi-select mode, we also have buttons to set and clear selections.          # For multi-select mode, we also have buttons to set and clear selections.
671          if ($multiSelect) {          if ($multiSelect) {
672              push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll('$menuID'); $showSelect\" />";              push @lines, "<INPUT type=\"button\" name=\"ClearAll\" class=\"bigButton\"  value=\"Clear All\" onClick=\"clearAll('$menuID'); $showSelect\" />";
# Line 667  Line 674 
674              push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome('$menuID', $nmpdrCount, true); $showSelect;\" />";              push @lines, "<INPUT type=\"button\" name=\"NMPDROnly\" class=\"bigButton\"  value=\"Select NMPDR\" onClick=\"selectSome('$menuID', $nmpdrCount, true); $showSelect;\" />";
675          }          }
676          # Add a hidden field we can use to generate organism page hyperlinks.          # Add a hidden field we can use to generate organism page hyperlinks.
677          push @lines, "<INPUT type=\"hidden\" id=\"$urlID\" value=\"$FIG_Config::cgi_url/seedviewer.cgi?page=Organism;organism=\" />";          push @lines, "<INPUT type=\"hidden\" id=\"$urlID\" value=\"$FIG_Config::cgi_url/wiki/rest.cgi/NmpdrPlugin/SeedViewer?page=Organism;organism=\" />";
678          # Add the status display. This tells the user what's selected no matter where the list is scrolled.          # Add the status display. This tells the user what's selected no matter where the list is scrolled.
679          push @lines, "<DIV id=\"$divID\" class=\"Panel\"></DIV>";          push @lines, "<DIV id=\"$divID\" class=\"Panel\"></DIV>";
680      }      }
# Line 678  Line 685 
685  }  }
686    
687    
688    =head3 Stem
689    
690        my $stem = $sprout->Stem($word);
691    
692    Return the stem of the specified word, or C<undef> if the word is not
693    stemmable. Note that even if the word is stemmable, the stem may be
694    the same as the original word.
695    
696    =over 4
697    
698    =item word
699    
700    Word to convert into a stem.
701    
702    =item RETURN
703    
704    Returns a stem of the word (which may be the word itself), or C<undef> if
705    the word is not stemmable.
706    
707    =back
708    
709    =cut
710    
711    sub Stem {
712        # Get the parameters.
713        my ($self, $word) = @_;
714        # Declare the return variable.
715        my $retVal;
716        # See if it's stemmable.
717        if ($word =~ /^[A-Za-z]+$/) {
718            # Compute the stem.
719            my $stemList = $self->{stemmer}->stem($word);
720            my $stem = $stemList->[0];
721            # Check to see if it's long enough.
722            if (length $stem >= 3) {
723                # Yes, keep it.
724                $retVal = $stem;
725            } else {
726                # No, use the original word.
727                $retVal = $word;
728            }
729        }
730        # Return the result.
731        return $retVal;
732    }
733    
734    
735  =head3 Build  =head3 Build
736    
737      $sprout->Build();      $sprout->Build();
# Line 1910  Line 1964 
1964      if ($featureID =~ /^fig\|(\d+\.\d+)/) {      if ($featureID =~ /^fig\|(\d+\.\d+)/) {
1965          $retVal = $1;          $retVal = $1;
1966      } else {      } else {
1967            # Find the feature by alias.
1968            my ($realFeatureID) = $self->FeaturesByAlias($featureID);
1969            if ($realFeatureID && $realFeatureID =~ /^fig\|(\d+\.\d+)/) {
1970                $retVal = $1;
1971            } else {
1972                # Use the external table.
1973                my ($org) = $self->GetFlat(['ExternalAliasOrg'], "ExternalAliasOrg(id) = ?",
1974                                           [$featureID], "ExternalAliasOrg(org)");
1975                if ($org) {
1976                    $retVal = $org;
1977                } else {
1978          Confess("Invalid feature ID $featureID.");          Confess("Invalid feature ID $featureID.");
1979      }      }
1980            }
1981        }
1982      # Return the value found.      # Return the value found.
1983      return $retVal;      return $retVal;
1984  }  }
# Line 2750  Line 2817 
2817      return @retVal;      return @retVal;
2818  }  }
2819    
 =head3 GetProperties  
   
     my @list = $sprout->GetProperties($fid, $key, $value, $url);  
   
 Return a list of the properties with the specified characteristics.  
   
 Properties are the Sprout analog of the FIG attributes. The call is  
 passed directly to the CustomAttributes or RemoteCustomAttributes object  
 contained in this object.  
   
 This method returns a series of tuples that match the specified criteria. Each tuple  
 will contain an object ID, a key, and one or more values. The parameters to this  
 method therefore correspond structurally to the values expected in each tuple. In  
 addition, you can ask for a generic search by suffixing a percent sign (C<%>) to any  
 of the parameters. So, for example,  
   
     my @attributeList = $sprout->GetProperties('fig|100226.1.peg.1004', 'structure%', 1, 2);  
   
 would return something like  
   
     ['fig}100226.1.peg.1004', 'structure', 1, 2]  
     ['fig}100226.1.peg.1004', 'structure1', 1, 2]  
     ['fig}100226.1.peg.1004', 'structure2', 1, 2]  
     ['fig}100226.1.peg.1004', 'structureA', 1, 2]  
   
 Use of C<undef> in any position acts as a wild card (all values). You can also specify  
 a list reference in the ID column. Thus,  
   
     my @attributeList = $sprout->GetProperties(['100226.1', 'fig|100226.1.%'], 'PUBMED');  
   
 would get the PUBMED attribute data for Streptomyces coelicolor A3(2) and all its  
 features.  
   
 In addition to values in multiple sections, a single attribute key can have multiple  
 values, so even  
   
     my @attributeList = $sprout->GetProperties($peg, 'virulent');  
   
 which has no wildcard in the key or the object ID, may return multiple tuples.  
   
 =over 4  
   
 =item objectID  
   
 ID of object whose attributes are desired. If the attributes are desired for multiple  
 objects, this parameter can be specified as a list reference. If the attributes are  
 desired for all objects, specify C<undef> or an empty string. Finally, you can specify  
 attributes for a range of object IDs by putting a percent sign (C<%>) at the end.  
   
 =item key  
   
 Attribute key name. A value of C<undef> or an empty string will match all  
 attribute keys. If the values are desired for multiple keys, this parameter can be  
 specified as a list reference. Finally, you can specify attributes for a range of  
 keys by putting a percent sign (C<%>) at the end.  
   
 =item values  
   
 List of the desired attribute values, section by section. If C<undef>  
 or an empty string is specified, all values in that section will match. A  
 generic match can be requested by placing a percent sign (C<%>) at the end.  
 In that case, all values that match up to and not including the percent sign  
 will match. You may also specify a regular expression enclosed  
 in slashes. All values that match the regular expression will be returned. For  
 performance reasons, only values have this extra capability.  
   
 =item RETURN  
   
 Returns a list of tuples. The first element in the tuple is an object ID, the  
 second is an attribute key, and the remaining elements are the sections of  
 the attribute value. All of the tuples will match the criteria set forth in  
 the parameter list.  
   
 =back  
   
 =cut  
   
 sub GetProperties {  
     # Get the parameters.  
     my ($self, @parms) = @_;  
     # Declare the return variable.  
     my @retVal = $self->{_ca}->GetAttributes(@parms);  
     # Return the result.  
     return @retVal;  
 }  
   
2820  =head3 FeatureProperties  =head3 FeatureProperties
2821    
2822      my @properties = $sprout->FeatureProperties($featureID);      my @properties = $sprout->FeatureProperties($featureID);
# Line 4033  Line 4014 
4014      # Get the parameters.      # Get the parameters.
4015      my ($self, $searchExpression) = @_;      my ($self, $searchExpression) = @_;
4016      # Perform the standard cleanup.      # Perform the standard cleanup.
4017      my $retVal = $self->ERDB::CleanKeywords($searchExpression);      my $words = $self->ERDB::CleanKeywords($searchExpression);
4018      # Fix the periods in EC and TC numbers.      # Fix the periods in EC and TC numbers.
4019      $retVal =~ s/(\d+|\-)\.(\d+|-)\.(\d+|-)\.(\d+|-)/$1_$2_$3_$4/g;      $words =~ s/(\d+|\-)\.(\d+|-)\.(\d+|-)\.(\d+|-)/$1_$2_$3_$4/g;
4020      # Fix non-trailing periods.      # Fix non-trailing periods.
4021      $retVal =~ s/\.(\w)/_$1/g;      $words =~ s/\.(\w)/_$1/g;
4022      # Fix non-leading minus signs.      # Fix non-leading minus signs.
4023      $retVal =~ s/(\w)[\-]/$1_/g;      $words =~ s/(\w)[\-]/$1_/g;
4024      # Fix the vertical bars and colons      # Fix the vertical bars and colons
4025      $retVal =~ s/(\w)[|:](\w)/$1'$2/g;      $words =~ s/(\w)[|:](\w)/$1'$2/g;
4026        # Now split up the list so that each keyword is in its own string. We keep the delimiters
4027        # because they may contain boolean expression data.
4028        my @words = split /([^A-Za-z'0-9_]+)/, $words;
4029        # We'll convert the stemmable words into stems and re-assemble the result.
4030        my $retVal = "";
4031        for my $word (@words) {
4032            my $stem = $self->Stem($word);
4033            if (defined $stem) {
4034                $retVal .= $stem;
4035            } else {
4036                $retVal .= $word;
4037            }
4038        }
4039        Trace("Cleaned keyword list for \"$searchExpression\" is \"$retVal\".") if T(3);
4040      # Return the result.      # Return the result.
4041      return $retVal;      return $retVal;
4042  }  }
# Line 4171  Line 4166 
4166  }  }
4167    
4168    
4169    =head3 Hint
4170    
4171        my $htmlText = SearchHelper::Hint($wikiPage, $hintText);
4172    
4173    Return the HTML for a small question mark that displays the specified hint text when it is clicked.
4174    This HTML can be put in forms to provide a useful hinting mechanism.
4175    
4176    =over 4
4177    
4178    =item wikiPage
4179    
4180    Name of the wiki page to be popped up when the hint mark is clicked.
4181    
4182    =item hintText
4183    
4184    Text to display for the hint. It is raw html, but may not contain any double quotes.
4185    
4186    =item RETURN
4187    
4188    Returns the html for the hint facility. The resulting html shows a small button-like thing that
4189    uses the standard FIG popup technology.
4190    
4191    =back
4192    
4193    =cut
4194    
4195    sub Hint {
4196        # Get the parameters.
4197        my ($wikiPage, $hintText) = @_;
4198        # Escape the single quotes in the hint text.
4199        my $quotedText = $hintText;
4200        $quotedText =~ s/'/\\'/g;
4201        # Convert the wiki page name to a URL.
4202        my $wikiURL = join("", map { ucfirst $_ } split /\s+/, $wikiPage);
4203        $wikiURL = "$FIG_Config::cgi_url/wiki/view.cgi/FIG/$wikiURL";
4204        # Compute the mouseover script.
4205        my $mouseOver = "doTooltip(this, '$quotedText')";
4206        # Create the html.
4207        my $retVal = "&nbsp;<a href=\"$wikiURL\"><img src=\"$FIG_Config::cgi_url/Html/button-h.png\" class=\"helpicon\" onmouseover=\"$mouseOver\"/></a>";
4208        # Return it.
4209        return $retVal;
4210    }
4211    
4212  1;  1;

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