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| 1 : | parrello | 1.1 | #!/usr/bin/perl -w |
| 2 : | |||
| 3 : | package SHSubSearch; | ||
| 4 : | |||
| 5 : | use strict; | ||
| 6 : | use Tracer; | ||
| 7 : | use CGI; | ||
| 8 : | use HTML; | ||
| 9 : | use Sprout; | ||
| 10 : | parrello | 1.6 | use RHFeatures; |
| 11 : | use base 'SearchHelper'; | ||
| 12 : | parrello | 1.1 | |
| 13 : | =head1 Subsystem Feature Search Helper | ||
| 14 : | |||
| 15 : | =head2 Introduction | ||
| 16 : | |||
| 17 : | This search helper displays a subsystem tree and allows the user to | ||
| 18 : | select any node in the tree to get back all of the features in a single | ||
| 19 : | subsystem or all the subsystems in a class. The tree will also have links to | ||
| 20 : | the subsystem display pages. | ||
| 21 : | |||
| 22 : | It has the following extra parameters. | ||
| 23 : | |||
| 24 : | =over 4 | ||
| 25 : | |||
| 26 : | =item specification | ||
| 27 : | |||
| 28 : | A string of the form C<id=>I<string> or C<classification=>I<string>. In the | ||
| 29 : | first case, I<string> is the ID of a subsystem. In the second case, | ||
| 30 : | I<string> is a LIKE-style string that can be used to get subsystems in the | ||
| 31 : | specified class. | ||
| 32 : | |||
| 33 : | =back | ||
| 34 : | |||
| 35 : | =head2 Virtual Methods | ||
| 36 : | |||
| 37 : | =head3 Form | ||
| 38 : | |||
| 39 : | parrello | 1.8 | my $html = $shelp->Form(); |
| 40 : | parrello | 1.1 | |
| 41 : | Generate the HTML for a form to request a new search. | ||
| 42 : | |||
| 43 : | =cut | ||
| 44 : | |||
| 45 : | sub Form { | ||
| 46 : | # Get the parameters. | ||
| 47 : | my ($self) = @_; | ||
| 48 : | # Get the CGI and sprout objects. | ||
| 49 : | my $cgi = $self->Q(); | ||
| 50 : | my $sprout = $self->DB(); | ||
| 51 : | # Start the form. | ||
| 52 : | parrello | 1.9 | my $retVal = $self->FormStart("Search for Genes by Subsystem or Class"); |
| 53 : | parrello | 1.1 | # Create a subsystem tree. |
| 54 : | my $tree = SearchHelper::SubsystemTree($sprout, radio => 1, links => 1); | ||
| 55 : | # Build a form field out of it. | ||
| 56 : | my $treeField = SearchHelper::SelectionTree($cgi, $tree, | ||
| 57 : | name => "specification", | ||
| 58 : | target => "_blank", | ||
| 59 : | selected => $cgi->param("specification")); | ||
| 60 : | # We'll accumulate the form table in here. | ||
| 61 : | my @rows = (); | ||
| 62 : | parrello | 1.3 | # Start with the subsystem tree. |
| 63 : | push @rows, $cgi->Tr($cgi->th({ colspan => 3, align => "center" }, "Subsystem Tree")), | ||
| 64 : | $cgi->Tr($cgi->td({ colspan => 3 }, $treeField)); | ||
| 65 : | parrello | 1.4 | # Put in the keyword search box. |
| 66 : | parrello | 1.1 | my $expressionString = $cgi->param('keywords') || ""; |
| 67 : | parrello | 1.6 | push @rows, RHFeatures::WordSearchRow($self); |
| 68 : | parrello | 1.1 | # Add the special options. |
| 69 : | parrello | 1.6 | push @rows, RHFeatures::FeatureFilterFormRows($self, 'options'); |
| 70 : | parrello | 1.1 | # Finish it off with the submit row. |
| 71 : | push @rows, $self->SubmitRow(); | ||
| 72 : | # Convert the form rows into a table. | ||
| 73 : | $retVal .= $self->MakeTable(\@rows); | ||
| 74 : | # Close the form. | ||
| 75 : | $retVal .= $self->FormEnd(); | ||
| 76 : | # Return the result. | ||
| 77 : | return $retVal; | ||
| 78 : | } | ||
| 79 : | |||
| 80 : | =head3 Find | ||
| 81 : | |||
| 82 : | parrello | 1.8 | my $resultCount = $shelp->Find(); |
| 83 : | parrello | 1.1 | |
| 84 : | Conduct a search based on the current CGI query parameters. The search results will | ||
| 85 : | be written to the session cache file and the number of results will be | ||
| 86 : | returned. If the search parameters are invalid, a result count of C<undef> will be | ||
| 87 : | returned and a result message will be stored in this object describing the problem. | ||
| 88 : | |||
| 89 : | =cut | ||
| 90 : | |||
| 91 : | sub Find { | ||
| 92 : | my ($self) = @_; | ||
| 93 : | # Get the CGI and Sprout objects. | ||
| 94 : | my $cgi = $self->Q(); | ||
| 95 : | my $sprout = $self->DB(); | ||
| 96 : | # Declare the return variable. If it remains undefined, the caller will | ||
| 97 : | # know that an error occurred. | ||
| 98 : | my $retVal; | ||
| 99 : | # Insure we have a specification. | ||
| 100 : | my $spec = $cgi->param('specification'); | ||
| 101 : | if (! $spec) { | ||
| 102 : | $self->SetMessage("No subsystem or class selected."); | ||
| 103 : | } else { | ||
| 104 : | parrello | 1.7 | # We need to build a query to get our features. This involves building |
| 105 : | # a filter clause and a parameter list. | ||
| 106 : | parrello | 1.1 | my ($filterClause, $parameter); |
| 107 : | if ($spec =~ /^id=(.+)$/) { | ||
| 108 : | # Here we're filtering for a single subsystem. | ||
| 109 : | $filterClause = "Subsystem(id) = ?"; | ||
| 110 : | $parameter = $1; | ||
| 111 : | } elsif ($spec =~ /^classification=(.+)$/) { | ||
| 112 : | # Here we're filtering for a class. | ||
| 113 : | $filterClause = "Subsystem(classification) LIKE ?"; | ||
| 114 : | $parameter = $1; | ||
| 115 : | } | ||
| 116 : | # Now we do some validation. | ||
| 117 : | my $keywords = $cgi->param('keywords') || ""; | ||
| 118 : | if (! defined($filterClause)) { | ||
| 119 : | $self->SetMessage("Invalid subsystem specification \"$spec\"."); | ||
| 120 : | } elsif ($self->ValidateKeywords($keywords)) { | ||
| 121 : | # We're valid, so we start by collecting the main parameters for the query. | ||
| 122 : | my @majorParms = (['Subsystem', 'HasRoleInSubsystem', 'Feature'], | ||
| 123 : | $filterClause, [$parameter]); | ||
| 124 : | # The way we execute the query is determined by whether or not | ||
| 125 : | # any keywords were specified. | ||
| 126 : | my $query; | ||
| 127 : | if ($keywords) { | ||
| 128 : | parrello | 1.5 | $self->PrintLine("Word search query submitted.<br />"); |
| 129 : | parrello | 1.1 | $query = $sprout->Search($keywords, 2, @majorParms); |
| 130 : | } else { | ||
| 131 : | parrello | 1.5 | $self->PrintLine("Standard search query submitted.<br />"); |
| 132 : | parrello | 1.1 | $query = $sprout->Get(@majorParms); |
| 133 : | } | ||
| 134 : | parrello | 1.6 | # Get the result helper for a feature search. |
| 135 : | my $rhelp = RHFeatures->new($self); | ||
| 136 : | # Compute the default columns. This is a very simple search which | ||
| 137 : | # has no extra columns. | ||
| 138 : | $self->DefaultColumns($rhelp); | ||
| 139 : | parrello | 1.1 | # Initialize the session file. |
| 140 : | parrello | 1.6 | $self->OpenSession($rhelp); |
| 141 : | parrello | 1.7 | # Clear the result counter. |
| 142 : | parrello | 1.1 | $retVal = 0; |
| 143 : | parrello | 1.7 | # Process the query results. |
| 144 : | parrello | 1.1 | while (my $record = $query->Fetch()) { |
| 145 : | parrello | 1.7 | # Compute the sort key. |
| 146 : | my $sort = $rhelp->SortKey($record); | ||
| 147 : | # Store this feature. | ||
| 148 : | $rhelp->PutData($sort, $record->PrimaryValue('Feature(id)'), $record); | ||
| 149 : | # Increment the result counter. | ||
| 150 : | parrello | 1.1 | $retVal++; |
| 151 : | } | ||
| 152 : | # Close the session file. | ||
| 153 : | $self->CloseSession(); | ||
| 154 : | } | ||
| 155 : | } | ||
| 156 : | # Return the result count. | ||
| 157 : | return $retVal; | ||
| 158 : | } | ||
| 159 : | |||
| 160 : | =head3 Description | ||
| 161 : | |||
| 162 : | parrello | 1.8 | my $htmlText = $shelp->Description(); |
| 163 : | parrello | 1.1 | |
| 164 : | Return a description of this search. The description is used for the table of contents | ||
| 165 : | on the main search tools page. It may contain HTML, but it should be character-level, | ||
| 166 : | not block-level, since the description is going to appear in a list. | ||
| 167 : | |||
| 168 : | =cut | ||
| 169 : | |||
| 170 : | sub Description { | ||
| 171 : | # Get the parameters. | ||
| 172 : | my ($self) = @_; | ||
| 173 : | # Return the result. | ||
| 174 : | return "Search for genes by keyword in a specified subsystem or subsystem class."; | ||
| 175 : | } | ||
| 176 : | |||
| 177 : | parrello | 1.8 | 1; |
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