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#!/usr/bin/perl |
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# |
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# @File GraphTraversal.pm |
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# @Author andriy |
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# @Created Jul 1, 2016 10:53:44 AM |
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# |
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use strict; |
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use warnings; |
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use SemMed::Interface::CUI; |
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use SemMed::Interface::Predicate; |
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use SemMed::Interface::DataAccess; |
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use Heap::Priority; |
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package GraphTraversal; |
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my $conn = ""; #used for data access |
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sub new{ |
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my $class = shift; |
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my $conn = shift; |
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my $self = {}; |
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bless $self, $class; |
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return $self; |
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} |
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#given a source CUI-ID and a destination CUI-ID this sub will return the destination CUI containing shortest path data or a |
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#-1 signifying no path was found. Path data in the returned CUI can be access through its methods (ie. $CUI->getPathLength()) |
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#Utilizes Dijktras for finding shortest path between CUI's |
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#INPUT: SOURCE_CUI(string), DESTINATION_CUI(St$gt = new GraphTraversal();ring), WEIGHT_STATISTICAL_MEASURE(string) |
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#OPTIONAL INPUT: , List of predicates to only include, List of Predicates to Ignore |
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sub findShortestPath{ |
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my $self = shift; |
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my $startCui = $conn->getCUI(shift); #ex. heart arrest C0018790 |
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my $endCui = $conn->getCUI(shift); #ex. traffic accidents C0000932 |
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my $statistic = shift; |
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my $includedPredicates = shift; #array reference to list of predicates to include |
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my $excludedPredicates = shift; #array reference to list of predicates to ignore |
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my $currentVertex = $startCui; #starting vertex |
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$currentVertex-> setPathLength(0); #mark first vertex as reached |
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my @edges = (); #this array contains all predicate connections found thus far |
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my $fringe = new Heap::Priority; #this PriorityQueue contains all CUI under consideration for the next shortest path. |
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$fringe->lowest_first(); #set priority to the smallest element |
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my @reached = (); #this array contains references to all CUI's that have already been reached. |
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## load initial set of predicate connections |
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my @query = $conn->getPredicateConnections($startCui, $statistic, $includedPredicates, $excludedPredicates); |
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foreach my $edge (@query){ |
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push @edges, $edge; |
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} |
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while($currentVertex->getId() ne $endCui->getId()){ #while we have not reached the vertex we're searching for |
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$currentVertex->_print(); |
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push @reached, $currentVertex; #add current vertex to reached vertices |
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# $currentVertex->printPath(); |
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foreach my $edge (@edges){ |
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if($edge->getSource()->getId() eq $currentVertex->getId() ){ |
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my $destVertex = $edge->getDestination(); |
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if( not(grep $_->getId() eq $destVertex->getId(), @reached) ){ #if destVertex has not been reached yet |
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if($destVertex->getPathLength() == -1){ |
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$destVertex->setPathLength( $currentVertex->getPathLength() + $edge->getWeight() ); #TODO implement own method |
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$destVertex->setPrevCUI($currentVertex); #save the vertex we arrived from |
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$destVertex->setPrevPredicate($edge -> getPredicate); |
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} |
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if($destVertex->getPathLength() >= ($currentVertex->getPathLength() + $edge->getWeight() ) ){ #TODO |
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$destVertex->setPathLength( $currentVertex->getPathLength() + $edge->getWeight() ); #TODO implement own method |
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$destVertex->setPrevCUI($currentVertex); #save the vertex we arrived fromcd |
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$destVertex->setPrevPredicate($edge -> getPredicate); |
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} |
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# if(not(grep $_->getId() eq $destVertex->getId(), @fringe) ){ |
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$fringe->add($destVertex, $destVertex->getPathLength()); |
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#push onto the queue giving it a priority equal to its edge weight. |
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# } |
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} |
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} |
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} |
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if($fringe->count()==0){ #if fringe is empty,break |
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return -1; |
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} |
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#set current vertex to CUI with smallest aggregate weight |
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$currentVertex = $fringe->pop(); |
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##loads new set of edges from databa$gt = new GraphTraversal();se |
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my @newedges = $conn->getPredicateConnections($currentVertex, $statistic); |
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foreach my $edge (@newedges){ |
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push @edges, $edge; |
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} |
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} |
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push @reached, $currentVertex; #push end cui onto reached as we have found it |
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return $currentVertex; |
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} |
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#finds a path between two given CUI's |
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#utilizes BFS |
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# |
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#INPUT: SOURCE_CUI(string), DESTINATION_CUI(string) |
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#OPTIONAL INPUT: , List of predicates to only include, List of Predicates to Ignore |
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# |
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#OUTPUT: PathLength from SOURCE_CUI to DESTINATION_CUI |
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# |
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# |
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sub findPath{ |
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my $self = shift; |
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my $startCui = shift; #String containing the start cui |
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my $endCui = shift; #String containing the end cui |
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my $includedPredicates = shift; #array reference to list of predicates to include |
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my $excludedPredicates = shift; #array reference to list of predicates to ignore |
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#shift will return head of the queue |
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#push will add element to the queue |
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my @reachedCUI = (); #this array(treated as a queue) will contain the next node we want to go to |
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my @reachedLength = (); #parallel array to hold the length to each cui |
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my $currentCUI = $startCui; |
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my $currentLength = 0; |
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while($currentCUI ne $endCui){ |
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if($currentLength == 10){ |
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return -1; |
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} |
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my @adjacentedges = $conn->getPredicateConnections($conn->getCUI($currentCUI), 1, $includedPredicates, $excludedPredicates); |
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#push new vertices to end of queue |
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foreach my $edge (@adjacentedges){ |
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push @reachedCUI, $edge->getDestination()->getId(); |
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push @reachedLength, ($currentLength + 1); |
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} |
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#pop next vertex from queue |
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$currentCUI = shift @reachedCUI; |
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$currentLength = shift @reachedLength; |
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} |
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return $currentLength; |
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} |
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#finds the aggregate path score between two given CUI's |
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#utilizes BFS |
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# |
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#INPUT: SOURCE_CUI(string), DESTINATION_CUI(string) |
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#OPTIONAL INPUT: statistical measure, List of predicates to only include, List of Predicates to Ignore |
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# |
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#OUTPUT: Aggregate relatedness score(measure specified in parameters) from SOURCE_CUI to DESTINATION_CUI |
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# |
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#TODO |
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sub findPathScore{ |
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my $self = shift; |
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my $startCui = shift; #String containing the start cui |
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my $endCui = shift; #String containing the end cui |
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my $measure = shift; |
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my $includedPredicates = shift; #array reference to list of predicates to include |
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my $excludedPredicates = shift; #array reference to list of predicates to ignore |
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#shift will return head of the queue |
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#push will add element to the queue |
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my @reachedCUI = (); #this array(treated as a queue) will contain the next node we want to go to |
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my @reachedScore = (); #parallel array to hold the score of each cui |
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199
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my $currentCUI = $startCui; |
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my $currentLength = 0; |
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my $iter = 0; |
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while($currentCUI ne $endCui){ |
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$iter++; |
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if($iter % 1000 == 0){ |
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# print STDERR "Buffered CUI's: ". scalar(@reachedCUI)." ==> $iter \n"; |
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} |
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208
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#TODO add threshold |
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# if($currentLength == 10){ |
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# return -1; |
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# } |
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213
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my @adjacentedges = $conn->getPredicateConnections($conn->getCUI($currentCUI), $measure, $includedPredicates, $excludedPredicates); |
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215
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#push new vertices to end of queue |
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foreach my $edge (@adjacentedges){ |
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push @reachedCUI, $edge->getDestination()->getId(); |
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push @reachedScore, ($currentLength + ($edge->getWeight())); |
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} |
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221
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#pop next vertex from queue |
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$currentCUI = shift @reachedCUI; |
223
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$currentLength = shift @reachedScore; |
224
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225
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226
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} |
227
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228
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return $currentLength; |
229
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230
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231
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} |
232
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233
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my @reachedCUI; #this array(treated as a queue) will contain the next node we want to go to |
234
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sub findPathR{ |
235
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my $self = shift; |
236
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my $startCui = shift; #String containing the start cui |
237
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my $endCui = shift; #String containing the end cui |
238
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my $measure = shift; |
239
|
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|
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my $includedPredicates = shift; #array reference to list of predicates to include |
240
|
|
|
|
|
|
|
my $excludedPredicates = shift; #array reference to list of predicates to ignore |
241
|
|
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|
|
|
|
|
242
|
|
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|
|
|
|
@reachedCUI = (); |
243
|
|
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|
|
|
|
|
244
|
|
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|
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|
|
my $pathString = _findPathHelper($endCui, $startCui, "$startCui", $measure, $includedPredicates, $excludedPredicates ); |
245
|
|
|
|
|
|
|
@reachedCUI = (); |
246
|
|
|
|
|
|
|
return $pathString; |
247
|
|
|
|
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|
|
|
248
|
|
|
|
|
|
|
|
249
|
|
|
|
|
|
|
|
250
|
|
|
|
|
|
|
} |
251
|
|
|
|
|
|
|
|
252
|
|
|
|
|
|
|
|
253
|
|
|
|
|
|
|
sub _findPathHelper{ |
254
|
|
|
|
|
|
|
my $self = shift; |
255
|
|
|
|
|
|
|
my $endCui = shift; |
256
|
|
|
|
|
|
|
my $currentCui = shift; |
257
|
|
|
|
|
|
|
my $currentString = shift; |
258
|
|
|
|
|
|
|
my $measure = shift; |
259
|
|
|
|
|
|
|
my $includedPredicates = shift; #array reference to list of predicates to include |
260
|
|
|
|
|
|
|
my $excludedPredicates = shift; #array reference to list of predicates to ignore |
261
|
|
|
|
|
|
|
|
262
|
|
|
|
|
|
|
if($endCui = $currentCui){ |
263
|
|
|
|
|
|
|
return $currentString; |
264
|
|
|
|
|
|
|
} |
265
|
|
|
|
|
|
|
|
266
|
|
|
|
|
|
|
my @adjacentedges = $conn->getPredicateConnections($conn->getCUI($currentCui), $measure, $includedPredicates, $excludedPredicates); |
267
|
|
|
|
|
|
|
|
268
|
|
|
|
|
|
|
#push new vertices to end of queue |
269
|
|
|
|
|
|
|
foreach my $edge (@adjacentedges) { |
270
|
|
|
|
|
|
|
push @reachedCUI, $edge->getDestination()->getId(); |
271
|
|
|
|
|
|
|
} |
272
|
|
|
|
|
|
|
|
273
|
|
|
|
|
|
|
$currentCui = shift @reachedCUI; |
274
|
|
|
|
|
|
|
|
275
|
|
|
|
|
|
|
return _findPathHelper($endCui, $currentCui,"$currentString $currentCui", $measure, $includedPredicates, $excludedPredicates); |
276
|
|
|
|
|
|
|
|
277
|
|
|
|
|
|
|
} |
278
|
|
|
|
|
|
|
1; |
279
|
|
|
|
|
|
|
|