#!/usr/local/bin/perl ############################################################################### # Program : GetInteractions # Author : Eric Deutsch # $Id$ # # Description : This program that allows users to # browse through the list of possible peptides # # SBEAMS is Copyright (C) 2000-2005 Institute for Systems Biology # This program is governed by the terms of the GNU General Public License (GPL) # version 2 as published by the Free Software Foundation. It is provided # WITHOUT ANY WARRANTY. See the full description of GPL terms in the # LICENSE file distributed with this software. # ############################################################################### ############################################################################### # Set up all needed modules and objects ############################################################################### use strict; use Getopt::Long; use FindBin; use lib "$FindBin::Bin/../../lib/perl"; use vars qw ($sbeams $sbeamsMOD $q $current_contact_id $current_username $PROG_NAME $USAGE %OPTIONS $QUIET $VERBOSE $DEBUG $DATABASE $TABLE_NAME $PROGRAM_FILE_NAME $CATEGORY $DB_TABLE_NAME @MENU_OPTIONS); use SBEAMS::Connection qw($q); use SBEAMS::Connection::Settings; use SBEAMS::Connection::Tables; use SBEAMS::Interactions; use SBEAMS::Interactions::Settings; use SBEAMS::Interactions::Tables; $sbeams = new SBEAMS::Connection; $sbeamsMOD = new SBEAMS::Interactions; $sbeamsMOD->setSBEAMS($sbeams); $sbeams->setSBEAMS_SUBDIR($SBEAMS_SUBDIR); #use CGI; #$q = new CGI; ############################################################################### # Set program name and usage banner for command like use ############################################################################### $PROG_NAME = $FindBin::Script; $USAGE = <Authenticate() and exit if it fails or continue if it works. ############################################################################### sub main { #### Do the SBEAMS authentication and exit if a username is not returned exit unless ($current_username = $sbeams->Authenticate( #permitted_work_groups_ref=>['Interactions_user','Interactions_admin', # 'Interactions_readonly'], #connect_read_only=>1, #allow_anonymous_access=>1, )); #### Read in the default input parameters my %parameters; my $n_params_found = $sbeams->parse_input_parameters( q=>$q,parameters_ref=>\%parameters); #$sbeams->printDebuggingInfo($q); #### Process generic "state" parameters before we start $sbeams->processStandardParameters(parameters_ref=>\%parameters); #### Decide what action to take based on information so far if ($parameters{action} eq "???") { # Some action } else { $sbeamsMOD->printPageHeader(); handle_request(ref_parameters=>\%parameters); $sbeamsMOD->printPageFooter(); } } # end main ############################################################################### # Handle Request ############################################################################### sub handle_request { my %args = @_; #### Process the arguments list my $ref_parameters = $args{'ref_parameters'} || die "ref_parameters not passed"; my %parameters = %{$ref_parameters}; #### Define some generic varibles my ($i,$element,$key,$value,$line,$result,$sql); #### Define some variables for a query and resultset my %resultset = (); my $resultset_ref = \%resultset; my (%url_cols,%hidden_cols,%max_widths,$show_sql); #### Read in the standard form values my $apply_action = $parameters{'action'} || $parameters{'apply_action'}; my $TABLE_NAME = $parameters{'QUERY_NAME'}; #### Set some specific settings for this program my $CATEGORY="Browse Interactions"; $TABLE_NAME="IN_GetInteractions" unless ($TABLE_NAME); ($PROGRAM_FILE_NAME) = $sbeamsMOD->returnTableInfo($TABLE_NAME,"PROGRAM_FILE_NAME"); my $base_url = "$CGI_BASE_DIR/$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME"; #### Get the columns and input types for this table/query my @columns = $sbeamsMOD->returnTableInfo($TABLE_NAME,"ordered_columns"); my %input_types = $sbeamsMOD->returnTableInfo($TABLE_NAME,"input_types"); #### Read the input parameters for each column my $n_params_found = $sbeams->parse_input_parameters( q=>$q,parameters_ref=>\%parameters, columns_ref=>\@columns,input_types_ref=>\%input_types); #### If the apply action was to recall a previous resultset, do it my %rs_params = $sbeams->parseResultSetParams(q=>$q); if ($apply_action eq "VIEWRESULTSET") { $sbeams->readResultSet(resultset_file=>$rs_params{set_name}, resultset_ref=>$resultset_ref,query_parameters_ref=>\%parameters); $n_params_found = 99; } #### Set some reasonable defaults if no parameters supplied unless ($n_params_found) { $parameters{input_form_format} = "minimum_detail"; } #### Apply any parameter adjustment logic unless ($parameters{project_id}) { $parameters{project_id} = $sbeams->getCurrent_project_id(); } #### Display the user-interaction input form $sbeams->display_input_form( TABLE_NAME=>$TABLE_NAME,CATEGORY=>$CATEGORY,apply_action=>$apply_action, PROGRAM_FILE_NAME=>$PROGRAM_FILE_NAME, parameters_ref=>\%parameters, input_types_ref=>\%input_types, ); #### Display the form action buttons $sbeams->display_form_buttons(TABLE_NAME=>$TABLE_NAME); #### Finish the upper part of the page and go begin the full-width #### data portion of the page $sbeams->display_page_footer(close_tables=>'YES', separator_bar=>'YES',display_footer=>'NO'); ######################################################################### #### Process all the constraints #build the interaction detail constraint # 1 = intra # 2 = inter # 3 = all this is the default my $detailedClause; if ($parameters{interactionDetailConstraintID} == 1) { $detailedClause = " AND (I.while_member_of_bioentity1_id is not NULL AND I.while_member_of_bioentity2_id is not NULL)"; } elsif ($parameters{interactionDetailConstraintID} == 2) { $detailedClause = "AND (I.while_member_of_bioentity1_id is NULL AND I.while_member_of_bioentity2_id is NULL)"; } #build the parent constraint # 4 = with parent constraint # 5 = no parent constraint this is the default my $parentString; my $parentWhere; my @parent1Array; my @parent2Array; my $parentFlag = $parameters{parentConstraintID}; @parent1Array = ["bioentity1_parent", "BE1P.bioentity_common_name", "BioEntity 1 Parent"] if $parentFlag == 4; @parent2Array = ["bioentity2_parent", "BE2P.bioentity_common_name", "BioEntity 2 Parent"] if $parentFlag == 4; $parentString =" LEFT JOIN $TBIN_BIOENTITY_MEMBER BEM1 ON ( BE1.bioentity_id = BEM1.child_bioentity_id) LEFT JOIN $TBIN_BIOENTITY BE1P ON ( BEM1.parent_bioentity_id = BE1P.bioentity_id ) LEFT JOIN $TBIN_BIOENTITY_MEMBER BEM2 ON ( BE2.bioentity_id = BEM2.child_bioentity_id) LEFT JOIN $TBIN_BIOENTITY BE2P ON ( BEM2.parent_bioentity_id = BE2P.bioentity_id )" if $parentFlag == 4; $parentWhere = " AND ( BEM1.record_status != 'D' OR BEM1.record_status IS NULL ) AND ( BEM2.record_status != 'D' OR BEM2.record_status IS NULL )" if $parentFlag == 4; #### Build PROJECT_ID constraint my $project_clause = $sbeams->parseConstraint2SQL( constraint_column=>"IG.project_id", constraint_type=>"int_list", constraint_name=>"Projects", constraint_value=>$parameters{project_id} ); return if ($project_clause eq '-1'); #### If no valid project_id was selected, stop here unless ($parameters{project_id}) { if (!$apply_action && $sbeams->output_mode() eq 'html') { print "

Begin by selecting one or more projects, selecting ". "any additional appropriate constraints, and pressing [QUERY]

\n"; return; } $sbeams->reportException( state => 'ERROR', type => 'INSUFFICIENT CONSTRAINTS', message => "You must select at least one valid Project", ); return; } #### Build ORGANISM_ID constraint my $organism_clause = $sbeams->parseConstraint2SQL( constraint_column=>"IG.organism_id", constraint_type=>"int_list", constraint_name=>"Organisms", constraint_value=>$parameters{organism_id} ); return if ($organism_clause eq '-1'); #### Build INTERACTION_GROUP_ID constraint my $interaction_group_clause = $sbeams->parseConstraint2SQL( constraint_column=>"IG.interaction_group_id", constraint_type=>"int_list", constraint_name=>"Interaction Groups", constraint_value=>$parameters{interaction_group_id} ); return if ($interaction_group_clause eq '-1'); #### Build BIOENTITY_ID constraint my $bioentity_clause = $sbeams->parseConstraint2SQL( constraint_column=>"bioentity_id", constraint_type=>"int_list", constraint_name=>"BioEntity List", constraint_value=>$parameters{bioentity_id} ); return if ($bioentity_clause eq '-1'); #### Translate to look in both sides if ($bioentity_clause =~ /(\s+AND )(bioentity_id IN \( [\d,]+ \))$/) { $bioentity_clause = $1."( BE1.$2 OR BE2.$2 )"; } #### Build BIOENTITY_NAME constraint my $bioentity_common_name_clause = $sbeams->parseConstraint2SQL( constraint_column=>"bioentity_common_name", constraint_type=>"plain_text", constraint_name=>"BioEntity Common Name", constraint_value=>$parameters{bioentity_common_name} ); return if ($bioentity_common_name_clause eq '-1'); #### Translate to look in both sides #if ($bioentity_common_name_clause =~ /(\s+AND )(bioentity_common_name LIKE .+)$/) { # $bioentity_common_name_clause = $1."( BE1.$2 OR BE2.$2 )"; #} #### Need more advanced replacer because of multi-param functionality while ($bioentity_common_name_clause =~ /(bioentity_common_name LIKE '.+?')/) { my $orig = $1; my $new = $orig; $new =~ s/common/xxyyzz/; $bioentity_common_name_clause =~ s/$orig/( BE1.$new OR BE2.$new )/; } $bioentity_common_name_clause =~ s/xxyyzz/common/g; #### Build INTERACTION_TYPE_ID constraint my $interaction_type_clause = $sbeams->parseConstraint2SQL( constraint_column=>"IT.interaction_type_id", constraint_type=>"int_list", constraint_name=>"Interaction Tyoe", constraint_value=>$parameters{interaction_type_id} ); return if ($interaction_type_clause eq '-1'); #### Build SORT ORDER my $order_by_clause = ""; if ($parameters{sort_order}) { if ($parameters{sort_order} =~ /SELECT|TRUNCATE|DROP|DELETE|FROM|GRANT/i) { print "

Cannot parse Sort Order! Check syntax.

\n\n"; return; } else { $order_by_clause = " ORDER BY $parameters{sort_order}"; } } #### Build ROWCOUNT constraint $parameters{row_limit} = 5000 unless ($parameters{row_limit} > 0 && $parameters{row_limit}<=1000000); my $limit_clause = $sbeams->buildLimitClause( row_limit=>$parameters{row_limit}); #### Define some variables needed to build the query my @column_array; my @additional_columns = (); #### Add in some extra columns if the user wants to see them if ( $parameters{display_options} =~ /ShowExtraProteinProps/ || $parameters{display_options} =~ /GroupCount/ ) { @additional_columns = ( ["fav_codon_frequency","STR(BPS.fav_codon_frequency,10,3)","Favored Codon Frequency"], ["n_transmembrane_regions","BPS.n_transmembrane_regions","Number of Transmembrane Regions"], ["protein_length","DATALENGTH(BS.biosequence_seq)","Protein Length"], @additional_columns, ); } #### Define the desired columns in the query #### [friendly name used in url_cols,SQL,displayed column title] @column_array = ( ["interaction_id","I.interaction_id","Interaction ID"], ["bioentity1_common_name","BE1.bioentity_common_name","BioEntity 1 Common Name"], ["bioentity1_link","'[Edit]'","BE1 Link"], ["bioentity1_url","'$SERVER_BASE_DIR$CGI_BASE_DIR/$SBEAMS_SUBDIR/ManageTable.cgi?TABLE_NAME=IN_Bioentity&bioentity_id='+STR(BE1.bioentity_id)","bioentity1_url"], ["bioentity1_canonical_name","BE1.bioentity_canonical_name","BioEntity 1 Canonical Name"], ["bioentity1_full_name","BE1.bioentity_full_name","BioEntity 1 Full Name"], ["bioentity1_state_name","BES1.bioentity_state_name","BioEntity 1 State Name"], ["bioentity1_organism", "O1.full_name", "BioEntity 1 Organism"], ["bioentity1_type", "BET1.bioentity_type_name", "BioEntity 1 Type"], @parent1Array, ["regulatory_feature_name1","RF1.regulatory_feature_name","Regulatory Feature 1 Name"], ["interaction_type_name","IT.interaction_type_name","Interaction Type Name"], ["bioentity2_common_name","BE2.bioentity_common_name","BioEntity 2 Common Name"], ["bioentity2_link","'[Edit]'","BE2 Link"], ["bioentity2_url","'$SERVER_BASE_DIR$CGI_BASE_DIR/$SBEAMS_SUBDIR/ManageTable.cgi?TABLE_NAME=IN_Bioentity&bioentity_id='+STR(BE2.bioentity_id)","bioentity2_url"], ["bioentity2_canonical_name","BE2.bioentity_canonical_name","BioEntity 2 Canonical Name"], ["bioentity2_full_name","BE2.bioentity_full_name","BioEntity 2 Full Name"], ["bioentity2_state_name","BES2.bioentity_state_name","BioEntity 2 State Name"], ["bioentity2_organism", "O2.full_name", "BioEntity 2 Organism"], ["bioentity2_type","BET2.bioentity_type_name", "BioEntity 2 Type"], @parent2Array, ["regulatory_feature_name2","RF2.regulatory_feature_name","Regulatory Feature 2 Name"], ["bioentity_id1","BE1.bioentity_id","BioEntity 1 ID"], ["bioentity_id2","BE2.bioentity_id","BioEntity 2 ID"], ["Publication_id","PUB.publication_name+ ' (PMID ' + PUB.pubmed_id +')'", "PubMed ID"], ["publication_url","PUB.pubmed_id","publication_url"], ["interaction_group_id","IG.interaction_group_id","interaction_group_id"], ["interaction_group_name","IG.interaction_group_name","interaction_group_name"], ["project_id","IG.project_id","project_id"], @additional_columns, ); ############# ## = = "http://www.ncbi.nlm.nih.gov/entrez/utils/pmfetch.fcgi?". ## "db=PubMed&id=$PubMedID&report=xml&mode=tex ########### #### Set flag to display SQL statement if user selected if ( $parameters{display_options} =~ /ShowSQL/ ) { $show_sql = 1; } #### Build the columns part of the SQL statement my %colnameidx = (); my @column_titles = (); my $columns_clause = $sbeams->build_SQL_columns_list( column_array_ref=>\@column_array, colnameidx_ref=>\%colnameidx, column_titles_ref=>\@column_titles ); #### Build the query $sql = qq~ SELECT $limit_clause->{top_clause} $columns_clause FROM $TBIN_INTERACTION I LEFT JOIN $TBIN_INTERACTION_GROUP IG ON ( I.interaction_group_id = IG.interaction_group_id ) LEFT JOIN $TBIN_INTERACTION_TYPE IT ON ( I.interaction_type_id = IT.interaction_type_id ) LEFT JOIN $TBIN_BIOENTITY BE1 ON ( I.bioentity1_id = BE1.bioentity_id ) LEFT JOIN $TB_ORGANISM O1 ON ( BE1.organism_id = O1.organism_id ) LEFT JOIN $TBIN_BIOENTITY BE2 ON ( I.bioentity2_id = BE2.bioentity_id ) LEFT JOIN $TB_ORGANISM O2 ON ( BE2.organism_id = O2.organism_id ) LEFT JOIN $TBIN_BIOENTITY_STATE BES1 ON ( I.bioentity1_state_id = BES1.bioentity_state_id ) LEFT JOIN $TBIN_BIOENTITY_STATE BES2 ON ( I.bioentity2_state_id = BES2.bioentity_state_id ) LEFT JOIN $TBIN_BIOENTITY_TYPE BET1 ON ( BE1.bioentity_type_id = BET1.bioentity_type_id) LEFT JOIN $TBIN_BIOENTITY_TYPE BET2 ON ( BE2.bioentity_type_id = BET2.bioentity_type_id) $parentString LEFT JOIN $TBIN_REGULATORY_FEATURE RF1 ON ( I.regulatory_feature1_id = RF1.regulatory_feature_id ) LEFT JOIN $TBIN_REGULATORY_FEATURE RF2 ON ( I.regulatory_feature2_id = RF2.regulatory_feature_id ) LEFT JOIN $TBIN_PUBLICATION PUB ON (I.publication_id = PUB.publication_id) WHERE 1 = 1 AND I.record_status != 'D' AND ( BE1.record_status != 'D' OR BE1.record_status IS NULL ) AND ( BE2.record_status != 'D' OR BE2.record_status IS NULL ) AND ( BES1.record_status != 'D' OR BES1.record_status IS NULL ) AND ( BES2.record_status != 'D' OR BES2.record_status IS NULL ) $parentWhere AND ( RF1.record_status != 'D' OR RF1.record_status IS NULL ) AND ( RF2.record_status != 'D' OR RF2.record_status IS NULL ) $project_clause $organism_clause $interaction_group_clause $bioentity_clause $bioentity_common_name_clause $interaction_type_clause $detailedClause $limit_clause->{trailing_limit_clause} ~; #AND $TBIN_INTERACTION.WHILE_MEMBER_OF_BIOENTITY1_ID IS NULL AND # $TBIN_INTERACTION.WHILE_MEMBER_OF_BIOENTITY2_ID IS NUL #### Certain types of actions should be passed to links my $pass_action = "QUERY"; $pass_action = $apply_action if ($apply_action =~ /QUERY/i); #### Pass nearly all of the constraints down to a child query my @parameters_to_pass; my $parameters_list = ''; while ( ($key,$value) = each %input_types ) { if ($key ne 'display_options' && $key ne 'n_occurrences' && $key ne 'biosequence_name_constraint' && $key ne 'xx_constraint' ) { if ($parameters{$key}) { push(@parameters_to_pass,"$key=$parameters{$key}"); } } } if (@parameters_to_pass) { $parameters_list = join('&',@parameters_to_pass); } #### Define the hypertext links for columns that need them %url_cols = ( 'Interaction ID' => "$CGI_BASE_DIR/$SBEAMS_SUBDIR/ManageTable.cgi?TABLE_NAME=IN_interaction&interaction_id=\%V", 'Interaction ID_ATAG' => 'TARGET="Win1"', 'BE1 Link' => "$CGI_BASE_DIR/$SBEAMS_SUBDIR/ManageTable.cgi?TABLE_NAME=IN_bioentity&bioentity_id=\%$colnameidx{bioentity_id1}V", 'BE1 Link_ATAG' => 'TARGET="Win1"', 'BE2 Link' => "$CGI_BASE_DIR/$SBEAMS_SUBDIR/ManageTable.cgi?TABLE_NAME=IN_bioentity&bioentity_id=\%$colnameidx{bioentity_id2}V", 'BE2 Link_ATAG' => 'TARGET="Win1"', 'BioEntity 1 Common Name' => "$base_url?bioentity_common_name=\%$colnameidx{bioentity_common_name1}V&apply_action=$pass_action", 'BioEntity 2 Common Name' => "$base_url?bioentity_common_name=\%$colnameidx{bioentity_common_name2}V&apply_action=$pass_action", 'PubMed ID' => "http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=\%$colnameidx{publication_url}V&dopt=Abstract", ); #### Define columns that should be hidden in the output table %hidden_cols = ('BioEntity 1 ID' => 1, 'BioEntity 2 ID' => 1, ); unless ( $parameters{display_options} =~ /ShowReg/) { %hidden_cols = ( %hidden_cols, 'Regulatory Feature 1 Name' => 1, 'Regulatory Feature 2 Name' => 1, 'bioentity1_url' => 1, 'bioentity2_url' => 1, 'publication_url'=> 1, 'interaction_group_id'=> 1, 'interaction_group_name'=> 1, 'project_id'=> 1, ); } ######################################################################### #### If QUERY or VIEWRESULTSET was selected, display the data if ($apply_action =~ /QUERY/i || $apply_action eq "VIEWRESULTSET") { #### If the action contained QUERY, then fetch the results from #### the database if ($apply_action =~ /QUERY/i) { #### Show the SQL that will be or was executed $sbeams->display_sql(sql=>$sql) if ($show_sql); #### Fetch the results from the database server $sbeams->fetchResultSet( sql_query=>$sql, resultset_ref=>$resultset_ref, ); #### Store the resultset and parameters to disk resultset cache $rs_params{set_name} = "SETME"; $sbeams->writeResultSet( resultset_file_ref=>\$rs_params{set_name}, resultset_ref=>$resultset_ref, query_parameters_ref=>\%parameters, resultset_params_ref=>\%rs_params, query_name=>"$SBEAMS_SUBDIR/$PROGRAM_FILE_NAME", ); } #### Display the resultset $sbeams->displayResultSet( resultset_ref=>$resultset_ref, query_parameters_ref=>\%parameters, rs_params_ref=>\%rs_params, url_cols_ref=>\%url_cols, hidden_cols_ref=>\%hidden_cols, max_widths=>\%max_widths, column_titles_ref=>\@column_titles, base_url=>$base_url, ); #### Display the resultset controls $sbeams->displayResultSetControls( resultset_ref=>$resultset_ref, query_parameters_ref=>\%parameters, rs_params_ref=>\%rs_params, base_url=>$base_url, ); #### If QUERY was not selected, then tell the user to enter some parameters } else { if ($sbeams->invocation_mode() eq 'http') { print "

Select parameters above and press QUERY

\n"; } else { print "You need to supply some parameters to contrain the query\n"; } } } # end handle_request ############################################################################### # evalSQL # # Callback for translating Perl variables into their values, # especially the global table variables to table names ############################################################################### sub evalSQL { my $sql = shift; print "
$sql
"; print eval "\"$sql\""; if ($@) { print "$@"; } return eval "\"$sql\""; } # end evalSQL