In case no -logic_name/-analysis_id was supplied, show the list of analyses...

In case no -logic_name/-analysis_id was supplied, show the list of analyses that have no incoming dataflow (and so are candidates for seeding)

scripts/seed_pipeline.pl

@@ -9,65 +9,84 @@ use Bio::EnsEMBL::Hive::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor;
 use Bio::EnsEMBL::Hive::Utils ('destringify', 'stringify', 'script_usage');
 
-my ($reg_conf, $reg_alias, $url, $analysis_id, $logic_name, $input_id);
-
-
-GetOptions(
-            # connect to the database:
-        'reg_conf|regfile=s'    => \$reg_conf,
-        'reg_alias|regname=s'   => \$reg_alias,
-        'url=s'                 => \$url,
-
-            # identify the analysis:
-        'analysis_id=i'         => \$analysis_id,
-        'logic_name=s'          => \$logic_name,
-
-            # specify the input_id (as a string):
-        'input_id=s'            => \$input_id,
-);
-
-my $hive_dba;
-if($reg_conf and $reg_alias) {
-    Bio::EnsEMBL::Registry->load_all($reg_conf);
-    $hive_dba = Bio::EnsEMBL::Registry->get_DBAdaptor($reg_alias, 'hive');
-} elsif($url) {
-    $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new(-url => $url);
-} else {
-    warn "\nERROR: Connection parameters (url or reg_conf+reg_alias) need to be specified\n";
-    script_usage(1);
+sub show_seedable_analyses {
+    my ($hive_dba) = @_;
+
+    my $analyses    = $hive_dba->get_AnalysisAdaptor->fetch_all();
+    my $incoming    = $hive_dba->get_DataflowRuleAdaptor->fetch_HASHED_FROM_to_analysis_url_TO_dataflow_rule_id();
+    my $job_adaptor = $hive_dba->get_AnalysisJobAdaptor;
+
+    print "\nYou haven't specified neither -logic_name nor -analysis_id of the analysis being seeded.\n";
+    print "\nSeedable analyses without incoming dataflow:\n";
+    foreach my $analysis (@$analyses) {
+        my $logic_name = $analysis->logic_name;
+        unless($incoming->{$logic_name}) {
+            print "\t".$logic_name." (".$analysis->dbID.")\n";
+        }
+    }
 }
 
-my $analysis_adaptor = $hive_dba->get_AnalysisAdaptor;
-my $analysis; 
-if($logic_name) {
-    $analysis = $analysis_adaptor->fetch_by_logic_name( $logic_name )
-        or die "Could not fetch analysis '$logic_name'";
-} else {
-    unless($analysis_id) {
-        $analysis_id = 1;
-        warn "Neither -logic_name nor -analysis_id was set, assuming analysis_id='$analysis_id'\n";
+
+sub main {
+    my ($reg_conf, $reg_alias, $url, $analysis_id, $logic_name, $input_id);
+
+    GetOptions(
+                # connect to the database:
+            'reg_conf|regfile=s'    => \$reg_conf,
+            'reg_alias|regname=s'   => \$reg_alias,
+            'url=s'                 => \$url,
+
+                # identify the analysis:
+            'analysis_id=i'         => \$analysis_id,
+            'logic_name=s'          => \$logic_name,
+
+                # specify the input_id (as a string):
+            'input_id=s'            => \$input_id,
+    );
+
+    my $hive_dba;
+    if($reg_conf and $reg_alias) {
+        Bio::EnsEMBL::Registry->load_all($reg_conf);
+        $hive_dba = Bio::EnsEMBL::Registry->get_DBAdaptor($reg_alias, 'hive');
+    } elsif($url) {
+        $hive_dba = Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->new(-url => $url);
+    } else {
+        warn "\nERROR: Connection parameters (url or reg_conf+reg_alias) need to be specified\n";
+        script_usage(1);
     }
-    $analysis = $analysis_adaptor->fetch_by_dbID( $analysis_id )
-        or die "Could not fetch analysis with dbID='$analysis_id'";
-}
 
-unless($input_id) {
-    $input_id = '{}';
-    warn "Since -input_id has not been set, assuming input_id='$input_id'\n";
-}
+    my $analysis_adaptor = $hive_dba->get_AnalysisAdaptor;
+    my $analysis; 
+    if($logic_name) {
+        $analysis = $analysis_adaptor->fetch_by_logic_name( $logic_name )
+            or die "Could not fetch analysis '$logic_name'";
+    } elsif($analysis_id) {
+        $analysis = $analysis_adaptor->fetch_by_dbID( $analysis_id )
+            or die "Could not fetch analysis with dbID='$analysis_id'";
+    } else {
+        show_seedable_analyses($hive_dba);
+        exit(0);
+    }
+
+    unless($input_id) {
+        $input_id = '{}';
+        warn "Since -input_id has not been set, assuming input_id='$input_id'\n";
+    }
 
-    # Make sure all job creations undergo re-stringification
-    # to avoid alternative "spellings" of the same input_id hash:
-$input_id = stringify( destringify( $input_id ) ); 
+        # Make sure all job creations undergo re-stringification
+        # to avoid alternative "spellings" of the same input_id hash:
+    $input_id = stringify( destringify( $input_id ) ); 
 
-Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor->CreateNewJob(
-    -analysis       => $analysis,
-    -input_id       => $input_id,
-    -prev_job_id    => undef,       # this job has been created by the initialization script, not by another job
-) or die "Could not create job '$input_id' (it could have been there already)\n";
+    Bio::EnsEMBL::Hive::DBSQL::AnalysisJobAdaptor->CreateNewJob(
+        -analysis       => $analysis,
+        -input_id       => $input_id,
+        -prev_job_id    => undef,       # this job has been created by the initialization script, not by another job
+    ) or die "Could not create job '$input_id' (it could have been there already)\n";
 
-warn "Job '$input_id' in analysis '".$analysis->logic_name."'(".$analysis->dbID.") has been created\n";
+    warn "Job '$input_id' in analysis '".$analysis->logic_name."'(".$analysis->dbID.") has been created\n";
+}
 
+main();
 
 __DATA__