stubs/DevSeedSeeder.php
public function up()
    {

        if ($this->landmark_file) {

            $run_args = [
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'seqtype' => $this->landmark_type,
                'method' => 2, //default insert and update
                'match_type' => 1, //unique name default
                //optional
                're_name' => null,
                're_uname' => null,
                're_accession' => null,
                'db_id' => null,
                'rel_type' => null,
                're_subject' => null,
                'parent_type' => null,
            ];
            $this->load_landmarks($run_args, $this->landmark_file);
        }

        if ($this->gff_file) {
            $run_args = [
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'organism_id' => $this->organism->organism_id,
                'use_transaction' => 1,
                'add_only' => 0,
                'update' => 1,
                'create_organism' => 0,
                'create_target' => 0,

                ///regexps for mRNA and protein.
                're_mrna' => null,
                're_protein' => $this->prot_regexp,
                //optional
                'target_organism_id' => null,
                'target_type' => null,
                'start_line' => null,
                'landmark_type' => null,
                'alt_id_attr' => null,
            ];
            $this->load_GFF($run_args, $this->gff_file);
        }

        if ($this->mRNA_file) {

            $run_args = [
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'seqtype' => 'mRNA',
                'method' => 2, //default insert and update
                'match_type' => 1, //unique name default
                //optional
                're_name' => null,
                're_uname' => null,
                're_accession' => null,
                'db_id' => null,
                'rel_type' => null,
                're_subject' => null,
                'parent_type' => null,
            ];
            $this->load_mRNA_FASTA($run_args, $this->mRNA_file);
        }

        if ($this->protein_file) {
            $run_args = [
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'seqtype' => 'polypeptide',
                'method' => 2,
                'match_type' => 1,
                //optional
                're_name' => null,
                're_uname' => null,
                're_accession' => null,
                'db_id' => null,
            ];

            if ($this->prot_regexp) {
                //links polypeptide to mRNA
                $run_args['rel_type'] = 'derives_from';
                $run_args['re_subject'] = $this->prot_regexp;
                $run_args['parent_type'] = 'mRNA';
            }
            $this->load_polypeptide_FASTA($run_args, $this->protein_file);
        }

        if ($this->interpro_file) {

            $run_args = [
                'analysis_id' => $this->sequence_analysis->analysis_id,
                //optional
                'query_type' => 'mRNA',
                'query_re' => $this->prot_regexp,
                'query_uniquename' => null,
                'parsego' => true,
            ];

            $this->load_interpro_annotations($run_args, $this->interpro_file);
        }

        if ($this->blast_file) {
            $run_args = [
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'no_parsed' => 25,//number results to parse
                'query_type' => 'mRNA',
                //optional
                'blastdb' => $this->blastdb->db_id,
                'blastfile_ext' => null,
                'is_concat' => 0,
                'query_re' => null,
                'query_uniquename' => 0,
            ];

            $this->load_blast_annotations($run_args, $this->blast_file);
        }

        if ($this->biomaterial_file) {
            $run_args = [
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
            ];
            //optional: specifies specific CVterms for properties/property values.  Not used here.
            //'cvterm_configuration' => NULL,
            //'cvalue_configuration' => NULL];

            $this->load_biomaterials($run_args, $this->biomaterial_file);
        }

        if ($this->expression_file) {
            $run_args = [
                'filetype' => 'mat', //matrix file type
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
                //optional
                'fileext' => null,
                're_start' => null,
                're_stop' => null,
                'feature_uniquenames' => null,
                'quantificationunits' => null,
                'seqtype' => 'mRNA',
            ];
            $this->load_expression($run_args, $this->expression_file);
        }
    }
public function up()
    {

        if ($this->landmark_file) {

            $run_args = [
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'seqtype' => $this->landmark_type,
                'method' => 2, //default insert and update
                'match_type' => 1, //unique name default
                //optional
                're_name' => null,
                're_uname' => null,
                're_accession' => null,
                'db_id' => null,
                'rel_type' => null,
                're_subject' => null,
                'parent_type' => null,
            ];
            $this->load_landmarks($run_args, $this->landmark_file);
        }

        if ($this->gff_file) {
            $run_args = [
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'organism_id' => $this->organism->organism_id,
                'use_transaction' => 1,
                'add_only' => 0,
                'update' => 1,
                'create_organism' => 0,
                'create_target' => 0,

                ///regexps for mRNA and protein.
                're_mrna' => null,
                're_protein' => $this->prot_regexp,
                //optional
                'target_organism_id' => null,
                'target_type' => null,
                'start_line' => null,
                'landmark_type' => null,
                'alt_id_attr' => null,
            ];
            $this->load_GFF($run_args, $this->gff_file);
        }

        if ($this->mRNA_file) {

            $run_args = [
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'seqtype' => 'mRNA',
                'method' => 2, //default insert and update
                'match_type' => 1, //unique name default
                //optional
                're_name' => null,
                're_uname' => null,
                're_accession' => null,
                'db_id' => null,
                'rel_type' => null,
                're_subject' => null,
                'parent_type' => null,
            ];
            $this->load_mRNA_FASTA($run_args, $this->mRNA_file);
        }

        if ($this->protein_file) {
            $run_args = [
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'seqtype' => 'polypeptide',
                'method' => 2,
                'match_type' => 1,
                //optional
                're_name' => null,
                're_uname' => null,
                're_accession' => null,
                'db_id' => null,
            ];

            if ($this->prot_regexp) {
                //links polypeptide to mRNA
                $run_args['rel_type'] = 'derives_from';
                $run_args['re_subject'] = $this->prot_regexp;
                $run_args['parent_type'] = 'mRNA';
            }
            $this->load_polypeptide_FASTA($run_args, $this->protein_file);
        }

        if ($this->interpro_file) {

            $run_args = [
                'analysis_id' => $this->sequence_analysis->analysis_id,
                //optional
                'query_type' => 'mRNA',
                'query_re' => $this->prot_regexp,
                'query_uniquename' => null,
                'parsego' => true,
            ];

            $this->load_interpro_annotations($run_args, $this->interpro_file);
        }

        if ($this->blast_file) {
            $run_args = [
                'analysis_id' => $this->sequence_analysis->analysis_id,
                'no_parsed' => 25,//number results to parse
                'query_type' => 'mRNA',
                //optional
                'blastdb' => $this->blastdb->db_id,
                'blastfile_ext' => null,
                'is_concat' => 0,
                'query_re' => null,
                'query_uniquename' => 0,
            ];

            $this->load_blast_annotations($run_args, $this->blast_file);
        }

        if ($this->biomaterial_file) {
            $run_args = [
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
            ];
            //optional: specifies specific CVterms for properties/property values.  Not used here.
            //'cvterm_configuration' => NULL,
            //'cvalue_configuration' => NULL];

            $this->load_biomaterials($run_args, $this->biomaterial_file);
        }

        if ($this->expression_file) {
            $run_args = [
                'filetype' => 'mat', //matrix file type
                'organism_id' => $this->organism->organism_id,
                'analysis_id' => $this->sequence_analysis->analysis_id,
                //optional
                'fileext' => null,
                're_start' => null,
                're_stop' => null,
                'feature_uniquenames' => null,
                'quantificationunits' => null,
                'seqtype' => 'mRNA',
            ];
            $this->load_expression($run_args, $this->expression_file);
        }
    }
Runs all loaders.
Will only run loaders where the files have been uncommented at the start
of the class.