GenomeFileUtil prod vs current diff

gfu-diff.diff

diff --git a/GenomeFileUtil.spec b/GenomeFileUtil.spec
index 9c8c209..d2cb40c 100644
--- a/GenomeFileUtil.spec
+++ b/GenomeFileUtil.spec
@@ -19,18 +19,18 @@ module GenomeFileUtil {
 
     typedef mapping<string, string> usermeta;
 
-    /*
+    /* 
     genome_name - becomes the name of the object
     workspace_name - the name of the workspace it gets saved to.
     source - Source of the file typically something like RefSeq or Ensembl
     taxon_ws_name - where the reference taxons are : ReferenceTaxons
     taxon_id - if defined, will try to link the Genome to the specified
         taxonomy id in lieu of performing the lookup during upload
-    release - Release or version number of the data
+    release - Release or version number of the data 
           per example Ensembl has numbered releases of all their data: Release 31
-    generate_ids_if_needed - If field used for feature id is not there,
+    generate_ids_if_needed - If field used for feature id is not there, 
           generate ids (default behavior is raising an exception)
-    genetic_code - Genetic code of organism. Overwrites determined GC from
+    genetic_code - Genetic code of organism. Overwrites determined GC from 
           taxon object
     scientific_name - will be used to set the scientific name of the genome
         and link to a taxon
@@ -66,7 +66,7 @@ module GenomeFileUtil {
                 returns (GenomeSaveResult result) authentication required;
 
     /*
-        is_gtf - optional flag switching export to GTF format (default is 0,
+        is_gtf - optional flag switching export to GTF format (default is 0, 
             which means GFF)
         target_dir - optional target directory to create file in (default is
             temporary folder with name 'gff_<timestamp>' created in scratch)
@@ -88,32 +88,6 @@ module GenomeFileUtil {
     funcdef genome_to_gff(GenomeToGFFParams params)
                 returns (GenomeToGFFResult result) authentication required;
 
-    /*
-        is_gtf - optional flag switching export to GTF format (default is 0,
-            which means GFF)
-        target_dir - optional target directory to create file in (default is
-            temporary folder with name 'gff_<timestamp>' created in scratch)
-    */
-
-    typedef structure {
-        string genome_ref;
-        list <string> ref_path_to_genome;
-        boolean is_gtf;
-        string target_dir;
-    } MetagenomeToGFFParams;
-
-    typedef structure {
-        string file_path;
-        boolean from_cache;
-    } MetagenomeToGFFResult;
-
-    typedef structure {
-        string metagenome_ref;
-    } MetagenomeSaveResult;
-
-    funcdef metagenome_to_gff(MetagenomeToGFFParams params)
-                returns (MetagenomeToGFFResult result) authentication required;
-
     typedef structure {
         string genome_ref;
         list <string> ref_path_to_genome;
@@ -196,16 +170,16 @@ module GenomeFileUtil {
     funcdef export_genome_features_protein_to_fasta(ExportParams params)
                 returns (ExportOutput output) authentication required;
 
-    /*
+    /* 
     genome_name - becomes the name of the object
     workspace_name - the name of the workspace it gets saved to.
     source - Source of the file typically something like RefSeq or Ensembl
     taxon_ws_name - where the reference taxons are : ReferenceTaxons
     taxon_id - if defined, will try to link the Genome to the specified
         taxonomy id in lieu of performing the lookup during upload
-    release - Release or version number of the data
+    release - Release or version number of the data 
           per example Ensembl has numbered releases of all their data: Release 31
-    genetic_code - Genetic code of organism. Overwrites determined GC from
+    genetic_code - Genetic code of organism. Overwrites determined GC from 
           taxon object
     scientific_name - will be used to set the scientific name of the genome
         and link to a taxon
@@ -236,39 +210,6 @@ module GenomeFileUtil {
     funcdef fasta_gff_to_genome_json(FastaGFFToGenomeParams params)
                 returns (UnspecifiedObject genome) authentication required;
 
-    /*
-    genome_name - becomes the name of the object
-    workspace_name - the name of the workspace it gets saved to.
-    source - Source of the file typically something like RefSeq or Ensembl
-    taxon_ws_name - where the reference taxons are : ReferenceTaxons
-    taxon_id - if defined, will try to link the Genome to the specified
-        taxonomy id in lieu of performing the lookup during upload
-    release - Release or version number of the data
-          per example Ensembl has numbered releases of all their data: Release 31
-    genetic_code - Genetic code of organism. Overwrites determined GC from
-          taxon object
-    scientific_name - will be used to set the scientific name of the genome
-        and link to a taxon
-    generate_missing_genes - If the file has CDS or mRNA with no corresponding
-        gene, generate a spoofed gene. Off by default
-    */
-
-    typedef structure {
-        File fasta_file;
-        File gff_file;
-
-        string genome_name;
-        string workspace_name;
-
-        string source;
-        string scientific_name;
-        usermeta metadata;
-        boolean generate_missing_genes;
-    } FastaGFFToMetagenomeParams;
-
-    funcdef fasta_gff_to_metagenome(FastaGFFToMetagenomeParams params)
-                returns (MetagenomeSaveResult returnVal) authentication required;
-
     typedef structure {
         string workspace;
         string name;