kb_uploadmethods.spec

/*
A KBase module: kb_uploadmethods
*/

module kb_uploadmethods {

  /* workspace name of the object */
  typedef string workspace_name;

  /*
    Indicates true or false values, false = 0, true = 1
    @range [0,1]
  */
  typedef int boolean;

  /* input and output file path/url */
  typedef string fwd_staging_file_name;
  typedef string rev_staging_file_name;
  typedef string download_type;
  typedef string fwd_file_url;
  typedef string rev_file_url;
  typedef string sequencing_tech;
  typedef string name;
  typedef string single_genome;
  typedef string interleaved;
  typedef string insert_size_mean;
  typedef string insert_size_std_dev;
  typedef string read_orientation_outward;
  typedef string obj_ref;
  typedef string report_name;
  typedef string report_ref;

  typedef structure {
    fwd_file_url fwd_file_url;
    rev_file_url rev_file_url;
    name name;
    single_genome single_genome;
    interleaved interleaved;
    insert_size_mean insert_size_mean;
    insert_size_std_dev insert_size_std_dev;
    read_orientation_outward read_orientation_outward;
  } urls_to_add;

  /*
    sequencing_tech: sequencing technology
    name: output reads file name
    workspace_name: workspace name/ID of the object

    For files in user's staging area:
    fwd_staging_file_name: single-end fastq file name or forward/left paired-end fastq file name from user's staging area
    rev_staging_file_name: reverse/right paired-end fastq file name user's staging area

    For files from web:
    download_type: download type for web source fastq file ('Direct Download', 'FTP', 'DropBox', 'Google Drive')
    fwd_file_url: single-end fastq file URL or forward/left paired-end fastq file URL
    rev_file_url: reverse/right paired-end fastq file URL

    urls_to_add: used for parameter-groups. dict of {fwd_file_url, rev_file_url, name,
          single_genome, interleaved, insert_size_mean and read_orientation_outward}

    Optional Params:
    single_genome: whether the reads are from a single genome or a metagenome.
    interleaved: whether reads is interleaved
    insert_size_mean: mean (average) insert length
    insert_size_std_dev: standard deviation of insert lengths
    read_orientation_outward: whether reads in a pair point outward
  */
  typedef structure {
    workspace_name workspace_name;
    fwd_staging_file_name fwd_staging_file_name;
    rev_staging_file_name rev_staging_file_name;
    download_type download_type;
    fwd_file_url fwd_file_url;
    rev_file_url rev_file_url;
    sequencing_tech sequencing_tech;
    name name;
    urls_to_add urls_to_add;
    single_genome single_genome;
    interleaved interleaved;
    insert_size_mean insert_size_mean;
    insert_size_std_dev insert_size_std_dev;
    read_orientation_outward read_orientation_outward;
  } UploadMethodParams;

  typedef structure {
    obj_ref obj_ref;
    report_name report_name;
    report_ref report_ref;
  } UploadMethodResult;

  funcdef upload_fastq_file(UploadMethodParams params)
    returns (UploadMethodResult returnVal) authentication required;

  /*
    Required:
    genome_name: output genome object name
    workspace_name: workspace name/ID of the object
    For staging area:
    fasta_file: fasta file containing assembled contigs/chromosomes
    gff_file: gff file containing predicted gene models and corresponding features

    Optional params:
    scientific_name - the scientific name of the genome.
    taxon_id - the numeric ID of the NCBI taxon to which this genome belongs.
               If defined, will try to link the Genome to the specified
               taxonomy id in lieu of performing the lookup during upload

    source: Source Of The GFF File. Default to 'User'
    taxon_wsname - where the reference taxons are. Default to 'ReferenceTaxons'
    release: Release Or Version Of The Source Data
    genetic_code: Genetic Code For The Organism
    type: 'Reference', 'User upload', 'Representative'
  */
  typedef structure {
    string fasta_file;
    string gff_file;
    string genome_name;
    workspace_name workspace_name;

    string genome_type;
    string scientific_name;
    string source;
    string taxon_wsname;
    string taxon_id;
    string release;
    int    genetic_code;
    string type;
    string generate_missing_genes;

  } UploadFastaGFFMethodParams;

  typedef structure {
    string genome_ref;
    string genome_info;
    report_name report_name;
    report_ref report_ref;
  } UploadFastaGFFMethodResult;

  funcdef upload_fasta_gff_file(UploadFastaGFFMethodParams params)
    returns (UploadFastaGFFMethodResult returnVal) authentication required;

  /*
    Required:
    genome_name: output metagenome object name
    workspace_name: workspace name/ID of the object
    For staging area:
    fasta_file: fasta file containing assembled contigs/chromosomes
    gff_file: gff file containing predicted gene models and corresponding features

    Optional params:
    source: Source Of The GFF File. Default to 'User'
    taxon_wsname - where the reference taxons are. Default to '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 Of The Source Data
    genetic_code: Genetic Code For The Organism
    type: 'Reference', 'User upload', 'Representative'
  */
  typedef structure {
    string fasta_file;
    string gff_file;
    string genome_name;
    workspace_name workspace_name;

    string source;
    string taxon_wsname;
    string taxon_id;
    string release;
    int    genetic_code;
    string type;
    string generate_missing_genes;
  } UploadMetagenomeFastaGFFMethodParams;

  typedef structure {
    string metagenome_ref;
    string metagenome_info;
    report_name report_name;
    report_ref report_ref;
  } UploadMetagenomeFastaGFFMethodResult;

  funcdef upload_metagenome_fasta_gff_file(UploadMetagenomeFastaGFFMethodParams params)
    returns (UploadMetagenomeFastaGFFMethodResult returnVal) authentication required;


  typedef structure {
    string staging_subdir;
    string genome_set_name;
    workspace_name workspace_name;

    string genome_type;
    string source;
    string taxon_wsname;
    string taxon_id;
    string release;
    int    genetic_code;
    string generate_missing_genes;
  } BatchGenomeImporterParams;

  typedef structure {
    string set_ref;
    report_name report_name;
    report_ref report_ref;
  } BatchImporterResult;

  funcdef batch_import_genomes_from_staging(BatchGenomeImporterParams params)
    returns (BatchImporterResult returnVal) authentication required;

  typedef structure {
    string staging_subdir;
    string assembly_set_name;
    workspace_name workspace_name;

    int min_contig_length;
    string type;
  } BatchAssemblyImporterParams;

  funcdef batch_import_assemblies_from_staging(BatchAssemblyImporterParams params)
    returns (BatchImporterResult returnVal) authentication required;

  /* Input parameters for the "unpack_staging_file" function.

      Required parameters:
      staging_file_subdir_path: subdirectory file path
      e.g.
        for file: /data/bulk/user_name/file_name
        staging_file_subdir_path is file_name
        for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
        staging_file_subdir_path is subdir_1/subdir_2/file_name
      workspace_name: workspace name/ID of the object
  */
  typedef structure {
    workspace_name workspace_name;
    string staging_file_subdir_path;
  }UnpackStagingFileParams;

  /* Results from the unpack_staging_file function.

    unpacked_file_path: unpacked file path(s) in staging area
  */
  typedef structure {
    string unpacked_file_path;
  }UnpackStagingFileOutput;

  /* Unpack a staging area file */
  funcdef unpack_staging_file(UnpackStagingFileParams params)
      returns(UnpackStagingFileOutput returnVal) authentication required;

  typedef structure{
    string file_url;
  }urls_to_add_web_unpack;

  /* Input parameters for the "unpack_web_file" function.

    Required parameters:
    workspace_name: workspace name/ID of the object
    file_url: file URL
    download_type: one of ['Direct Download', 'FTP', 'DropBox', 'Google Drive']

    Optional:
    urls_to_add_web_unpack: used for parameter-groups. dict of {file_url}

  */
  typedef structure {
    workspace_name workspace_name;
    string file_url;
    string download_type;
    urls_to_add_web_unpack urls_to_add_web_unpack;
  }UnpackWebFileParams;

  /* Results from the unpack_web_file function.

    unpacked_file_path: unpacked file path(s) in staging area
  */
  typedef structure {
    string unpacked_file_path;
  }UnpackWebFileOutput;

  /* Download and unpack a web file to staging area */
  funcdef unpack_web_file(UnpackWebFileParams params)
      returns(UnpackWebFileOutput returnVal) authentication required;

  /*
  import_genbank_from_staging: wrapper method for GenomeFileUtil.genbank_to_genome

    required params:
    staging_file_subdir_path - subdirectory file path
    e.g.
      for file: /data/bulk/user_name/file_name
      staging_file_subdir_path is file_name
      for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
      staging_file_subdir_path is subdir_1/subdir_2/file_name
    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

    optional params:
    scientific_name - the scientific name of the genome.
    taxon_id - the numeric ID of the NCBI taxon to which this genome belongs.
               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
    generate_ids_if_needed - If field used for feature id is not there,
        generate ids (default behavior is raising an exception)
    generate_missing_genes - Generate gene feature for CDSs that do not have
        a parent in file
    genetic_code - Genetic code of organism. Overwrites determined GC from
        taxon object
    type - Reference, Representative or User upload
  */
  typedef structure {
    string staging_file_subdir_path;
    string genome_name;
    string workspace_name;
    string source;
    string genome_type;

    string release;
    int    genetic_code;
    string type;
    string scientific_name;
    string taxon_id;
    string generate_ids_if_needed;
    string generate_missing_genes;
  } GenbankToGenomeParams;

  typedef structure {
      string genome_ref;
  } GenomeSaveResult;

  funcdef import_genbank_from_staging(GenbankToGenomeParams params)
          returns (GenomeSaveResult returnVal) authentication required;

  /*
    required params:
    staging_file_subdir_path: subdirectory file path
    e.g.
      for file: /data/bulk/user_name/file_name
      staging_file_subdir_path is file_name
      for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
      staging_file_subdir_path is subdir_1/subdir_2/file_name
    sequencing_tech: sequencing technology
    name: output reads file name
    workspace_name: workspace name/ID of the object

    Optional Params:
    single_genome: whether the reads are from a single genome or a metagenome.
    insert_size_mean: mean (average) insert length
    insert_size_std_dev: standard deviation of insert lengths
    read_orientation_outward: whether reads in a pair point outward
  */
  typedef structure {
    string staging_file_subdir_path;
    sequencing_tech sequencing_tech;
    name name;
    workspace_name workspace_name;

    single_genome single_genome;
    insert_size_mean insert_size_mean;
    insert_size_std_dev insert_size_std_dev;
    read_orientation_outward read_orientation_outward;
  } SRAToReadsParams;

  funcdef import_sra_from_staging(SRAToReadsParams params)
          returns (UploadMethodResult returnVal) authentication required;

  /*
    download_type: download type for web source fastq file
                       ('Direct Download', 'FTP', 'DropBox', 'Google Drive')

    sra_urls_to_add: dict of SRA file URLs
        required params:
        file_url: SRA file URL
        sequencing_tech: sequencing technology
        name: output reads file name
        workspace_name: workspace name/ID of the object

        Optional Params:
        single_genome: whether the reads are from a single genome or a metagenome.
        insert_size_mean: mean (average) insert length
        insert_size_std_dev: standard deviation of insert lengths
        read_orientation_outward: whether reads in a pair point outward
  */
  typedef structure {
    string file_url;
    sequencing_tech sequencing_tech;
    name name;

    single_genome single_genome;
    insert_size_mean insert_size_mean;
    insert_size_std_dev insert_size_std_dev;
    read_orientation_outward read_orientation_outward;
  }sra_urls_to_add;

  typedef structure {
    string download_type;
    sra_urls_to_add sra_urls_to_add;
    workspace_name workspace_name;
  } WebSRAToReadsParams;

  typedef structure {
    list<string> obj_refs;
    report_name report_name;
    report_ref report_ref;
  } WebSRAToReadsResult;

  funcdef import_sra_from_web(WebSRAToReadsParams params)
          returns (WebSRAToReadsResult returnVal) authentication required;

  /*
    required params:
    staging_file_subdir_path: subdirectory file path
    e.g.
      for file: /data/bulk/user_name/file_name
      staging_file_subdir_path is file_name
      for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
      staging_file_subdir_path is subdir_1/subdir_2/file_name
    assembly_name: output Assembly file name
    workspace_name: workspace name/ID of the object
  */
  typedef structure {
    string staging_file_subdir_path;
    string assembly_name;
    workspace_name workspace_name;
    int min_contig_length;
    string type;
  } FastaToAssemblyParams;

  funcdef import_fasta_as_assembly_from_staging(FastaToAssemblyParams params)
          returns (UploadMethodResult returnVal) authentication required;

  /*
    required params:
    staging_file_subdir_path: subdirectory file path
    e.g.
      for file: /data/bulk/user_name/file_name
      staging_file_subdir_path is file_name
      for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
      staging_file_subdir_path is subdir_1/subdir_2/file_name
    media_name: output Media file name
    workspace_name: workspace name/ID of the object
  */
  typedef structure {
    string staging_file_subdir_path;
    string media_name;
    workspace_name workspace_name;
  } FileToMediaParams;

  funcdef import_tsv_as_media_from_staging(FileToMediaParams params)
          returns (UploadMethodResult returnVal) authentication required;

  funcdef import_excel_as_media_from_staging(FileToMediaParams params)
          returns (UploadMethodResult returnVal) authentication required;

  funcdef import_tsv_or_excel_as_media_from_staging(FileToMediaParams params)
          returns (UploadMethodResult returnVal) authentication required;

  /*
  required params:
  model_file: subdirectory file path for model file
  e.g.
    for file: /data/bulk/user_name/file_name
    staging_file_subdir_path is file_name
    for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
    staging_file_subdir_path is subdir_1/subdir_2/file_name
  compounds_file: same as above for compound (only used for tsv)
  file_type: one of "tsv", "excel", "sbml"
  genome: the associated species genome
  biomasses: one or more biomass reactions in model
  model_name: output FBAModel object name
  workspace_name: workspace name/ID of the object
  */

  typedef structure {
    string model_file;
    string compounds_file;
    string file_type;
    string genome;
    string biomass;
    string model_name;
    workspace_name workspace_name;
  } FileToFBAModelParams;

  funcdef import_file_as_fba_model_from_staging(FileToFBAModelParams params)
        returns (UploadMethodResult returnVal) authentication required;

  /*
    required params:
    staging_file_subdir_path: subdirectory file path
    e.g.
      for file: /data/bulk/user_name/file_name
      staging_file_subdir_path is file_name
      for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
      staging_file_subdir_path is subdir_1/subdir_2/file_name
    matrix_name: output Expressin Matirx file name
    workspace_name: workspace name/ID of the object

    genome_ref: optional reference to a Genome object that will be
        used for mapping feature IDs to
    fill_missing_values: optional flag for filling in missing
          values in matrix (default value is false)
    data_type: optional filed, value is one of 'untransformed',
          'log2_level', 'log10_level', 'log2_ratio', 'log10_ratio' or
          'unknown' (last one is default value)
    data_scale: optional parameter (default value is '1.0')
  */
  typedef structure {
    string staging_file_subdir_path;
    workspace_name workspace_name;
    string matrix_name;
    string genome_ref;
    boolean fill_missing_values;
    string data_type;
    string data_scale;
  } FileToMatrixParams;

  funcdef import_tsv_as_expression_matrix_from_staging(FileToMatrixParams params)
          returns (UploadMethodResult returnVal) authentication required;

  /*
    sequencing_tech: sequencing technology
    name: output reads file name
    workspace_name: workspace name/ID of the object
    import_type: either FASTQ or SRA

    For files in user's staging area:
    fastq_fwd_or_sra_staging_file_name: single-end fastq file name Or forward/left paired-end fastq file name from user's staging area Or SRA staging file
    fastq_rev_staging_file_name: reverse/right paired-end fastq file name user's staging area
    e.g.
      for file: /data/bulk/user_name/file_name
      staging_file_subdir_path is file_name
      for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
      staging_file_subdir_path is subdir_1/subdir_2/file_name

    Optional Params:
    single_genome: whether the reads are from a single genome or a metagenome.
    interleaved: whether reads is interleaved
    insert_size_mean: mean (average) insert length
    insert_size_std_dev: standard deviation of insert lengths
    read_orientation_outward: whether reads in a pair point outward
  */
  typedef structure {
    string import_type;
    string fastq_fwd_staging_file_name;
    string fastq_rev_staging_file_name;
    string sra_staging_file_name;
    sequencing_tech sequencing_tech;
    workspace_name workspace_name;
    string name;
    single_genome single_genome;
    interleaved interleaved;
    insert_size_mean insert_size_mean;
    insert_size_std_dev insert_size_std_dev;
    read_orientation_outward read_orientation_outward;
  } UploadReadsParams;

  funcdef import_reads_from_staging(UploadReadsParams params)
    returns (UploadMethodResult returnVal) authentication required;

  /*
    required params:
    staging_file_subdir_path: subdirectory file path
    e.g.
      for file: /data/bulk/user_name/file_name
      staging_file_subdir_path is file_name
      for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
      staging_file_subdir_path is subdir_1/subdir_2/file_name
    phenotype_set_name: output PhenotypeSet object name
    workspace_name: workspace name/ID of the object

    optional:
    genome: Genome object that contains features referenced by the Phenotype Set
  */
  typedef structure {
    string staging_file_subdir_path;
    workspace_name workspace_name;
    string phenotype_set_name;
    obj_ref genome;
  } FileToPhenotypeSetParams;

  funcdef import_tsv_as_phenotype_set_from_staging(FileToPhenotypeSetParams params)
          returns (UploadMethodResult returnVal) authentication required;

  /*
    required params:
    staging_file_subdir_path: subdirectory file path
    e.g.
      for file: /data/bulk/user_name/file_name
      staging_file_subdir_path is file_name
      for file: /data/bulk/user_name/subdir_1/subdir_2/file_name
      staging_file_subdir_path is subdir_1/subdir_2/file_name
    attribute_mapping_name: output ConditionSet object name
    workspace_id: workspace name/ID of the object
  */
  typedef structure {
    string staging_file_subdir_path;
    workspace_name workspace_name;
    string attribute_mapping_name;
  } FileToConditionSetParams;

  funcdef import_attribute_mapping_from_staging(FileToConditionSetParams params)
          returns (UploadMethodResult returnVal) authentication required;

  typedef structure {
    string staging_file_subdir_path;
    int workspace_id;
    string escher_map_name;
  } EscherMapParams;

  funcdef import_eschermap_from_staging(EscherMapParams params)
          returns (UploadMethodResult returnVal) authentication required;
          
  typedef structure {
    string staging_file_subdir_path;
    string workspace_name;
    list<string> genome_refs;
    string description;
    int lookup_gene_matches;
    float min_similarity_threshold;
    int filter_nomatch;
    string seqset_name;
  } FASTAToSeqSetParams;

  funcdef import_fasta_as_seqset_from_staging(FASTAToSeqSetParams params)
          returns (UploadMethodResult returnVal) authentication required;

};