search

kbase / execution_engine2

KBase Execution Engine
http://www.kbase.us/services/ee2
MIT License
0 stars 7 forks source link

Expose clientgroups in ee2 #231

Closed bio-boris closed 4 years ago

bio-boris commented 4 years ago
bio-boris commented 4 years ago

Exposed them in the check_jobs_all_range endpoint... here

https://github.com/kbase/execution_engine2/pull/230

Need to also save a snapshot of them for posterity

AssemblyRAST run_arast bigmem, request_cpus=32  
kb_uploadmethods unpack_staging_file kb_upload, request_cpus=1, request_memory=6000  
ReferenceDataManager index_genomes_in_solr kb_upload, request_cpus=1, request_memory=6000  
ReferenceDataManager index_taxa_in_solr kb_upload, request_cpus=1, request_memory=6042  
ReferenceDataManager update_loaded_genomes kb_upload, request_cpus=1, request_memory=6042  
jgi_mg_assembly run_mg_assembly_pipeline bigmemlong, request_cpus=32  
kb_uploadmethods import_file_as_fba_model_from_staging kb_upload, request_cpus=1, request_memory=6042  
kb_uploadmethods import_tsv_as_phenotype_set_from_staging kb_upload, request_cpus=1, request_memory=6042  
RAST_SDK reannotate_microbial_genome bigmem, request_cpus=32  
RAST_SDK annotate_genome bigmem, request_cpus=32  
kb_diamond diamond_blast_search bigmemlong, request_cpus=16  
kb_diamond Diamond_Blast_Search bigmemlong, request_cpus=16  
AssemblyRAST run_velvet bigmemlong, request_cpus=32  
AssemblyRAST run_a6 bigmemlong, request_cpus=32  
AssemblyRAST run_kiki bigmemlong, request_cpus=32  
AssemblyRAST run_miniasm bigmemlong, request_cpus=32  
AssemblyRAST run_a5 bigmemlong, request_cpus=32  
AssemblyRAST run_spades bigmemlong, request_cpus=32  
AssemblyRAST run_idba bigmemlong, request_cpus=32  
AssemblyRAST run_ray bigmemlong, request_cpus=32  
AssemblyRAST run_masurca bigmemlong, request_cpus=32  
BBTools run_RQCFilter_app bigmemlong, request_cpus=32  
kb_staging_exporter export_to_staging kb_upload, request_cpus=1, request_memory=6042  
kb_variation_importer import_variation kb_upload, request_cpus=1, request_memory=6042  
GenericsAPI import_matrix_from_excel kb_upload, request_cpus=1, request_memory=6042  
GenericsAPI import_matrix_from_biom kb_upload, request_cpus=1, request_memory=6042  
MotifUtils importFromNarrative kb_upload, request_cpus=1, request_memory=6041  
kb_SPAdes run_metaSPAdes bigmemlong, request_cpus=32  
kb_uploadmethods import_attribute_mapping_from_staging kb_upload, request_cpus=1, request_memory=6041  
kb_gtdbtk run_kb_gtdbtk bigmem, request_cpus=16, request_memory=110000  
kb_uploadmethods upload_fastq_file kb_upload, request_cpus=1, request_memory=6041  
genome_transform genbank_to_genome_GFU kb_upload, request_cpus=1, request_memory=6041  
genome_transform sra_reads_to_library kb_upload, request_cpus=1, request_memory=6041  
genome_transform reads_to_library kb_upload, request_cpus=1, request_memory=6041  
genome_transform narrative_genbank_to_genome kb_upload, request_cpus=1, request_memory=6041  
kb_uploadmethods import_genbank_from_staging kb_upload, request_cpus=1, request_memory=6041  
kb_uploadmethods upload_fasta_gff_file kb_upload, request_cpus=1, request_memory=6041  
kb_uploadmethods import_sra_from_staging kb_upload, request_cpus=1, request_memory=6041  
hipmer run_hipmer_hpc hpc  
kb_uploadmethods import_fasta_as_assembly_from_staging kb_upload, request_cpus=3  
kb_uploadmethods import_tsv_or_excel_as_media_from_staging kb_upload, request_cpus=1, request_memory=6041  
RAST_SDK annotate_genomes bigmem, request_cpus=32  
RAST_SDK reannotate_microbial_genomes bigmem, request_cpus=32  
kb_uploadmethods import_reads_from_staging kb_upload, request_cpus=1, request_memory=6041  
kb_IDBA run_idba_ud bigmemlong, request_cpus=32  
CompoundSetUtils compound_set_from_file kb_upload, request_cpus=1, request_memory=6041  
kb_orthofinder annotate_plant_transcripts bigmem, request_cpus=32  
megahit run_megahit bigmem, request_cpus=16, request_memory= 100000  
kb_SPAdes run_SPAdes bigmem, request_cpus=32  
ProteinStructureUtils import_model_pdb_file kb_upload, request_cpus=1, request_memory=6041  
GenericsAPI update_matrix_attribute_mapping kb_upload, request_cpus=1, request_memory=6041  
MSAUtils import_msa_file kb_upload, request_cpus=1, request_memory=6041  
MergeMetabolicAnnotations import_annotations kb_upload, request_cpus=1, request_memory=6041  
FamaProfiling run_FamaProfiling bigmem, request_cpus=32  
simpleapp simple_add bigmemlong_extreme  
kb_uploadmethods batch_import_assemblies_from_staging kb_upload, request_cpus=3  
kb_uploadmethods batch_import_genomes_from_staging kb_upload, request_cpus=1, request_memory=6041  
VariationUtil import_variation_from_vcf kb_upload, request_cpus=1, request_memory=6041  
VariationUtil save_variation_from_vcf kb_upload, request_cpus=1, request_memory=6041  
kb_rnaseq_export export_rna_seq_alignment_as_bam_to_staging kb_upload, request_cpus=1, request_memory=6042  
kb_uploadmethods import_tsv_as_expression_matrix_from_staging kb_upload, request_cpus=1, request_memory=6041  
SBMLTools sbml_importer kb_upload, request_cpus=1, request_memory=6042  
KBaseFeatureValues cluster_k_means bigmem, request_cpus=32  
stressTest run_stressTest stressTest  
stressTest run_stressTest2 stressTest  
stressTest run_stressTest3 stressTest  
kb_SPAdes run_hybridSPAdes bigmem, request_cpus=32  
kb_SPAdes run_HybridSPAdes bigmem, request_cpus=32  
kb_MaSuRCA run_masurca_assembler bigmem, request_cpus=32  
RAST_SDK annotate_contigset bigmem, request_cpus=32  
RAST_SDK annotate_contigsets bigmem, request_cpus=32  
kb_genomeclassification upload_trainingset kb_upload, request_cpus=1, request_memory=6041  
KBase2IMG_submit run_KBase2IMG_submit kb_upload, request_cpus=1, request_memory=6042  
kb_uploadmethods import_gff_fasta_as_metagenome_from_staging kb_upload, request_cpus=1, request_memory=6000  
kb_uploadmethods upload_metagenome_fasta_gff_file kb_upload, request_cpus=1, request_memory=6000  
simple_app simple_add kb_upload_bulk  
simple_app simple_add_multiprocessing kb_upload_bulk  
simpleapp simple_add_multiprocessing kb_upload_bulk  
ReadsUtils export_reads njs, request_cpus=4, request_disk=400000  
DomainAnnotation search_domains njs, request_cpus=8, request_disk=400000  
kb_Bowtie2 align_reads_to_assembly_app bigmem, request_cpus=32  
kb_ReadsUtilities KButil_Random_Subsample_Reads njs, request_cpus=8, request_disk=400000  
CoExpression expression_toolkit_cluster_WGCNA njs, request_cpus=8, request_disk=400000  
CoExpression const_coex_net_clust njs, request_cpus=8, request_disk=400000  
dRep dereplicate njs, request_cpus=8  
CompMolNWChem run_CompMolNWChem kb_upload, request_cpus=1, request_memory=6000  
kb_model_analysis model_heatmap_analysis kb_upload, request_cpus=1, request_memory=6000  
simple_app simpleadd bigmemlong  
MergeMetabolicAnnotations import_bulk_annotations kb_upload, request_cpus=1, request_memory=6000  
kb_model_analysis import_fbamodel_attribute_mapping_from_staging kb_upload, request_cpus=1, request_memory=6000  
fba_tools build_metagenome_model njs, request_cpus=4, request_disk=400000, request_memory=6000  
PFLOTRAN upload_pflotran_model kb_upload, request_cpus=1, request_memory=6000  
kb_uploadmethods import_eschermap_from_staging kb_upload, request_cpus=1, request_memory=6000  
kb_Msuite run_checkM_lineage_wf njs, request_cpus=8  
poolfileupload run_poolfileupload kb_upload, request_cpus=3, request_memory=6000  
kb_kaiju run_kaiju njs, request_cpus=8, request_memory=53248
bio-boris commented 4 years ago

created simple endpoint

bio-boris commented 3 years ago
Module Name Function Name Client Groups  
AssemblyRAST run_arast bigmem  
kb_uploadmethods unpack_staging_file kb_upload, request_cpus=1, request_memory=6000  
ReferenceDataManager index_genomes_in_solr kb_upload, request_cpus=1, request_memory=6000  
ReferenceDataManager index_taxa_in_solr kb_upload, request_cpus=1, request_memory=6042  
ReferenceDataManager update_loaded_genomes kb_upload, request_cpus=1, request_memory=6042  
jgi_mg_assembly run_mg_assembly_pipeline {"request_cpus": "32", "client_group": "extreme"}  
kb_uploadmethods import_file_as_fba_model_from_staging kb_upload, request_cpus=1, request_memory=6042  
kb_uploadmethods import_tsv_as_phenotype_set_from_staging kb_upload, request_cpus=1, request_memory=6042  
RAST_SDK reannotate_microbial_genome {"request_cpus": "32", "client_group": "bigmem"}  
RAST_SDK annotate_genome {"request_cpus": "32", "client_group": "bigmem"}  
AssemblyRAST run_velvet bigmemlong, request_cpus=32  
AssemblyRAST run_a6 bigmemlong, request_cpus=32  
AssemblyRAST run_kiki bigmemlong, request_cpus=32  
AssemblyRAST run_miniasm bigmemlong, request_cpus=32  
AssemblyRAST run_a5 bigmemlong, request_cpus=32  
AssemblyRAST run_spades bigmemlong, request_cpus=32  
AssemblyRAST run_idba bigmemlong, request_cpus=32  
AssemblyRAST run_ray bigmemlong, request_cpus=32  
AssemblyRAST run_masurca bigmemlong, request_cpus=32  
BBTools run_RQCFilter_app {"request_cpus": "32", "client_group": "extreme"}  
kb_staging_exporter export_to_staging kb_upload, request_cpus=1, request_memory=6042  
kb_variation_importer import_variation kb_upload, request_cpus=1, request_memory=6042  
GenericsAPI import_matrix_from_excel kb_upload, request_cpus=1, request_memory=6042  
GenericsAPI import_matrix_from_biom kb_upload, request_cpus=1, request_memory=6042  
MotifUtils importFromNarrative kb_upload, request_cpus=1, request_memory=6041  
kb_SPAdes run_metaSPAdes {"request_cpus": "32", "client_group": "extreme"}  
kb_uploadmethods import_attribute_mapping_from_staging kb_upload, request_cpus=1, request_memory=6041  
kb_gtdbtk run_kb_gtdbtk bigmem, request_cpus=16, request_memory=110000  
kb_uploadmethods upload_fastq_file kb_upload, request_cpus=1, request_memory=6041  
FunctionalProfileUtil import_func_profile kb_upload, request_cpus=1, request_memory=6000  
kb_checkV run_kb_checkV {"request_cpus": "32", "client_group": "bigmem"}  
genome_transform genbank_to_genome_GFU kb_upload, request_cpus=1, request_memory=6041  
genome_transform sra_reads_to_library kb_upload, request_cpus=1, request_memory=6041  
genome_transform reads_to_library kb_upload, request_cpus=1, request_memory=6041  
genome_transform narrative_genbank_to_genome kb_upload, request_cpus=1, request_memory=6041  
kb_uploadmethods import_genbank_from_staging kb_upload, request_cpus=1, request_memory=6041  
kb_uploadmethods upload_fasta_gff_file kb_upload, request_cpus=1, request_memory=6041  
kb_uploadmethods import_sra_from_staging kb_upload, request_cpus=1, request_memory=6041  
hipmer run_hipmer_hpc hpc  
kb_uploadmethods import_fasta_as_assembly_from_staging kb_upload, request_cpus=3  
kb_uploadmethods import_tsv_or_excel_as_media_from_staging kb_upload, request_cpus=1, request_memory=6041  
RAST_SDK annotate_genomes {"request_cpus": "32", "client_group": "bigmem"}  
RAST_SDK reannotate_microbial_genomes bigmem, request_cpus=32  
kb_uploadmethods import_reads_from_staging kb_upload, request_cpus=1, request_memory=6041  
kb_IDBA run_idba_ud {"request_cpus": "32", "client_group": "extreme"}  
CompoundSetUtils compound_set_from_file kb_upload, request_cpus=1, request_memory=6041  
kb_orthofinder annotate_plant_transcripts bigmem, request_cpus=32  
megahit run_megahit bigmem, request_cpus=16, request_memory=100000  
kb_SPAdes run_SPAdes bigmem, request_cpus=32  
ProteinStructureUtils import_model_pdb_file kb_upload, request_cpus=1, request_memory=6041  
GenericsAPI update_matrix_attribute_mapping kb_upload, request_cpus=1, request_memory=6041  
MSAUtils import_msa_file kb_upload, request_cpus=1, request_memory=6041  
MergeMetabolicAnnotations import_annotations kb_upload, request_cpus=1, request_memory=6041  
FamaProfiling run_FamaProfiling bigmem, request_cpus=32  
kb_uploadmethods batch_import_assemblies_from_staging kb_upload, request_cpus=3  
kb_uploadmethods batch_import_genomes_from_staging kb_upload, request_cpus=1, request_memory=6041  
VariationUtil import_variation_from_vcf kb_upload, request_cpus=1, request_memory=6041  
VariationUtil save_variation_from_vcf kb_upload, request_cpus=1, request_memory=6041  
kb_rnaseq_export export_rna_seq_alignment_as_bam_to_staging kb_upload, request_cpus=1, request_memory=6042  
kb_uploadmethods import_tsv_as_expression_matrix_from_staging kb_upload, request_cpus=1, request_memory=6041  
SBMLTools sbml_importer kb_upload, request_cpus=1, request_memory=6041  
stressTest run_stressTest stressTest  
stressTest run_stressTest2 stressTest  
stressTest run_stressTest3 stressTest  
kb_SPAdes run_hybridSPAdes bigmem, request_cpus=32  
kb_SPAdes run_HybridSPAdes bigmem, request_cpus=32  
kb_MaSuRCA run_masurca_assembler bigmem, request_cpus=32  
RAST_SDK annotate_contigset bigmem, request_cpus=32  
RAST_SDK annotate_contigsets bigmem, request_cpus=32  
kb_genomeclassification upload_trainingset kb_upload, request_cpus=1, request_memory=6041  
KBase2IMG_submit run_KBase2IMG_submit kb_upload, request_cpus=1, request_memory=6042  
kb_uploadmethods import_gff_fasta_as_metagenome_from_staging kb_upload, request_cpus=1, request_memory=6000  
kb_uploadmethods upload_metagenome_fasta_gff_file kb_upload, request_cpus=1, request_memory=6000  
simple_app simple_add kb_upload_bulk  
simple_app simple_add_multiprocessing kb_upload_bulk  
simpleapp simple_add_multiprocessing kb_upload_bulk  
kb_Bowtie2 align_reads_to_assembly_app bigmem, request_cpus=32  
CompMolNWChem run_CompMolNWChem kb_upload, request_cpus=1, request_memory=6000  
kb_model_analysis model_heatmap_analysis {"request_cpus": "12", "client_group": "njs"}  
MergeMetabolicAnnotations import_bulk_annotations kb_upload, request_cpus=1, request_memory=6000  
PFLOTRAN upload_pflotran_model kb_upload, request_cpus=1, request_memory=6000  
kb_uploadmethods import_eschermap_from_staging kb_upload, request_cpus=1, request_memory=6000  
poolfileupload run_poolfileupload kb_upload, request_cpus=3, request_memory=6000  
kb_kaiju run_kaiju bigmem, request_cpus=16, request_memory=100000  
kb_fastqc runFastQC bigmem, request_cpus=16  
kb_trimmomatic run_trimmomatic bigmem, request_cpus=16  
RAST_SDK annotate_genome_assembly bigmem, request_cpus=32  
sample_uploader import_samples kb_upload  
kb_stringtie run_stringtie {"request_cpus": "32", "client_group": "bigmem"}  
kb_stringtie run_stringtie_app {"request_cpus": "32", "client_group": "bigmem"}  
kb_genomeclassification predict_phenotype kb_upload, request_cpus=1, request_memory=6041  
CompMolNWChem_Thermo run_CompMolNWChem_Thermo kb_upload, request_cpus=1, request_memory=6000  
RAST_SDK annotate_metagenome {"request_cpus": "32", "client_group": "bigmem"}  
RAST_SDK rast_genome_assembly {"request_cpus": "32", "client_group": "bigmem"}  
simpleapp simple_add bigmem, request_cpus=999, request_memory=999, color=blue  
RAST_SDK rast_genome_assemblies {"request_cpus": "32", "client_group": "bigmem"}  
kb_model_analysis import_fbamodel_set_from_staging kb_upload, request_cpus=1, request_memory=6000  
kb_ReadsUtilities KButil_Random_Subsample_Reads {"request_cpus": "32", "client_group": "bigmem"}  
kb_genomeclassification rast_annotate_trainingset {"request_cpus": "32", "client_group": "bigmem"}  
KBaseFeatureValues expression_toolkit_estimate_k {"request_cpus": "32", "client_group": "bigmem"}  
KBaseFeatureValues estimate_k_new {"request_cpus": "32", "client_group": "bigmem"}  
kb_virmatcher run_kb_virmatcher {"request_cpus": "16", "client_group": "bigmem", "request_memory" : "150000"}  
kb_meta_decoder map_reads_to_reference {"request_cpus": "16", "client_group": "bigmem", "request_memory": "110000"}  
kb_meta_decoder calculate_population_statistics {"request_cpus": "16", "client_group": "bigmem", "request_memory": "110000"}  
kb_meta_decoder call_variants {"request_cpus": "16", "client_group": "bigmem", "request_memory": "110000"}  
kb_meta_decoder call_variants_single {"request_cpus": "16", "client_group": "bigmem", "request_memory": "110000"}  
FamaProfiling run_FamaReadProfiling {"request_cpus": "16", "client_group": "bigmem", "request_memory": "110000"}  
nmdc_metaassembly run_nmdc_metaassembly {"machine": "kc42-p.chicago.kbase.us", "client_group": "bigmem"}