/* $Id: validrules.inc,v 1.3 2013/05/30 18:48:05 kans Exp $ * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government have not placed any restriction on its use or reproduction. * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * Please cite the author in any work or product based on this material. * * =========================================================================== * * Author: Jonathan Kans et al. * * File Description: * Built-in copy of validrules.txt. * */ static const char* const s_Defaultvalidrules[] = { "Comment-set ::= {", " {", " prefix \"##MIGS-Data-START##\" ,", " fields {", " {", " field-name \"investigation_type\" ,", " match-expression \"^\\(eukaryote\\|bacteria_archaea\\|plasmid\\|virus\\|orga", "nelle\\)$\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"project_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"collection_date\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"lat_lon\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"depth\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"alt_elev\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"country\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"environment\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"isol_growth_condt\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"sequencing_meth\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"assembly\" ,", " required TRUE ,", " severity info } } ,", " require-order FALSE ,", " allow-unlisted TRUE ,", " dependent-rules {", " {", " match-name \"investigation_type\" ,", " value-constraint \"^eukaryote$\" ,", " other-fields {", " {", " field-name \"ploidy\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"num_replicons\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"estimated_size\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"trophic_level\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"propagation\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"finishing_strategy\" ,", " required TRUE ,", " severity info } } } ,", " {", " match-name \"investigation_type\" ,", " value-constraint \"^bacteria_archaea$\" ,", " other-fields {", " {", " field-name \"num_replicons\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"ref_biomaterial\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"biotic_relationship\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"trophic_level\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"rel_to_oxygen\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"finishing_strategy\" ,", " required TRUE ,", " severity info } } } ,", " {", " match-name \"investigation_type\" ,", " value-constraint \"^plasmid$\" ,", " other-fields {", " {", " field-name \"propagation\" ,", " required TRUE ,", " severity info } } } ,", " {", " match-name \"investigation_type\" ,", " value-constraint \"^virus$\" ,", " other-fields {", " {", " field-name \"propagation\" ,", " required TRUE ,", " severity info } } } } } ,", " {", " prefix \"##MIMS-Data-START##\" ,", " fields {", " {", " field-name \"investigation_type\" ,", " match-expression \"^metagenome$\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"project_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"collection_date\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"lat_lon\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"depth\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"alt_elev\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"country\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"environment\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"samp_size\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"sequencing_meth\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"assembly\" ,", " required TRUE ,", " severity info } } ,", " require-order FALSE ,", " allow-unlisted TRUE } ,", " {", " prefix \"##MIENS-Data-START##\" ,", " fields {", " {", " field-name \"investigation_type\" ,", " match-expression \"^\\(miens-survey\\|miens-culture\\)$\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"project_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"collection_date\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"lat_lon\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"depth\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"alt_elev\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"country\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"environment\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"target_gene\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"sequencing_meth\" ,", " required TRUE ,", " severity info } } ,", " require-order FALSE ,", " allow-unlisted TRUE ,", " dependent-rules {", " {", " match-name \"investigation_type\" ,", " value-constraint \"^miens-survey$\" ,", " other-fields {", " {", " field-name \"project_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"collection_date\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"lat_lon\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"depth\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"alt_elev\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"country\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"environment\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"samp_size\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"target_gene\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"sequencing_meth\" ,", " required TRUE ,", " severity info } } } ,", " {", " match-name \"investigation_type\" ,", " value-constraint \"^miens-culture$\" ,", " other-fields {", " {", " field-name \"project_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"collection_date\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"lat_lon\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"depth\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"alt_elev\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"country\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"environment\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"biotic_relationship\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"trophic_level\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"rel_to_oxygen\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"isol_growth_condt\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"target_gene\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"sequencing_meth\" ,", " required TRUE ,", " severity info } } } } } ,", " {", " prefix \"##MIGS:3.0-Data-START##\" ,", " fields {", " {", " field-name \"investigation_type\" ,", " match-expression \"^\\(eukaryote\\|bacteria_archaea\\|plasmid\\|virus\\|orga", "nelle\\)$\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"project_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"lat_lon\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"geo_loc_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"collection_date\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"biome\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"feature\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"material\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"env_package\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"isol_growth_condt\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"seq_meth\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"assembly\" ,", " required TRUE ,", " severity info } } ,", " require-order FALSE ,", " allow-unlisted TRUE ,", " dependent-rules {", " {", " match-name \"investigation_type\" ,", " value-constraint \"^eukaryote$\" ,", " other-fields {", " {", " field-name \"num_replicons\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"ploidy\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"estimated_size\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"propagation\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"finishing_strategy\" ,", " required TRUE ,", " severity info } } } ,", " {", " match-name \"investigation_type\" ,", " value-constraint \"^bacteria_archaea$\" ,", " other-fields {", " {", " field-name \"num_replicons\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"ref_biomaterial\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"finishing_strategy\" ,", " required TRUE ,", " severity info } } } ,", " {", " match-name \"investigation_type\" ,", " value-constraint \"^plasmid$\" ,", " other-fields {", " {", " field-name \"propagation\" ,", " required TRUE ,", " severity info } } } ,", " {", " match-name \"investigation_type\" ,", " value-constraint \"^virus$\" ,", " other-fields {", " {", " field-name \"propagation\" ,", " required TRUE ,", " severity info } } } } } ,", " {", " prefix \"##MIMS:3.0-Data-START##\" ,", " fields {", " {", " field-name \"investigation_type\" ,", " match-expression \"^metagenome$\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"project_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"lat_lon\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"geo_loc_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"collection_date\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"biome\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"feature\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"material\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"env_package\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"seq_meth\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"assembly\" ,", " required TRUE ,", " severity info } } ,", " require-order FALSE ,", " allow-unlisted TRUE } ,", " {", " prefix \"##MIMARKS:3.0-Data-START##\" ,", " fields {", " {", " field-name \"investigation_type\" ,", " match-expression \"^\\(mimarks-survey\\|mimarks-culture\\)$\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"project_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"lat_lon\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"geo_loc_name\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"collection_date\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"biome\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"feature\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"material\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"env_package\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"target_gene\" ,", " required TRUE ,", " severity info } ,", " {", " field-name \"seq_meth\" ,", " required TRUE ,", " severity info } } ,", " require-order FALSE ,", " allow-unlisted TRUE ,", " dependent-rules {", " {", " match-name \"investigation_type\" ,", " value-constraint \"^mimarks-culture$\" ,", " other-fields {", " {", " field-name \"isol_growth_condt\" ,", " required TRUE ,", " severity info } } } } } ,", " {", " prefix \"##Genome-Assembly-Data-START##\" ,", " fields {", " {", " field-name \"Finishing Goal\" ,", " match-expression \"^\\(Standard Draft\\|High-Quality Draft\\|Improved", " High-Quality Draft\\|Annotation-Directed Improvement\\|Noncontiguous", " Finished\\|Finished\\)$\" ,", " severity info } ,", " {", " field-name \"Current Finishing Status\" ,", " match-expression \"^\\(Standard Draft\\|High-Quality Draft\\|Improved", " High-Quality Draft\\|Annotation-Directed Improvement\\|Noncontiguous", " Finished\\|Finished\\)$\" ,", " severity info } ,", " {", " field-name \"Assembly Date\" ,", " match-expression \"^\\(\\(\\(0\\|1\\|2\\|3\\)\\(0\\|1\\|2\\|3\\|4\\|5\\|6\\|7\\|8\\|9\\)-", "\\(JAN\\|FEB\\|MAR\\|APR\\|MAY\\|JUN\\|JUL\\|AUG\\|SEP\\|OCT\\|NOV\\|DEC\\)-\\(19\\|20\\)\\(0\\|", "1\\|2\\|3\\|4\\|5\\|6\\|7\\|8\\|9\\)\\(0\\|1\\|2\\|3\\|4\\|5\\|6\\|7\\|8\\|9\\)\\)\\|\\(\\(JAN\\|FEB\\|M", "AR\\|APR\\|MAY\\|JUN\\|JUL\\|AUG\\|SEP\\|OCT\\|NOV\\|DEC\\)-\\(19\\|20\\)\\(0\\|1\\|2\\|3\\|4\\|5", "\\|6\\|7\\|8\\|9\\)\\(0\\|1\\|2\\|3\\|4\\|5\\|6\\|7\\|8\\|9\\)\\)\\|\\(\\(19\\|20\\)\\(0\\|1\\|2\\|3\\|4\\", "|5\\|6\\|7\\|8\\|9\\)\\(0\\|1\\|2\\|3\\|4\\|5\\|6\\|7\\|8\\|9\\)\\)\\)$\" ,", " severity error } ,", " {", " field-name \"Assembly Method\" ,", " match-expression \".+ v\\. .+\",", " required TRUE } ,", " {", " field-name \"Assembly Name\" } ,", " {", " field-name \"Long Assembly Name\" } ,", " {", " field-name \"Genome Representation\" ,", " match-expression \"^\\(Full\\|Partial\\)$\" ,", " required FALSE } ,", " {", " field-name \"Expected Final Version\" ,", " match-expression \"^\\(Yes\\|No\\)$\" ,", " required FALSE } ,", " {", " field-name \"Reference-guided Assembly\" } ,", " {", " field-name \"Single-cell Amplification\" } ,", " {", " field-name \"Corresponding 16S rRNA\" ,", " match-expression \"^.+\\.\\(0\\|1\\|2\\|3\\|4\\|5\\|6\\|7\\|8\\|9\\)+$\",", " required FALSE } ,", " {", " field-name \"Genome Coverage\" ,", " required TRUE } ,", " {", " field-name \"Sequencing Technology\" ,", " required TRUE } } ,", " dependent-rules {", " {", " match-name \"Finishing Goal\" ,", " value-constraint \"^Standard Draft$\" ,", " other-fields {", " {", " field-name \"Current Finishing Status\" ,", " match-expression \"^Standard Draft$\" } } } ,", " {", " match-name \"Finishing Goal\" ,", " value-constraint \"^High-Quality Draft$\" ,", " other-fields {", " {", " field-name \"Current Finishing Status\" ,", " match-expression \"^\\(Standard Draft\\|High-Quality Draft\\)$\" } } } ,", " {", " match-name \"Finishing Goal\" ,", " value-constraint \"^Improved High-Quality Draft$\" ,", " other-fields {", " {", " field-name \"Current Finishing Status\" ,", " match-expression \"^\\(Standard Draft\\|High-Quality Draft\\|Improved", " High-Quality Draft\\)$\" } } } ,", " {", " match-name \"Finishing Goal\" ,", " value-constraint \"^Annotation-Directed Improvement$\" ,", " other-fields {", " {", " field-name \"Current Finishing Status\" ,", " match-expression \"^\\(Standard Draft\\|High-Quality Draft\\|Improved", " High-Quality Draft\\|Annotation-Directed Improvement\\)$\" } } } ,", " {", " match-name \"Finishing Goal\" ,", " value-constraint \"^Noncontiguous Finished$\" ,", " other-fields {", " {", " field-name \"Current Finishing Status\" ,", " match-expression \"^\\(Standard Draft\\|High-Quality Draft\\|Improved", " High-Quality Draft\\|Annotation-Directed Improvement\\|Noncontiguous", " Finished\\)$\" } } } ,", " {", " match-name \"Finishing Goal\" ,", " value-constraint \"^Finished$\" ,", " other-fields {", " {", " field-name \"Current Finishing Status\" ,", " match-expression \"^\\(Standard Draft\\|High-Quality Draft\\|Improved", " High-Quality Draft\\|Annotation-Directed Improvement\\|Noncontiguous", " Finished\\|Finished\\)$\" } } } ,", " {", " match-name \"Sequencing Technology\" ,", " value-constraint \"^\\(w\\|W\\)\\(g\\|G\\)\\(s\\|S\\)$\" ,", " other-fields {", " {", " field-name \"Assembly Date\" ,", " required TRUE ,", " severity warning } } } } } ,", " {", " prefix \"##Assembly-Data-START##\" ,", " fields {", " {", " field-name \"Assembly Method\" ,", " required FALSE } ,", " {", " field-name \"Assembly Name\" ,", " required FALSE } ,", " {", " field-name \"Coverage\" ,", " required FALSE } ,", " {", " field-name \"Sequencing Technology\" ,", " required TRUE } } ,", " allow-unlisted TRUE ,", " dependent-rules {", " {", " match-name \"Sequencing Technology\" ,", " value-constraint \"\\(Sanger dideoxy sequencing\\|ABI PRISM\\|Sanger\\|Sanger sequencing\\)\",", " invert-match TRUE ,", " other-fields {", " {", " field-name \"Assembly Method\" ,", " required TRUE } } } } } ,", " {", " prefix \"##International Barcode of Life (iBOL)Data-START##\" ,", " fields {", " {", " field-name \"Barcode Index Number\" ,", " required FALSE } ,", " {", " field-name \"Order Assignment\" ,", " required FALSE } ,", " {", " field-name \"iBOL Working Group\" ,", " required FALSE } ,", " {", " field-name \"iBOL Release Status\" ,", " required FALSE } ,", " { field-name \"Tentative Name\" ,", " required FALSE } } ,", " allow-unlisted TRUE } ,", " {", " prefix \"##Genome-Annotation-Data-START##\" ,", " fields {", " {", " field-name \"Annotation Provider\" ,", " required TRUE } ,", " {", " field-name \"Annotation Status\" ,", " required FALSE } ,", " {", " field-name \"Annotation Version\" ,", " required FALSE } ,", " {", " field-name \"Annotation Date\" ,", " required FALSE } ,", " {", " field-name \"Annotation Pipeline\" ,", " required FALSE } ,", " {", " field-name \"Annotation Method\" ,", " required FALSE } ,", " {", " field-name \"Annotation Software Version\" ,", " required FALSE } ,", " {", " field-name \"Features Annotated\" ,", " required FALSE } ,", " {", " field-name \"Update Version\" ,", " required FALSE } ,", " {", " field-name \"Input Data\" ,", " required FALSE } ,", " { ", " field-name \"URL\" ,", " required FALSE } } ,", " require-order FALSE ,", " allow-unlisted TRUE } ,", " {", " prefix \"##RefSeq-Attributes-START##\" ,", " fields {", " {", " field-name \"Transcript_exon_combination_evidence\" ,", " required FALSE } } ,", " allow-unlisted TRUE } ", "}", "" };