1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146

use crate::utils::expression::{Function, TypeOf, Variable};
use lazy_static::lazy_static;
use std::collections::BTreeMap;

// https://stackoverflow.com/questions/27582739/how-do-i-create-a-hashmap-literal

/// Makes a static [`BTreeMap`] from the input of `GOAT_VARIABLE_DATA`.
macro_rules! collection {
    // map-like
    ($($k:expr => $v:expr),* $(,)?) => {{
        use std::iter::{Iterator, IntoIterator};
        Iterator::collect(IntoIterator::into_iter([$(($k, $v),)*]))
    }};
}

// this is data for the `taxon` index.

lazy_static! {
    /// Automatically generated GoaT variable data from a Bash script in the
    /// `/vars` directory.
    pub static ref GOAT_TAXON_VARIABLE_DATA: BTreeMap<&'static str, Variable<'static>> = collection!(
        // automated input start taxon
		"c_value" => Variable { display_name: "C value", type_of: TypeOf::HalfFloat, functions: Function::Some(vec!["min", "max"]) },
		"c_value_method" => Variable { display_name: "C value method", type_of: TypeOf::Keyword(vec!["biochemical analysis", "bulk fluorometric assay", "complete genome sequencing", "feulgen densitometry", "feulgen image analysis densitometry", "flow cytometry", "flow karyotyping", "fluorescence fading analysis", "gallocyanin chrom alum densitometry", "methyl green densitometry", "not specified", "static cell fluorometry", "ultraviolet microscopy", "unknown", "biochemical analysis", "feulgen image analysis densitometry", "flow cytometry", "feulgen densitometry", "feulgen densitometry & flow cytometry", "microdensitometry", "pulse field gel electrophoresis", "reassociation kinetics", "whole genome sequencing"]), functions: Function::None },
		"c_value_cell_type" => Variable { display_name: "C value cell type", type_of: TypeOf::Keyword(vec!["antennae", "antennal gland", "blood cells", "brain", "buccal epithelium", "coelomocytes", "corneal epithelium", "digestive gland", "dorsal fin clip", "egg", "embyro", "epidermis", "exopodite", "fibroblasts", "fin clips", "germarium", "gills", "haemocytes", "heart cells", "individual chromosomes", "intestine", "kidney cells", "legs", "leukocytes", "liver", "lung (culture)", "mantle", "midgut", "muscle cells", "ne", "not specified", "oocytes", "ovaries", "pancreas", "pharynx", "polypide cells in suspension", "red blood cells", "retinal cells", "salivary gland", "somatic cells", "sperm", "spleen", "tentacles", "testes", "thymus", "tissue culture", "various", "ventral hypodermal chord", "whole body", "whole body squash"]), functions: Function::None },
		"genome_size" => Variable { display_name: "Genome size", type_of: TypeOf::Long, functions: Function::Some(vec!["min", "max"]) },
		"genome_size_kmer" => Variable { display_name: "Genome size kmer", type_of: TypeOf::Long, functions: Function::Some(vec!["min", "max"]) },
		"genome_size_draft" => Variable { display_name: "Genome size draft", type_of: TypeOf::Long, functions: Function::Some(vec!["min", "max"]) },
		"assembly_level" => Variable { display_name: "Assembly level", type_of: TypeOf::Keyword(vec!["complete genome", "chromosome", "scaffold", "contig"]), functions: Function::None },
		"assembly_span" => Variable { display_name: "Assembly span", type_of: TypeOf::Long, functions: Function::Some(vec!["min", "max"]) },
		"bioproject" => Variable { display_name: "bioproject", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"biosample" => Variable { display_name: "biosample", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"contig_n50" => Variable { display_name: "Contig N50", type_of: TypeOf::Long, functions: Function::Some(vec!["min", "max"]) },
		"assembly_date" => Variable { display_name: "Last updated", type_of: TypeOf::Date, functions: Function::Some(vec!["min", "max"]) },
		"scaffold_n50" => Variable { display_name: "Scaffold N50", type_of: TypeOf::Long, functions: Function::Some(vec!["min", "max"]) },
		"gene_count" => Variable { display_name: "Gene count", type_of: TypeOf::Integer, functions: Function::Some(vec!["min", "max"]) },
		"ebp_metric_date" => Variable { display_name: "EBP metric date", type_of: TypeOf::Date, functions: Function::Some(vec!["min", "max"]) },
		"mitochondrion_assembly_span" => Variable { display_name: "mitochondrion span", type_of: TypeOf::Long, functions: Function::None },
		"mitochondrion_gc_percent" => Variable { display_name: "mitochondrion GC%", type_of: TypeOf::TwoDP, functions: Function::None },
		"plastid_assembly_span" => Variable { display_name: "plastid span", type_of: TypeOf::Long, functions: Function::None },
		"plastid_gc_percent" => Variable { display_name: "plastid GC%", type_of: TypeOf::TwoDP, functions: Function::None },
		"chromosome_number" => Variable { display_name: "Chromosome number", type_of: TypeOf::Short, functions: Function::Some(vec!["min", "max"]) },
		"haploid_number" => Variable { display_name: "Haploid number", type_of: TypeOf::Short, functions: Function::Some(vec!["min", "max"]) },
		"sex_determination" => Variable { display_name: "Sex Determination", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"ploidy" => Variable { display_name: "Ploidy", type_of: TypeOf::Short, functions: Function::Some(vec!["min", "max"]) },
		"echabs92" => Variable { display_name: "EC Habitats Directive 1992", type_of: TypeOf::Keyword(vec!["echabs92_annex_iib", "echabs92_annex_ivb", "echabs92_annex_iva"]), functions: Function::None },
		"habreg_2017" => Variable { display_name: "Conservation of Habitats and Species Regulations 2017", type_of: TypeOf::Keyword(vec!["habreg-sch2", "habreg-sch5"]), functions: Function::None },
		"marhabreg-2017" => Variable { display_name: "Conservation of Offshore Marine Habitats and Species Regulations 2017", type_of: TypeOf::Keyword(vec!["marhabreg-sch1"]), functions: Function::None },
		"waca_1981" => Variable { display_name: "Wildlife and Countryside Act 1981", type_of: TypeOf::Keyword(vec!["waca-sch1", "waca-sch5"]), functions: Function::None },
		"isb_wildlife_act_1976" => Variable { display_name: "Irish Statute Book Wildlife Act, 1976", type_of: TypeOf::Keyword(vec!["iwa-nsch3", "iwa-sch5"]), functions: Function::None },
		"protection_of_badgers_act_1992" => Variable { display_name: "Protection of Badgers Act 1992", type_of: TypeOf::Keyword(vec!["badgers92"]), functions: Function::None },
		"sample_sex" => Variable { display_name: "Sample sex", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"sample_location" => Variable { display_name: "location", type_of: TypeOf::None, functions: Function::None },
		"country_list" => Variable { display_name: "Country list", type_of: TypeOf::Keyword(vec!["gb", "ie"]), functions: Function::None },
		"btk_nohit" => Variable { display_name: "BTK no hit", type_of: TypeOf::OneDP, functions: Function::None },
		"btk_target" => Variable { display_name: "BTK_target", type_of: TypeOf::OneDP, functions: Function::None },
		"busco_completeness" => Variable { display_name: "BUSCO completeness", type_of: TypeOf::OneDP, functions: Function::None },
		"busco_lineage" => Variable { display_name: "BUSCO lineage", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"busco_string" => Variable { display_name: "BUSCO string", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"gc_percent" => Variable { display_name: "GC percent", type_of: TypeOf::OneDP, functions: Function::None },
		"n_percent" => Variable { display_name: "N percent", type_of: TypeOf::OneDP, functions: Function::None },
		"odb10_lineage" => Variable { display_name: "Busco_odb10 lineage", type_of: TypeOf::Keyword(vec!["aconoidasida_odb10", "actinopterygii_odb10", "agaricales_odb10", "agaricomycetes_odb10", "alveolata_odb10", "apicomplexa_odb10", "arachnida_odb10", "arthropoda_odb10", "ascomycota_odb10", "aves_odb10", "basidiomycota_odb10", "boletales_odb10", "brassicales_odb10", "capnodiales_odb10", "carnivora_odb10", "cetartiodactyla_odb10", "chaetothyriales_odb10", "chlorophyta_odb10", "coccidia_odb10", "cyprinodontiformes_odb10", "diptera_odb10", "dothideomycetes_odb10", "embryophyta_odb10", "endopterygota_odb10", "euarchontoglires_odb10", "eudicots_odb10", "euglenozoa_odb10", "eukaryota_odb10", "eurotiales_odb10", "eurotiomycetes_odb10", "eutheria_odb10", "fabales_odb10", "fungi_odb10", "glires_odb10", "glomerellales_odb10", "helotiales_odb10", "hemiptera_odb10", "hymenoptera_odb10", "hypocreales_odb10", "insecta_odb10", "laurasiatheria_odb10", "leotiomycetes_odb10", "lepidoptera_odb10", "liliopsida_odb10", "mammalia_odb10", "metazoa_odb10", "microsporidia_odb10", "mollusca_odb10", "mucorales_odb10", "mucoromycota_odb10", "nematoda_odb10", "onygenales_odb10", "passeriformes_odb10", "plasmodium_odb10", "pleosporales_odb10", "poales_odb10", "polyporales_odb10", "primates_odb10", "saccharomycetes_odb10", "sauropsida_odb10", "solanales_odb10", "sordariomycetes_odb10", "stramenopiles_odb10", "tetrapoda_odb10", "tremellomycetes_odb10", "vertebrata_odb10", "viridiplantae_odb10"]), functions: Function::None },
		"sample_collected" => Variable { display_name: "sample_collected", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"sample_collected_by" => Variable { display_name: "sample_collected_by", type_of: TypeOf::Keyword(vec!["dalu", "ghc", "mba", "nhm", "nsu", "psu", "qmul", "rbge", "kew", "san", "ubc", "derb", "oxf", "vien"]), functions: Function::None },
		"sample_acquired" => Variable { display_name: "sample_acquired", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"in_progress" => Variable { display_name: "in_progress", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"insdc_open" => Variable { display_name: "insdc_open", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"published" => Variable { display_name: "published", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"sequencing_status" => Variable { display_name: "sequencing_status", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_ag100pest" => Variable { display_name: "sequencing_status_ag100pest", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_asg" => Variable { display_name: "sequencing_status_asg", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_b10k" => Variable { display_name: "sequencing_status_b10k", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_canbp" => Variable { display_name: "sequencing_status_canbp", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_cbp" => Variable { display_name: "sequencing_status_cbp", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_ccgp" => Variable { display_name: "sequencing_status_ccgp", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_cfgp" => Variable { display_name: "sequencing_status_cfgp", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_dtol" => Variable { display_name: "sequencing_status_dtol", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_ebpn" => Variable { display_name: "sequencing_status_ebpn", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_endemixit" => Variable { display_name: "sequencing_status_endemixit", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_erga" => Variable { display_name: "sequencing_status_erga", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_eurofish" => Variable { display_name: "sequencing_status_eurofish", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_gaga" => Variable { display_name: "sequencing_status_gaga", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_giga" => Variable { display_name: "sequencing_status_giga", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_ilebp" => Variable { display_name: "sequencing_status_ilebp", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_metainvert" => Variable { display_name: "sequencing_status_metainvert", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_pgp" => Variable { display_name: "sequencing_status_pgp", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_squalomix" => Variable { display_name: "sequencing_status_squalomix", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_vgp" => Variable { display_name: "sequencing_status_vgp", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_zoonomia" => Variable { display_name: "sequencing_status_zoonomia", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_omg" => Variable { display_name: "sequencing_status_omg", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_arg" => Variable { display_name: "sequencing_status_arg", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_agi" => Variable { display_name: "sequencing_status_agi", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_tsi" => Variable { display_name: "sequencing_status_tsi", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_gap" => Variable { display_name: "sequencing_status_gap", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"sequencing_status_gbr" => Variable { display_name: "sequencing_status_gbr", type_of: TypeOf::Keyword(vec!["published", "insdc_open", "in_progress", "sample_acquired", "sample_collected"]), functions: Function::None },
		"long_list" => Variable { display_name: "long_list", type_of: TypeOf::Keyword(vec!["africabp", "ag100pest", "agi", "arg", "asg", "b10k", "canbp", "cbp", "ccgp", "cfgp", "dtol", "ebpn", "ein", "endemixit", "erga", "eurofish", "gaga", "gap", "gbr", "giga", "ilebp", "metainvert", "omg", "pgp", "squalomix", "tsi", "vgp", "zoonomia"]), functions: Function::None },
		"other_priority" => Variable { display_name: "other_priority", type_of: TypeOf::Keyword(vec!["africabp", "ag100pest", "agi", "arg", "asg", "b10k", "canbp", "cbp", "ccgp", "cfgp", "dtol", "ebpn", "ein", "endemixit", "erga", "eurofish", "gaga", "gap", "gbr", "giga", "ilebp", "metainvert", "omg", "pgp", "squalomix", "tsi", "vgp", "zoonomia"]), functions: Function::None },
		"family_representative" => Variable { display_name: "family_representative", type_of: TypeOf::Keyword(vec!["africabp", "ag100pest", "agi", "arg", "asg", "b10k", "canbp", "cbp", "ccgp", "cfgp", "dtol", "ebpn", "ein", "endemixit", "erga", "eurofish", "gaga", "gap", "gbr", "giga", "ilebp", "metainvert", "omg", "pgp", "squalomix", "tsi", "vgp", "zoonomia"]), functions: Function::None },
		"sequencing_status_ebp" => Variable { display_name: "sequencing_status_ebp", type_of: TypeOf::None, functions: Function::None },
        // automated input end taxon
    );
}

// this is the data for `assembly` index.

lazy_static! {
    /// Automatically generated GoaT variable data from a Bash script in the
    /// `/vars` directory.
    pub static ref GOAT_ASSEMBLY_VARIABLE_DATA: BTreeMap<&'static str, Variable<'static>> = collection!(
        // automated input start assembly
		"assembly_level" => Variable { display_name: "Assembly level", type_of: TypeOf::Keyword(vec!["complete genome", "chromosome", "scaffold", "contig"]), functions: Function::None },
		"assembly_span" => Variable { display_name: "Assembly span", type_of: TypeOf::Long, functions: Function::None },
		"assembly_type" => Variable { display_name: "Assembly type", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"bioproject" => Variable { display_name: "bioproject", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"biosample" => Variable { display_name: "biosample", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"chromosome_count" => Variable { display_name: "Chromosome count", type_of: TypeOf::Long, functions: Function::None },
		"contig_count" => Variable { display_name: "Contig count", type_of: TypeOf::Long, functions: Function::None },
		"contig_l50" => Variable { display_name: "Contig L50", type_of: TypeOf::Long, functions: Function::None },
		"contig_n50" => Variable { display_name: "Contig N50", type_of: TypeOf::Long, functions: Function::None },
		"ebp_metric_date" => Variable { display_name: "EBP metric date", type_of: TypeOf::Date, functions: Function::None },
		"gene_count" => Variable { display_name: "Gene count", type_of: TypeOf::Integer, functions: Function::None },
		"isolate" => Variable { display_name: "Isolate", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"last_updated" => Variable { display_name: "Last updated", type_of: TypeOf::Date, functions: Function::None },
		"noncoding_gene_count" => Variable { display_name: "Non-coding gene count", type_of: TypeOf::Integer, functions: Function::None },
		"organelle" => Variable { display_name: "organelle", type_of: TypeOf::None, functions: Function::None },
		"protein_count" => Variable { display_name: "Protein count", type_of: TypeOf::Integer, functions: Function::None },
		"pseudogene_count" => Variable { display_name: "Pseudogene count", type_of: TypeOf::Integer, functions: Function::None },
		"refseq_category" => Variable { display_name: "RefSeq category", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"sample_sex" => Variable { display_name: "Sample sex", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"scaffold_count" => Variable { display_name: "Scaffold count", type_of: TypeOf::Long, functions: Function::None },
		"scaffold_l50" => Variable { display_name: "Scaffold L50", type_of: TypeOf::Long, functions: Function::None },
		"scaffold_n50" => Variable { display_name: "Scaffold N50", type_of: TypeOf::Long, functions: Function::None },
		"sequence_count" => Variable { display_name: "Sequence count", type_of: TypeOf::Long, functions: Function::None },
		"submitter" => Variable { display_name: "Submitter", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"ungapped_span" => Variable { display_name: "Ungapped span", type_of: TypeOf::Long, functions: Function::None },
		"btk_nohit" => Variable { display_name: "BTK no hit", type_of: TypeOf::OneDP, functions: Function::None },
		"btk_target" => Variable { display_name: "BTK_target", type_of: TypeOf::OneDP, functions: Function::None },
		"busco_completeness" => Variable { display_name: "BUSCO completeness", type_of: TypeOf::OneDP, functions: Function::None },
		"busco_lineage" => Variable { display_name: "BUSCO lineage", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"busco_string" => Variable { display_name: "BUSCO string", type_of: TypeOf::Keyword(vec![""]), functions: Function::None },
		"gc_percent" => Variable { display_name: "gc_percent", type_of: TypeOf::TwoDP, functions: Function::None },
		"n_percent" => Variable { display_name: "n_percent", type_of: TypeOf::TwoDP, functions: Function::None },
		"sample_location" => Variable { display_name: "sample_location", type_of: TypeOf::None, functions: Function::None },
        // automated input end assembly
    );
}