-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #7 from COBREXA/compathelper/new_version/2024-06-1…
…0-12-48-43-523-00499766618 CompatHelper: bump compat for AbstractFBCModels to 0.3, (keep existing compat)
- Loading branch information
Showing
9 changed files
with
366 additions
and
32 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,192 @@ | ||
|
|
||
| # note: this file is a copy from JSONFBCModels. Might be nice to have some | ||
| # kindof mechanism to keep them roughly in sync. Maybe sink to the Abstract | ||
| # interface? | ||
|
|
||
| import PikaParser as PP | ||
|
|
||
| """ | ||
| `PikaParser.jl` grammar for stringy GRR expressions. | ||
| """ | ||
| const grr_grammar = begin | ||
| # characters that typically form the identifiers | ||
| isident(x::Char) = | ||
| isletter(x) || | ||
| isdigit(x) || | ||
| x == '_' || | ||
| x == '-' || | ||
| x == ':' || | ||
| x == '.' || | ||
| x == '@' || | ||
| x == '#' || | ||
| x == '\'' || | ||
| x == '[' || | ||
| x == ']' | ||
|
|
||
| # scanner helpers | ||
| eat(p) = m -> begin | ||
| last = 0 | ||
| for i in eachindex(m) | ||
| p(m[i]) || break | ||
| last = i | ||
| end | ||
| return last | ||
| end | ||
|
|
||
| # eat one of keywords | ||
| kws(w...) = m -> begin | ||
| last = eat(isident)(m) | ||
| m[begin:last] in w ? last : 0 | ||
| end | ||
|
|
||
| PP.make_grammar( | ||
| [:expr], | ||
| PP.flatten( | ||
| Dict( | ||
| :space => PP.first(PP.scan(eat(isspace)), PP.epsilon), | ||
| :id => PP.scan(eat(isident)), | ||
| :orop => | ||
| PP.first(PP.tokens("||"), PP.token('|'), PP.scan(kws("OR", "or"))), | ||
| :andop => PP.first( | ||
| PP.tokens("&&"), | ||
| PP.token('&'), | ||
| PP.scan(kws("AND", "and")), | ||
| ), | ||
| :expr => PP.seq(:space, :orexpr, :space, PP.end_of_input), | ||
| :orexpr => PP.first( | ||
| :or => PP.seq(:andexpr, :space, :orop, :space, :orexpr), | ||
| :andexpr, | ||
| ), | ||
| :andexpr => PP.first( | ||
| :and => PP.seq(:baseexpr, :space, :andop, :space, :andexpr), | ||
| :baseexpr, | ||
| ), | ||
| :baseexpr => PP.first( | ||
| :id, | ||
| :parenexpr => PP.seq( | ||
| PP.token('('), | ||
| :space, | ||
| :orexpr, | ||
| :space, | ||
| PP.token(')'), | ||
| ), | ||
| ), | ||
| ), | ||
| Char, | ||
| ), | ||
| ) | ||
| end | ||
|
|
||
| grr_grammar_open(m, _) = | ||
| m.rule == :expr ? Bool[0, 1, 0, 0] : | ||
| m.rule == :parenexpr ? Bool[0, 0, 1, 0, 0] : | ||
| m.rule in [:or, :and] ? Bool[1, 0, 0, 0, 1] : | ||
| m.rule in [:andexpr, :orexpr, :notexpr, :baseexpr] ? Bool[1] : | ||
| (false for _ in m.submatches) | ||
|
|
||
| grr_grammar_fold(m, _, subvals) = | ||
| m.rule == :id ? Expr(:call, :gene, String(m.view)) : | ||
| m.rule == :and ? Expr(:call, :and, subvals[1], subvals[5]) : | ||
| m.rule == :or ? Expr(:call, :or, subvals[1], subvals[5]) : | ||
| m.rule == :parenexpr ? subvals[3] : | ||
| m.rule == :expr ? subvals[2] : isempty(subvals) ? nothing : subvals[1] | ||
|
|
||
| """ | ||
| $(TYPEDSIGNATURES) | ||
| Parses a JSON-ish data reference to a `Expr`-typed gene association. Contains | ||
| "calls" to `gene`, `and` and `or` functions that describe the association. | ||
| """ | ||
| function parse_gene_association(str::String)::Maybe{Expr} | ||
| all(isspace, str) && return nothing | ||
| tree = PP.parse_lex(grr_grammar, str) | ||
| match = PP.find_match_at!(tree, :expr, 1) | ||
| match > 0 || throw(DomainError(str, "cannot parse GRR")) | ||
| PP.traverse_match(tree, match, open = grr_grammar_open, fold = grr_grammar_fold) | ||
| end | ||
|
|
||
| """ | ||
| $(TYPEDSIGNATURES) | ||
| Evaluate the gene association expression with the reference values given by the | ||
| `val` function. | ||
| """ | ||
| function eval_gene_association(ga::Expr, val::Function)::Bool | ||
| (ga.head == :call && length(ga.args) >= 2) || | ||
| throw(DomainError(ga, "invalid gene association expr")) | ||
| if ga.args[1] == :gene && length(ga.args) == 2 | ||
| val(ga.args[2]) | ||
| elseif ga.args[1] == :and | ||
| all(eval_gene_association.(ga.args[2:end], Ref(val))) | ||
| elseif ga.args[1] == :or | ||
| any(eval_gene_association.(ga.args[2:end], Ref(val))) | ||
| else | ||
| throw(DomainError(ga, "unsupported gene association function")) | ||
| end | ||
| end | ||
|
|
||
| """ | ||
| $(TYPEDSIGNATURES) | ||
| A helper for producing predictable unique sequences. Might be faster if | ||
| compacting would be done directly in sort(). | ||
| """ | ||
| function sortunique(x) | ||
| o = collect(x) | ||
| sort!(o) | ||
| put = prevind(o, firstindex(o)) | ||
| for i in eachindex(o) | ||
| if put >= firstindex(o) && o[i] == o[put] | ||
| # we already have this one | ||
| continue | ||
| else | ||
| put = nextind(o, put) | ||
| if put != i | ||
| o[put] = o[i] | ||
| end | ||
| end | ||
| end | ||
| o[begin:put] | ||
| end | ||
|
|
||
| """ | ||
| $(TYPEDSIGNATURES) | ||
| Convert the given gene association expression to DNF. | ||
| """ | ||
| function flatten_gene_association(ga::Expr)::A.GeneAssociationDNF | ||
| function fold_and(dnfs::Vector{Vector{Vector{String}}})::Vector{Vector{String}} | ||
| if isempty(dnfs) | ||
| [String[]] | ||
| else | ||
| sortunique( | ||
| sortunique(String[l; r]) for l in dnfs[1] for r in fold_and(dnfs[2:end]) | ||
| ) | ||
| end | ||
| end | ||
|
|
||
| (ga.head == :call && length(ga.args) >= 2) || | ||
| throw(DomainError(ga, "invalid gene association expr")) | ||
| if ga.args[1] == :gene && length(ga.args) == 2 | ||
| [[ga.args[2]]] | ||
| elseif ga.args[1] == :and | ||
| fold_and(flatten_gene_association.(ga.args[2:end])) | ||
| elseif ga.args[1] == :or | ||
| sortunique(vcat(flatten_gene_association.(ga.args[2:end])...)) | ||
| else | ||
| throw(DomainError(ga, "unsupported gene association function")) | ||
| end | ||
| end | ||
|
|
||
| """ | ||
| $(TYPEDSIGNATURES) | ||
| Formats a DNF gene association as a `String`. | ||
| """ | ||
| function format_gene_association_dnf( | ||
| grr::A.GeneAssociationDNF; | ||
| and = " && ", | ||
| or = " || ", | ||
| )::String | ||
| return join(("(" * join(gr, and) * ")" for gr in grr), or) | ||
| end |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.
ea240ccThere was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
@JuliaRegistrator register
ea240ccThere was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Registration pull request created: JuliaRegistries/General/108869
Tip: Release Notes
Did you know you can add release notes too? Just add markdown formatted text underneath the comment after the text
"Release notes:" and it will be added to the registry PR, and if TagBot is installed it will also be added to the
release that TagBot creates. i.e.
To add them here just re-invoke and the PR will be updated.
Tagging
After the above pull request is merged, it is recommended that a tag is created on this repository for the registered package version.
This will be done automatically if the Julia TagBot GitHub Action is installed, or can be done manually through the github interface, or via: