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pubchem.jl's Introduction

PubChem.jl

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PubChem.jl is a powerful Julia package that facilitates easy access to chemical data from the PubChem database and associates it with chemical species defined using the Catalyst.jl package. This allows you to seamlessly integrate chemical metadata into your computational workflows.

Example Usage

Suppose we want to retrieve chemical properties for the species H2O. First, we define the species and attach the appropriate metadata:

using PubChem, Catalyst
@variables t
@species H2O(t)
@attach_metadata H2O

Now, our species H2O holds chemical data fetched from PubChem as its metadata. We can query this data:

julia> chemical_properties(H2O)
Dict{Any, Any} with 7 entries:
  "IUPAC_Name_Preferred"   => "oxidane"
  "IUPAC_Name_Traditional" => "water"
  "Charge"                 => 0
  "Molecular_formula"      => "H2O"
  "Molecular_mass"         => 18.0106
  "Molecular_weight"       => 18.015
  "Smiles"                 => "O"

Chemical Calculations

You can now utilize these chemical properties to perform various calculations, such as determining the limiting reactant and calculating theoretical yields in a balanced Catalyst reaction.

As an example, let's consider the reaction 2Al + 3Cl2 --> 2AlCl3 and suppose we have the masses of Al and Cl2 as 2.80g and 4.15g, respectively.

# Define the species involved in the reaction
@variables t
@species Al(t), Cl2(t), AlCl3(t)

# Attach metadata to the species
@attach_metadata Al 
@attach_metadata Cl2 
@attach_metadata AlCl3 

# Define a balanced Catalyst reaction 
rx = Reaction(1.0, [Al, Cl2], [AlCl3], [2, 3], [2])

# Get limiting reagent given the masses of the reactants
julia> limiting_reagent(rx,[2.80,4.15])
(Cl2(t), 0.05853314527503526) # Returns the limiting reagent and it's number of moles

# Calculate theoretical yield given the masses of the reactants and the product for which to calculate
julia> theoretical_yield(rx,[2.80,4.15],AlCl3)
5.203206393982134 # 5.2g of AlCl3 is produced 

pubchem.jl's People

Contributors

lalitchauhan56 avatar anandijain avatar

Stargazers

allan avatar  avatar Andrés Riedemann avatar Huo Ruiqing avatar  avatar Sasikumar Palanisamy avatar

Watchers

Sam Isaacson avatar  avatar Andrés Riedemann avatar  avatar

pubchem.jl's Issues

1

[ Info: Precompiling Symbolics [0c5d862f-8b57-4792-8d23-62f2024744c7]
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Compat [34da2185-b29b-5c13-b0c7-acf172513d20]
│   exception = Required dependency DelimitedFiles [8bb1440f-4735-579b-a4ab-409b98df4dab] failed to load from a cache file.
└ @ Base loading.jl:1783
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for DataStructures [864edb3b-99cc-5e75-8d2d-829cb0a9cfe8]
│   exception = Required dependency DelimitedFiles [8bb1440f-4735-579b-a4ab-409b98df4dab] failed to load from a cache file.
└ @ Base loading.jl:1783
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Compat [34da2185-b29b-5c13-b0c7-acf172513d20]
│   exception = Required dependency DelimitedFiles [8bb1440f-4735-579b-a4ab-409b98df4dab] failed to load from a cache file.
└ @ Base loading.jl:1783
┌ Warning: Module Compat with build ID ffffffff-ffff-ffff-0000-1dcae73c1618 is missing from the cache.
│ This may mean Compat [34da2185-b29b-5c13-b0c7-acf172513d20] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module Compat with build ID ffffffff-ffff-ffff-0000-1dcae73c1618 is missing from the cache.
│ This may mean Compat [34da2185-b29b-5c13-b0c7-acf172513d20] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module Compat with build ID ffffffff-ffff-ffff-0000-1dcae73c1618 is missing from the cache.
│ This may mean Compat [34da2185-b29b-5c13-b0c7-acf172513d20] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module BangBang with build ID ffffffff-ffff-ffff-0000-1dcca3d5442a is missing from the cache.
│ This may mean BangBang [198e06fe-97b7-11e9-32a5-e1d131e6ad66] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
WARNING: method definition for OneHotArray at C:\Users\lalit\.julia\packages\MicroCollections\Qsg6U\src\onehot.jl:79 declares type variable N but does not use it.
┌ Warning: Module BangBang with build ID ffffffff-ffff-ffff-0000-1dcca3d5442a is missing from the cache.
│ This may mean BangBang [198e06fe-97b7-11e9-32a5-e1d131e6ad66] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
WARNING: method definition for adapt_structure at C:\Users\lalit\.julia\packages\Transducers\HBMTc\src\partitionby.jl:50 declares type variable inbounds but does not use it.
WARNING: method definition for _foldl_array at C:\Users\lalit\.julia\packages\Transducers\HBMTc\src\processes.jl:222 declares type variable T but does not use it.
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Metatheory [e9d8d322-4543-424a-9be4-0cc815abe26c]
│   exception = Required dependency DelimitedFiles [8bb1440f-4735-579b-a4ab-409b98df4dab] failed to load from a cache file.
└ @ Base loading.jl:1783
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Compat [34da2185-b29b-5c13-b0c7-acf172513d20]
│   exception = Required dependency DelimitedFiles [8bb1440f-4735-579b-a4ab-409b98df4dab] failed to load from a cache file.
└ @ Base loading.jl:1783
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for DataStructures [864edb3b-99cc-5e75-8d2d-829cb0a9cfe8]
│   exception = Required dependency DelimitedFiles [8bb1440f-4735-579b-a4ab-409b98df4dab] failed to load from a cache file.
└ @ Base loading.jl:1783
┌ Warning: The call to compilecache failed to create a usable precompiled cache file for Compat [34da2185-b29b-5c13-b0c7-acf172513d20]
│   exception = Required dependency DelimitedFiles [8bb1440f-4735-579b-a4ab-409b98df4dab] failed to load from a cache file.
└ @ Base loading.jl:1783
┌ Warning: Module Compat with build ID ffffffff-ffff-ffff-0000-1dd2c7ee1a25 is missing from the cache.
│ This may mean Compat [34da2185-b29b-5c13-b0c7-acf172513d20] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module Compat with build ID ffffffff-ffff-ffff-0000-1dd2c7ee1a25 is missing from the cache.
│ This may mean Compat [34da2185-b29b-5c13-b0c7-acf172513d20] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module Compat with build ID ffffffff-ffff-ffff-0000-1dd2c7ee1a25 is missing from the cache.
│ This may mean Compat [34da2185-b29b-5c13-b0c7-acf172513d20] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module BangBang with build ID ffffffff-ffff-ffff-0000-1dd4957209a7 is missing from the cache.
│ This may mean BangBang [198e06fe-97b7-11e9-32a5-e1d131e6ad66] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
WARNING: method definition for OneHotArray at C:\Users\lalit\.julia\packages\MicroCollections\Qsg6U\src\onehot.jl:79 declares type variable N but does not use it.
┌ Warning: Module BangBang with build ID ffffffff-ffff-ffff-0000-1dd4957209a7 is missing from the cache.
│ This may mean BangBang [198e06fe-97b7-11e9-32a5-e1d131e6ad66] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
WARNING: method definition for adapt_structure at C:\Users\lalit\.julia\packages\Transducers\HBMTc\src\partitionby.jl:50 declares type variable inbounds but does not use it.
WARNING: method definition for _foldl_array at C:\Users\lalit\.julia\packages\Transducers\HBMTc\src\processes.jl:222 declares type variable T but does not use it.
┌ Warning: Module Metatheory with build ID ffffffff-ffff-ffff-0000-1dd0b56a8096 is missing from the cache.
│ This may mean Metatheory [e9d8d322-4543-424a-9be4-0cc815abe26c] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module Compat with build ID ffffffff-ffff-ffff-0000-1dd2c7ee1a25 is missing from the cache.
│ This may mean Compat [34da2185-b29b-5c13-b0c7-acf172513d20] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module Compat with build ID ffffffff-ffff-ffff-0000-1dd2c7ee1a25 is missing from the cache.
│ This may mean Compat [34da2185-b29b-5c13-b0c7-acf172513d20] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module Compat with build ID ffffffff-ffff-ffff-0000-1dd2c7ee1a25 is missing from the cache.
│ This may mean Compat [34da2185-b29b-5c13-b0c7-acf172513d20] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
WARNING: method definition for == at C:\Users\lalit\.julia\packages\ChainRulesCore\6Sl9y\src\tangent_types\tangent.jl:68 declares type variable T but does not use it.
WARNING: method definition for getindex at C:\Users\lalit\.julia\packages\ChainRulesCore\6Sl9y\src\tangent_types\tangent.jl:120 declares type variable T but does not use it.
WARNING: method definition for getindex at C:\Users\lalit\.julia\packages\ChainRulesCore\6Sl9y\src\tangent_types\tangent.jl:120 declares type variable P but does not use it.       
WARNING: method definition for canonicalize at C:\Users\lalit\.julia\packages\ChainRulesCore\6Sl9y\src\tangent_types\tangent.jl:240 declares type variable L but does not use it.
WARNING: method definition for canonicalize at C:\Users\lalit\.julia\packages\ChainRulesCore\6Sl9y\src\tangent_types\tangent.jl:241 declares type variable L but does not use it.   
┌ Warning: Module ChainRulesCore with build ID ffffffff-ffff-ffff-0000-1dd986eef669 is missing from the cache.
│ This may mean ChainRulesCore [d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module ChainRulesCore with build ID ffffffff-ffff-ffff-0000-1dd986eef669 is missing from the cache.
│ This may mean ChainRulesCore [d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module DataStructures with build ID ffffffff-ffff-ffff-0000-1dd2719f84dc is missing from the cache.
│ This may mean DataStructures [864edb3b-99cc-5e75-8d2d-829cb0a9cfe8] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module MultivariatePolynomials with build ID ffffffff-ffff-ffff-0000-1dddb6a76908 is missing from the cache.
│ This may mean MultivariatePolynomials [102ac46a-7ee4-5c85-9060-abc95bfdeaa3] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
WARNING: method definition for multiplyexistingvar at C:\Users\lalit\.julia\packages\DynamicPolynomials\juS7t\src\mult.jl:1 declares type variable C but does not use it.
WARNING: method definition for multiplyexistingvar at C:\Users\lalit\.julia\packages\DynamicPolynomials\juS7t\src\mult.jl:6 declares type variable C but does not use it.
┌ Warning: Module ChainRulesCore with build ID ffffffff-ffff-ffff-0000-1dd986eef669 is missing from the cache.
│ This may mean ChainRulesCore [d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module ChainRulesCore with build ID ffffffff-ffff-ffff-0000-1dd986eef669 is missing from the cache.
│ This may mean ChainRulesCore [d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module ChainRulesCore with build ID ffffffff-ffff-ffff-0000-1dd986eef669 is missing from the cache.
│ This may mean ChainRulesCore [d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module SpecialFunctions with build ID ffffffff-ffff-ffff-0000-1dd94bc309a8 is missing from the cache.
│ This may mean SpecialFunctions [276daf66-3868-5448-9aa4-cd146d93841b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module SpecialFunctions with build ID ffffffff-ffff-ffff-0000-1dd94bc309a8 is missing from the cache.
│ This may mean SpecialFunctions [276daf66-3868-5448-9aa4-cd146d93841b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module SpecialFunctions with build ID ffffffff-ffff-ffff-0000-1dd94bc309a8 is missing from the cache.
│ This may mean SpecialFunctions [276daf66-3868-5448-9aa4-cd146d93841b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module SpecialFunctions with build ID ffffffff-ffff-ffff-0000-1dd94bc309a8 is missing from the cache.
│ This may mean SpecialFunctions [276daf66-3868-5448-9aa4-cd146d93841b] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module RecursiveArrayTools with build ID ffffffff-ffff-ffff-0000-1de40315d50c is missing from the cache.
│ This may mean RecursiveArrayTools [731186ca-8d62-57ce-b412-fbd966d074cd] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
WARNING: method definition for supremum at C:\Users\lalit\.julia\packages\Symbolics\J8IHJ\src\domains.jl:22 declares type variable T but does not use it.
┌ Warning: Module MultivariatePolynomials with build ID ffffffff-ffff-ffff-0000-1dddb6a76908 is missing from the cache.
│ This may mean MultivariatePolynomials [102ac46a-7ee4-5c85-9060-abc95bfdeaa3] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
WARNING: method definition for convert_to_output at C:\Users\lalit\.julia\packages\Groebner\yLVEZ\src\io.jl:483 declares type variable T but does not use it.
WARNING: method definition for groebner at C:\Users\lalit\.julia\packages\Groebner\yLVEZ\src\gb\groebner.jl:93 declares type variable Rng but does not use it.
WARNING: method definition for fglm_f4 at C:\Users\lalit\.julia\packages\Groebner\yLVEZ\src\fglm\fglm.jl:184 declares type variable Rng but does not use it.
WARNING: method definition for kbase_f4 at C:\Users\lalit\.julia\packages\Groebner\yLVEZ\src\fglm\fglm.jl:226 declares type variable Rng but does not use it.
┌ Warning: Module DataStructures with build ID ffffffff-ffff-ffff-0000-1dd2719f84dc is missing from the cache.
│ This may mean DataStructures [864edb3b-99cc-5e75-8d2d-829cb0a9cfe8] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module DataStructures with build ID ffffffff-ffff-ffff-0000-1dd2719f84dc is missing from the cache.
│ This may mean DataStructures [864edb3b-99cc-5e75-8d2d-829cb0a9cfe8] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module DataStructures with build ID ffffffff-ffff-ffff-0000-1dd2719f84dc is missing from the cache.
│ This may mean DataStructures [864edb3b-99cc-5e75-8d2d-829cb0a9cfe8] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
┌ Warning: Module DataStructures with build ID ffffffff-ffff-ffff-0000-1dd2719f84dc is missing from the cache.
│ This may mean DataStructures [864edb3b-99cc-5e75-8d2d-829cb0a9cfe8] does not support precompilation but is imported by a module that does.
└ @ Base loading.jl:1758
ERROR: LoadError: UndefVarError: `Float` not defined
Stacktrace:
  [1] getproperty(x::Module, f::Symbol)
    @ Base .\Base.jl:31
  [2] top-level scope
    @ C:\Users\lalit\.julia\packages\SortingAlgorithms\PEcBU\src\SortingAlgorithms.jl:125
  [3] include
    @ .\Base.jl:457 [inlined]
  [4] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:1801
  [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:1625
  [6] macro expansion
    @ .\loading.jl:1613 [inlined]
  [7] macro expansion
    @ .\lock.jl:267 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:1576
  [9] include
    @ .\Base.jl:457 [inlined]
 [10] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:1801
 [11] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:1625
 [12] macro expansion
    @ .\loading.jl:1613 [inlined]
 [13] macro expansion
    @ .\lock.jl:267 [inlined]
 [14] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:1576
 [15] include
    @ .\Base.jl:457 [inlined]
 [16] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:1801
 [17] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:1625
 [18] macro expansion
    @ .\loading.jl:1613 [inlined]
 [19] macro expansion
    @ .\lock.jl:267 [inlined]
 [20] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:1576
 [21] include
    @ .\Base.jl:457 [inlined]
 [22] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt128}}, source::String)
    @ Base .\loading.jl:2010
 [23] top-level scope
    @ stdin:2
in expression starting at C:\Users\lalit\.julia\packages\SortingAlgorithms\PEcBU\src\SortingAlgorithms.jl:3
in expression starting at C:\Users\lalit\.julia\packages\StatsBase\XgjIN\src\StatsBase.jl:1
in expression starting at C:\Users\lalit\.julia\packages\Distributions\39PV5\src\Distributions.jl:1
in expression starting at C:\Users\lalit\.julia\packages\Symbolics\J8IHJ\src\Symbolics.jl:1
in expression starting at stdin:2
ERROR: Failed to precompile Symbolics [0c5d862f-8b57-4792-8d23-62f2024744c7] to "C:\\Users\\lalit\\.julia\\compiled\\v1.9\\Symbolics\\jl_AD0D.tmp".
Stacktrace:
  [1] error(s::String)
    @ Base .\error.jl:35
  [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool)
    @ Base .\loading.jl:2260
  [3] compilecache
    @ .\loading.jl:2127 [inlined]
  [4] _require(pkg::Base.PkgId, env::String)
    @ Base .\loading.jl:1770
  [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base .\loading.jl:1625
  [6] macro expansion
    @ .\loading.jl:1613 [inlined]
  [7] macro expansion
    @ .\lock.jl:267 [inlined]
  [8] require(into::Module, mod::Symbol)
    @ Base .\loading.jl:1576
  [9] eval
    @ .\boot.jl:370 [inlined]
 [10] include_string(mapexpr::typeof(REPL.softscope), mod::Module, code::String, filename::String)
    @ Base .\loading.jl:1864
 [11] invokelatest(::Any, ::Any, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}})
    @ Base .\essentials.jl:816
 [12] invokelatest(::Any, ::Any, ::Vararg{Any})
    @ Base .\essentials.jl:813
 [13] inlineeval(m::Module, code::String, code_line::Int64, code_column::Int64, file::String; softscope::Bool)
    @ VSCodeServer c:\Users\lalit\.vscode\extensions\julialang.language-julia-1.38.2\scripts\packages\VSCodeServer\src\eval.jl:233
 [14] (::VSCodeServer.var"#66#70"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})()
    @ VSCodeServer c:\Users\lalit\.vscode\extensions\julialang.language-julia-1.38.2\scripts\packages\VSCodeServer\src\eval.jl:157
 [15] withpath(f::VSCodeServer.var"#66#70"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams}, path::String)
    @ VSCodeServer c:\Users\lalit\.vscode\extensions\julialang.language-julia-1.38.2\scripts\packages\VSCodeServer\src\repl.jl:249
 [16] (::VSCodeServer.var"#65#69"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})()
    @ VSCodeServer c:\Users\lalit\.vscode\extensions\julialang.language-julia-1.38.2\scripts\packages\VSCodeServer\src\eval.jl:155
 [17] hideprompt(f::VSCodeServer.var"#65#69"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})
    @ VSCodeServer c:\Users\lalit\.vscode\extensions\julialang.language-julia-1.38.2\scripts\packages\VSCodeServer\src\repl.jl:38
 [18] (::VSCodeServer.var"#64#68"{Bool, Bool, Bool, Module, String, Int64, Int64, String, VSCodeServer.ReplRunCodeRequestParams})()
    @ VSCodeServer c:\Users\lalit\.vscode\extensions\julialang.language-julia-1.38.2\scripts\packages\VSCodeServer\src\eval.jl:126
 [19] with_logstate(f::Function, logstate::Any)
    @ Base.CoreLogging .\logging.jl:514
 [20] with_logger
    @ .\logging.jl:626 [inlined]
 [21] (::VSCodeServer.var"#63#67"{VSCodeServer.ReplRunCodeRequestParams})()
    @ VSCodeServer c:\Users\lalit\.vscode\extensions\julialang.language-julia-1.38.2\scripts\packages\VSCodeServer\src\eval.jl:225
 [22] #invokelatest#2
    @ .\essentials.jl:816 [inlined]
 [23] invokelatest(::Any)
    @ Base .\essentials.jl:813
 [24] macro expansion
    @ c:\Users\lalit\.vscode\extensions\julialang.language-julia-1.38.2\scripts\packages\VSCodeServer\src\eval.jl:34 [inlined]
 [25] (::VSCodeServer.var"#61#62")()
    @ VSCodeServer .\task.jl:514

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