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23 Commits
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e8511c01b0
| Author | SHA1 | Date |
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 Emilia Allison
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e8511c01b0
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Emilia Allison
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83d74cfc6f
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Emilia Allison
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9aad876a31
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Emilia Allison
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b25d1eb0c6
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Emilia Allison
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c6d3b86237
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Emilia Allison
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51093f5efd
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Emilia Allison
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a1d4cc74c5
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Emilia Allison
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e88fdb0cdd
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Emilia Allison
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7771ce1786
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Emilia Allison
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ca142ef594
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Emilia Allison
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deac725fdb
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Emilia Allison
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7031ae33dc
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Emilia Allison
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63790c2145
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Emilia Allison
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7e321a78c4
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Emilia Allison
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06baf0a053
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Emilia Allison
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52b28aabb1
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Emilia Allison
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9e1abdc8bb
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Emilia Allison
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e829a49424
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Emilia Allison
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2ccb84041b
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Emilia Allison
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caf10f10c1
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Emilia Allison
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98d2d92b49
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Emilia Allison
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ce6e88a347
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Emilia Allison
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94386a0485
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@ -26,6 +26,21 @@ dependencies = [
|
|||
"memchr",
|
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]
|
||||
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||||
[[package]]
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||||
name = "android-tzdata"
|
||||
version = "0.1.1"
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||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "e999941b234f3131b00bc13c22d06e8c5ff726d1b6318ac7eb276997bbb4fef0"
|
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|
||||
[[package]]
|
||||
name = "android_system_properties"
|
||||
version = "0.1.5"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311"
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||||
dependencies = [
|
||||
"libc",
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||||
]
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||||
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||||
[[package]]
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||||
name = "anymap"
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version = "1.0.0-beta.2"
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@ -76,6 +91,12 @@ dependencies = [
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"rustc-demangle",
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||||
]
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[[package]]
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||||
name = "base64"
|
||||
version = "0.22.1"
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||||
source = "registry+https://github.com/rust-lang/crates.io-index"
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||||
checksum = "72b3254f16251a8381aa12e40e3c4d2f0199f8c6508fbecb9d91f575e0fbb8c6"
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[[package]]
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name = "bincode"
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version = "1.3.3"
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@ -118,6 +139,19 @@ version = "1.0.0"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
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||||
[[package]]
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||||
name = "chrono"
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||||
version = "0.4.38"
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||||
source = "registry+https://github.com/rust-lang/crates.io-index"
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||||
checksum = "a21f936df1771bf62b77f047b726c4625ff2e8aa607c01ec06e5a05bd8463401"
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dependencies = [
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||||
"android-tzdata",
|
||||
"iana-time-zone",
|
||||
"num-traits",
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||||
"serde",
|
||||
"windows-targets",
|
||||
]
|
||||
|
||||
[[package]]
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||||
name = "console_error_panic_hook"
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||||
version = "0.1.7"
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||||
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@ -128,6 +162,12 @@ dependencies = [
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|||
"wasm-bindgen",
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||||
]
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||||
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||||
[[package]]
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||||
name = "core-foundation-sys"
|
||||
version = "0.8.6"
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||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "06ea2b9bc92be3c2baa9334a323ebca2d6f074ff852cd1d7b11064035cd3868f"
|
||||
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||||
[[package]]
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||||
name = "csv"
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||||
version = "1.3.0"
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@ -184,6 +224,22 @@ dependencies = [
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"syn 2.0.48",
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||||
]
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||||
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||||
[[package]]
|
||||
name = "deranged"
|
||||
version = "0.3.11"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "b42b6fa04a440b495c8b04d0e71b707c585f83cb9cb28cf8cd0d976c315e31b4"
|
||||
dependencies = [
|
||||
"powerfmt",
|
||||
"serde",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "equivalent"
|
||||
version = "1.0.1"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "5443807d6dff69373d433ab9ef5378ad8df50ca6298caf15de6e52e24aaf54d5"
|
||||
|
||||
[[package]]
|
||||
name = "fnv"
|
||||
version = "1.0.7"
|
||||
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@ -467,12 +523,24 @@ version = "0.12.3"
|
|||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "8a9ee70c43aaf417c914396645a0fa852624801b24ebb7ae78fe8272889ac888"
|
||||
|
||||
[[package]]
|
||||
name = "hashbrown"
|
||||
version = "0.14.5"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "e5274423e17b7c9fc20b6e7e208532f9b19825d82dfd615708b70edd83df41f1"
|
||||
|
||||
[[package]]
|
||||
name = "hermit-abi"
|
||||
version = "0.3.5"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "d0c62115964e08cb8039170eb33c1d0e2388a256930279edca206fff675f82c3"
|
||||
|
||||
[[package]]
|
||||
name = "hex"
|
||||
version = "0.4.3"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "7f24254aa9a54b5c858eaee2f5bccdb46aaf0e486a595ed5fd8f86ba55232a70"
|
||||
|
||||
[[package]]
|
||||
name = "http"
|
||||
version = "0.2.11"
|
||||
|
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@ -484,6 +552,29 @@ dependencies = [
|
|||
"itoa",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "iana-time-zone"
|
||||
version = "0.1.60"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "e7ffbb5a1b541ea2561f8c41c087286cc091e21e556a4f09a8f6cbf17b69b141"
|
||||
dependencies = [
|
||||
"android_system_properties",
|
||||
"core-foundation-sys",
|
||||
"iana-time-zone-haiku",
|
||||
"js-sys",
|
||||
"wasm-bindgen",
|
||||
"windows-core",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "iana-time-zone-haiku"
|
||||
version = "0.1.2"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "f31827a206f56af32e590ba56d5d2d085f558508192593743f16b2306495269f"
|
||||
dependencies = [
|
||||
"cc",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "ident_case"
|
||||
version = "1.0.1"
|
||||
|
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@ -496,7 +587,7 @@ version = "0.3.9"
|
|||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "cfd6201e7c30ccb24773cac7efa6fec1e06189d414b7439ce756a481c8bfbf53"
|
||||
dependencies = [
|
||||
"indexmap",
|
||||
"indexmap 1.9.3",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
|
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@ -506,7 +597,19 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
|
|||
checksum = "bd070e393353796e801d209ad339e89596eb4c8d430d18ede6a1cced8fafbd99"
|
||||
dependencies = [
|
||||
"autocfg",
|
||||
"hashbrown",
|
||||
"hashbrown 0.12.3",
|
||||
"serde",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "indexmap"
|
||||
version = "2.3.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "de3fc2e30ba82dd1b3911c8de1ffc143c74a914a14e99514d7637e3099df5ea0"
|
||||
dependencies = [
|
||||
"equivalent",
|
||||
"hashbrown 0.14.5",
|
||||
"serde",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
|
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@ -557,6 +660,21 @@ dependencies = [
|
|||
"adler",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "num-conv"
|
||||
version = "0.1.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "51d515d32fb182ee37cda2ccdcb92950d6a3c2893aa280e540671c2cd0f3b1d9"
|
||||
|
||||
[[package]]
|
||||
name = "num-traits"
|
||||
version = "0.2.19"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "071dfc062690e90b734c0b2273ce72ad0ffa95f0c74596bc250dcfd960262841"
|
||||
dependencies = [
|
||||
"autocfg",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "num_cpus"
|
||||
version = "1.16.0"
|
||||
|
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@ -633,7 +751,7 @@ dependencies = [
|
|||
|
||||
[[package]]
|
||||
name = "plate-tool-lib"
|
||||
version = "0.4.0"
|
||||
version = "0.5.0"
|
||||
dependencies = [
|
||||
"csv",
|
||||
"getrandom",
|
||||
|
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@ -643,12 +761,14 @@ dependencies = [
|
|||
"regex",
|
||||
"serde",
|
||||
"serde_json",
|
||||
"serde_with",
|
||||
"serde_yaml",
|
||||
"uuid",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "plate-tool-web"
|
||||
version = "0.4.0"
|
||||
version = "0.5.0"
|
||||
dependencies = [
|
||||
"csv",
|
||||
"getrandom",
|
||||
|
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@ -669,6 +789,12 @@ dependencies = [
|
|||
"yewdux",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "powerfmt"
|
||||
version = "0.2.0"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "439ee305def115ba05938db6eb1644ff94165c5ab5e9420d1c1bcedbba909391"
|
||||
|
||||
[[package]]
|
||||
name = "ppv-lite86"
|
||||
version = "0.2.17"
|
||||
|
|
@ -881,6 +1007,49 @@ dependencies = [
|
|||
"serde",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "serde_with"
|
||||
version = "3.9.0"
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
|
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checksum = "69cecfa94848272156ea67b2b1a53f20fc7bc638c4a46d2f8abde08f05f4b857"
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dependencies = [
|
||||
"base64",
|
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"chrono",
|
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"hex",
|
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"indexmap 1.9.3",
|
||||
"indexmap 2.3.0",
|
||||
"serde",
|
||||
"serde_derive",
|
||||
"serde_json",
|
||||
"serde_with_macros",
|
||||
"time",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "serde_with_macros"
|
||||
version = "3.9.0"
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
|
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|
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|
||||
"darling",
|
||||
"proc-macro2",
|
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"quote",
|
||||
"syn 2.0.48",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "serde_yaml"
|
||||
version = "0.9.34+deprecated"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "6a8b1a1a2ebf674015cc02edccce75287f1a0130d394307b36743c2f5d504b47"
|
||||
dependencies = [
|
||||
"indexmap 2.3.0",
|
||||
"itoa",
|
||||
"ryu",
|
||||
"serde",
|
||||
"unsafe-libyaml",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "slab"
|
||||
version = "0.4.9"
|
||||
|
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@ -938,6 +1107,37 @@ dependencies = [
|
|||
"syn 2.0.48",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "time"
|
||||
version = "0.3.36"
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
|
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checksum = "5dfd88e563464686c916c7e46e623e520ddc6d79fa6641390f2e3fa86e83e885"
|
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dependencies = [
|
||||
"deranged",
|
||||
"itoa",
|
||||
"num-conv",
|
||||
"powerfmt",
|
||||
"serde",
|
||||
"time-core",
|
||||
"time-macros",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "time-core"
|
||||
version = "0.1.2"
|
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source = "registry+https://github.com/rust-lang/crates.io-index"
|
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checksum = "ef927ca75afb808a4d64dd374f00a2adf8d0fcff8e7b184af886c3c87ec4a3f3"
|
||||
|
||||
[[package]]
|
||||
name = "time-macros"
|
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|
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source = "registry+https://github.com/rust-lang/crates.io-index"
|
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checksum = "3f252a68540fde3a3877aeea552b832b40ab9a69e318efd078774a01ddee1ccf"
|
||||
dependencies = [
|
||||
"num-conv",
|
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"time-core",
|
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]
|
||||
|
||||
[[package]]
|
||||
name = "tokio"
|
||||
version = "1.36.0"
|
||||
|
|
@ -996,6 +1196,12 @@ version = "1.0.12"
|
|||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
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checksum = "3354b9ac3fae1ff6755cb6db53683adb661634f67557942dea4facebec0fee4b"
|
||||
|
||||
[[package]]
|
||||
name = "unsafe-libyaml"
|
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|
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|
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checksum = "673aac59facbab8a9007c7f6108d11f63b603f7cabff99fabf650fea5c32b861"
|
||||
|
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[[package]]
|
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name = "uuid"
|
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version = "1.7.0"
|
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|
|
@ -1145,6 +1351,79 @@ dependencies = [
|
|||
"wasm-bindgen",
|
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]
|
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|
||||
[[package]]
|
||||
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"windows-targets",
|
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|
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|
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[[package]]
|
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||||
dependencies = [
|
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"windows_aarch64_gnullvm",
|
||||
"windows_aarch64_msvc",
|
||||
"windows_i686_gnu",
|
||||
"windows_i686_gnullvm",
|
||||
"windows_i686_msvc",
|
||||
"windows_x86_64_gnu",
|
||||
"windows_x86_64_gnullvm",
|
||||
"windows_x86_64_msvc",
|
||||
]
|
||||
|
||||
[[package]]
|
||||
name = "windows_aarch64_gnullvm"
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version = "0.52.6"
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source = "registry+https://github.com/rust-lang/crates.io-index"
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||||
checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
|
||||
|
||||
[[package]]
|
||||
name = "windows_aarch64_msvc"
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||||
|
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|
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|
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|
||||
[[package]]
|
||||
name = "windows_x86_64_gnu"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
|
||||
|
||||
[[package]]
|
||||
name = "windows_x86_64_gnullvm"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
|
||||
|
||||
[[package]]
|
||||
name = "windows_x86_64_msvc"
|
||||
version = "0.52.6"
|
||||
source = "registry+https://github.com/rust-lang/crates.io-index"
|
||||
checksum = "589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec"
|
||||
|
||||
[[package]]
|
||||
name = "yew"
|
||||
version = "0.20.0"
|
||||
|
|
@ -1155,7 +1434,7 @@ dependencies = [
|
|||
"futures",
|
||||
"gloo",
|
||||
"implicit-clone",
|
||||
"indexmap",
|
||||
"indexmap 1.9.3",
|
||||
"js-sys",
|
||||
"prokio",
|
||||
"rustversion",
|
||||
|
|
|
|||
274
README.md
274
README.md
|
|
@ -1,147 +1,193 @@
|
|||
# plate-tool
|
||||
|
||||
A web-based tool for creating assays for your favorite (acoustic) liquid handler.
|
||||
A web-based tool for creating and visualizing picklists for your favorite (possibly acoustic) liquid handler.
|
||||
|
||||
## Table of Contents
|
||||
- [Usage](#Usage)
|
||||
- [Installation](#Installation)
|
||||
- [Usage](#usage)
|
||||
- [Plates](#plates)
|
||||
- [Adding plates](#adding-plates)
|
||||
- [Modifying plates](#modifying-plates)
|
||||
- [Transfers](#transfers)
|
||||
- [Adding a transfer](#adding-a-transfer)
|
||||
- [Modifying transfers](#modifying-transfers)
|
||||
- [Importing and Exporting](#importing-and-Exporting)
|
||||
- [Export as CSV](#export-as-csv)
|
||||
- [Export as JSON](#export-as-json)
|
||||
- [Import from JSON](#import-from-json)
|
||||
- [Import Transfer from CSV](#import-transfer-from-csv)
|
||||
- [Other Neat Features](#other-neat-features)
|
||||
- [Installation](#installation)
|
||||
|
||||
## Usage
|
||||
|
||||
### Adding plates
|
||||
### Plates
|
||||
#### Adding plates
|
||||
When you open plate tool for the first time,
|
||||
you'll be greeted by a message informing you that no plates are selected.
|
||||
|
||||
To add a new plate, click the "New Plate" button:
|
||||
|
||||
Once you've added at least one source plate and one destination plate,
|
||||
click one of each to select them.
|
||||
The right-most pane will now display these plates.
|
||||
|
||||
### Modifying and deleting plates
|
||||
Suppose you erroneously created a plate, or misspelled its name.
|
||||
Double click on that plate in the list (top-left pane) and a new modal will open.
|
||||
Here you can rename a plate or delete it.
|
||||
You may also change the format of a plate
|
||||
(note that this will not delete any data if you accidentally switch to a smaller format).
|
||||
|
||||
### Adding a transfer
|
||||
Now that you have two plates selected,
|
||||
it's time to add a transfer.
|
||||
We can see all of the properties of our transfer in the bottom-left pane.
|
||||
You should first name your transfer (this name is only used for your reference, and is not passed to the liquid handler).
|
||||
You can enter your source and destination regions in their respective fields;
|
||||
the accepted format should be familiar—capital letters for the row and arabic numerals for the column.
|
||||
|
||||
However, it is much easier to click-and-drag the desired region.
|
||||
If we click and hold on a well (see right pane), that specifies our start well.
|
||||
Then, we can drag and subsequently release on our desired end well.
|
||||
|
||||
Our selected wells will be highlighted in light blue for our source plate and light red for our destination plate.
|
||||
You might also notice that some wells are hatched:
|
||||
this indicates wells that will be used in the transfer.
|
||||
Not all selected wells will necessarily be hatched,
|
||||
depending on the transfer type and interleave settings.
|
||||
|
||||
When all of the settings are to your liking, click the "Save" button.
|
||||
Note that it now appears in the "Transfers" section of the list pane.
|
||||
To add a new plate, click the "Add" button for the corresponding plate type:
|
||||
|
||||
Once you've added at least one source plate and one destination plate,
|
||||
click one of each to select them.
|
||||
The right-most pane will now display these plates.
|
||||
|
||||
### Modifying and deleting transfers
|
||||
If you already saved a transfer and would like to change it,
|
||||
click on its entry in the list.
|
||||
Now change the properties of the transfer as you did during initial creation.
|
||||
When finished, click the "Save" button to commit these changes.
|
||||
|
||||
If you no longer need a transfer, select it as above and then click the "Delete" button.
|
||||
|
||||
### Importing and Exporting
|
||||
#### Modifying plates
|
||||
Suppose you erroneously created a plate, or misspelled its name.
|
||||
Double click on that plate in the list (top-left pane) and a new modal will open.
|
||||
Here you can rename a plate or delete it.
|
||||
You may also change the format of a plate
|
||||
(note that this will not delete any data if you accidentally switch to a smaller format).
|
||||
|
||||
#### Export as CSV
|
||||
Exporting the transfers we have created to a CSV format is the primary (if not sole) usage of Plate Tool.
|
||||
To do so, first note the "File" tab at the top-left of the screen (above the list pane).
|
||||
Mouse over this tab, and a few more options will be revealed.
|
||||
We want to export: mouse over export and select "Export as CSV".
|
||||
You will be reminded that this is a one-way export (see JSON export/import below),
|
||||
and then prompted by your browser to select a location for your file.
|
||||
### Transfers
|
||||
#### Adding a transfer
|
||||
Now that you have two plates selected,
|
||||
it's time to add a transfer.
|
||||
We can see all of the properties of our transfer in the bottom-left pane.
|
||||
You should first name your transfer (this name is only used for your reference, and is not passed to the liquid handler).
|
||||
You can enter your source and destination regions in their respective fields;
|
||||
the accepted format should be familiar—capital letters for the row and arabic numerals for the column.
|
||||
|
||||
#### Export as JSON (Saving Your Work)
|
||||
Currently, it is not possible to export to a format produced by other similar software.
|
||||
However, you might reasonably want to save a copy of your work
|
||||
either as a backup or to share.
|
||||
Mouse over the "File" tab, then "Export" as above, then alternatively select "Export as JSON".
|
||||
Your browser will then prompt you to pick a suitable location to save your work as a file.
|
||||
(See note 1 below)
|
||||
However, it is much easier to click-and-drag the desired region.
|
||||
If we click and hold on a well (see right pane), that specifies our start well.
|
||||
Then, we can drag and subsequently release on our desired end well.
|
||||
|
||||
#### Import from JSON (Recovering Your Work)
|
||||
If we want to import one such file, mouse over the "File" tab as before
|
||||
and select "Import", and finally click "Import from JSON".
|
||||
This opens a modal where you are prompted to upload (see note 2)
|
||||
your file; it will then be processed and loaded.
|
||||
Keep in mind that this will overwrite any work you currently have open,
|
||||
so you may wish to export first (see above).
|
||||
Our selected wells will be highlighted in light blue for our source plate and light red for our destination plate.
|
||||
You might also notice that some wells are hatched:
|
||||
this indicates wells that will be used in the transfer.
|
||||
Not all selected wells will necessarily be hatched,
|
||||
depending on the transfer type and interleave settings.
|
||||
|
||||
_Note 1_: JSON files are plaintext!
|
||||
By default there is little whitespace (this makes comprehending them a challenge)
|
||||
but if we pass it through a "JSON Beautifier" (enter this into your search engine of choice)
|
||||
it immediately becomes more readable.
|
||||
It is encouraged (although by no means necessary) to take a look at your export;
|
||||
you will see that the representation here very closely mirrors the representation presented
|
||||
in Plate Tool.
|
||||
|
||||
_Note 2_: Use of the word "upload" might imply that your data is leaving your computer.
|
||||
It does not.
|
||||
You are welcome to verify (use your browser's developer tools, it should have a network tab)
|
||||
that this application does not "phone home".
|
||||
Your data is stored locally (unless you choose to export it and distribute it yourself).
|
||||
When all of the settings are to your liking, click the "Save" button.
|
||||
Note that it now appears in the "Transfers" section of the list pane.
|
||||
|
||||
#### Import Transfer from CSV (Using a picklist as a transfer)
|
||||
If you have a CSV generated by another tool (or plate-tool),
|
||||
you can import it as a single transfer.
|
||||
To do so, mouse over the "File" tab, then "Import", and finally "Import Transfer from CSV".
|
||||
When creating transfers via this method, the transfer cannot be edited.
|
||||
This is useful if you have a pre-existing picklist that you would like to visualize in plate-tool.
|
||||
#### Modifying transfers
|
||||
If you already saved a transfer and would like to change it,
|
||||
click on its entry in the list.
|
||||
Now change the properties of the transfer as you did during initial creation.
|
||||
When finished, click the "Save" button to commit these changes.
|
||||
|
||||
You may either manually map plates in a picklist to plates you've already created, or click "Auto" to:
|
||||
1. Generate all plates in the picklist
|
||||
2. Generate transfers for all source:destination pairs.
|
||||
|
||||
_Note_: If you try to use this feature and no plates are available to select,
|
||||
there was likely an issue parsing your picklist.
|
||||
Your browser's console may have guidance as to why parsing failed;
|
||||
plate-tool was probably expecting a different name for a column than was in your file.
|
||||
If you no longer need a transfer, select it as above and then click the "Delete" button.
|
||||
|
||||
### Importing and Exporting
|
||||
|
||||
#### Export as CSV
|
||||
Exporting the transfers we have created to a CSV format is the primary (if not sole) usage of Plate Tool.
|
||||
To do so, first note the "File" tab at the top-left of the screen (above the list pane).
|
||||
Mouse over this tab, and a few more options will be revealed.
|
||||
We want to export: mouse over export and select "Export as CSV".
|
||||
You will be prompted by your browser to select a location for your file.
|
||||
|
||||
As of version `0.4.0`, it is possible to pick a CSV export format:
|
||||
Mouse over options, then export, then click "Change CSV export type".
|
||||
In the dialog that opens, select your desired export type.
|
||||
Currently, plate-tool supports:
|
||||
- Normal
|
||||
- This format can be imported by Cellario's cherrypick hook.
|
||||
- Echo Client
|
||||
- This format is useful if you want to run a picklist directly from the
|
||||
Echo Client software.
|
||||
This will export just the transfers between the currently selected plates;
|
||||
I assume you'd be using this feature in a non-automation context
|
||||
and know to load your plates into your Echo yourself.
|
||||
|
||||
#### Export as JSON
|
||||
##### (Saving Your Work)
|
||||
Currently, it is not possible to export to a format produced by other similar software.
|
||||
However, you might reasonably want to save a copy of your work
|
||||
either as a backup or to share.
|
||||
Mouse over the "File" tab, then "Export" as above, then alternatively select "Export as JSON".
|
||||
Your browser will then prompt you to pick a suitable location to save your work as a file.
|
||||
(See note 1 below)
|
||||
|
||||
#### Import from JSON
|
||||
##### (Recovering Your Work)
|
||||
If we want to import one such file, mouse over the "File" tab as before
|
||||
and select "Import", and finally click "Import from JSON".
|
||||
This opens a modal where you are prompted to upload (see note 2)
|
||||
your file; it will then be processed and loaded.
|
||||
Keep in mind that this will overwrite any work you currently have open,
|
||||
so you may wish to export first (see above).
|
||||
|
||||
_Note 1_: JSON files are plaintext!
|
||||
By default there is little whitespace (this makes comprehending them a challenge)
|
||||
but if we pass it through a "JSON Beautifier" (enter this into your search engine of choice)
|
||||
it immediately becomes more readable.
|
||||
It is encouraged (although by no means necessary) to take a look at your export;
|
||||
you will see that the representation here very closely mirrors the representation presented
|
||||
in Plate Tool.
|
||||
|
||||
_Note 2_: Use of the word "upload" might imply that your data is leaving your computer.
|
||||
It does not.
|
||||
You are welcome to verify (use your browser's developer tools, it should have a network tab)
|
||||
that this application does not "phone home".
|
||||
Your data is stored locally (unless you choose to export it and distribute it yourself).
|
||||
|
||||
#### Import Transfer from CSV
|
||||
##### (Using a picklist as a transfer)
|
||||
If you have a CSV generated by another tool (or plate-tool),
|
||||
you can import it as a single transfer.
|
||||
To do so, mouse over the "File" tab, then "Import", and finally "Import Transfer from CSV".
|
||||
When creating transfers via this method, the transfer cannot be edited.
|
||||
This is useful if you have a pre-existing picklist that you would like to visualize in plate-tool.
|
||||
|
||||
You may either manually map plates in a picklist to plates you've already created, or click "Auto" to:
|
||||
1. Generate all plates in the picklist
|
||||
2. Generate transfers for all source:destination pairs.
|
||||
|
||||
_Note_: If you try to use this feature and no plates are available to select,
|
||||
there was likely an issue parsing your picklist.
|
||||
Your browser's console may have guidance as to why parsing failed;
|
||||
plate-tool was probably expecting a different name for a column than was in your file.
|
||||
|
||||
_Note_: If you find a picklist that Cellario *can* import that plate-tool cannot,
|
||||
please email me!
|
||||
Odds are your picklist contains a weird edge case I've not considered,
|
||||
and I would like to fix that!
|
||||
|
||||
### Other Neat Features
|
||||
|
||||
#### Taking Pictures of Plates
|
||||
If you double click on a plate
|
||||
(try to avoid clicking a well since that will change your selection)
|
||||
plate-tool will do some magic to take a screenshot of your plate
|
||||
and deposit it in your clipboard for you.
|
||||
You can then paste this into PowerPoint, GIMP, or whereever else
|
||||
you want a pretty picture of a plate.
|
||||
#### Taking Pictures of Plates
|
||||
If you double click on a plate
|
||||
(try to avoid clicking a well since that will change your selection)
|
||||
plate-tool will do some magic to take a screenshot of your plate
|
||||
and deposit it in your clipboard for you.
|
||||
You can then paste this into PowerPoint, GIMP, or whereever else
|
||||
you want a pretty picture of a plate.
|
||||
I hope this is helpful for arts and crafts.
|
||||
|
||||
_NOTE:_ I won't guarantee this feature will work in all contexts;
|
||||
it relies on your browser thinking that you have plate-tool open
|
||||
in a "secure context" (localhost or https).
|
||||
_NOTE:_ I won't guarantee this feature will work in all contexts;
|
||||
it relies on your browser thinking that you have plate-tool open
|
||||
in a "secure context" (localhost or https).
|
||||
|
||||
#### Turn off the in-transfer hashes
|
||||
Have you noticed that when you select a transfer, the wells to
|
||||
be used in that transfer have little diagonal lines over them?
|
||||
Hopefully you have, because this is supposed to happen!
|
||||
However, if you want to take a Pretty Plate Picture (see above),
|
||||
you might want these indicators turned off.
|
||||
#### Turn off the in-transfer hashes
|
||||
Have you noticed that when you select a transfer, the wells to
|
||||
be used in that transfer have little diagonal lines over them?
|
||||
Hopefully you have, because this is supposed to happen!
|
||||
However, if you want to take a Pretty Plate Picture (see above),
|
||||
you might want these indicators turned off.
|
||||
|
||||
To disable the indicators, mouse over "Options" (top-left of screen), then "Styles",
|
||||
then click "Toggle transfer hashes".
|
||||
To turn them back on, do the exact same thing.
|
||||
To disable the indicators, mouse over "Options" (top-left of screen), then "Styles",
|
||||
then click "Toggle transfer hashes".
|
||||
To turn them back on, do the exact same thing.
|
||||
|
||||
#### Transfer Volume Heatmap (Experimental)
|
||||
This can be used to verify that all of the wells in a plate will have the same volume
|
||||
transferred at a glance.
|
||||
Wells will be colored based on the sum of all transfers using that plate.
|
||||
|
||||
To toggle this feature, mouse over "Options", then "Styles", then click "Toggle volume heatmap".
|
||||
|
||||
_NOTE_: The scale for the colors is spaced linearly; if you have a well that is being used
|
||||
significantly more than some others, it may be difficult to see the difference between other wells
|
||||
with more similar volumes.
|
||||
If you have a use case that would benefit from a logarithmic scale here, please let me know.
|
||||
|
||||
## Installation
|
||||
|
||||
Plate tool is hosted [here](https://ilia.moe/cool-stuff/plate-tool/) for your convenience.
|
||||
However, you're absolutely welcome to host your own instance (even locally).
|
||||
Here's how:
|
||||
(_Note:_ ~~If you run Windows you're probably best off doing the following in WSL2~~ You're absolutely fine to install rustup in Powershell, and the subsequent steps should be very similar but likely with different filepaths.)
|
||||
(_Note:_ If you run Windows you're absolutely fine to install rustup in Powershell, and the subsequent steps should be very similar but likely with different filepaths. I haven't personally validated this. )
|
||||
|
||||
1. Make sure you have a working Rust toolchain
|
||||
1. Installing `rustup` is the easiest way to do this. See [their website](https://rustup.rs/),
|
||||
|
|
|
|||
|
|
@ -1,6 +1,6 @@
|
|||
[package]
|
||||
name = "plate-tool-lib"
|
||||
version = "0.4.0"
|
||||
version = "0.5.0"
|
||||
edition = "2021"
|
||||
|
||||
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
|
||||
|
|
@ -15,3 +15,5 @@ csv = "1.2"
|
|||
getrandom = { version = "0.2", features = ["js"] }
|
||||
rand = { version = "0.8", features = ["small_rng"] }
|
||||
lazy_static = "1.4"
|
||||
serde_with = { version = "3.9.0", features = ["json"] }
|
||||
serde_yaml = "0.9.34"
|
||||
|
|
|
|||
|
|
@ -2,9 +2,10 @@ use serde::Serialize;
|
|||
|
||||
use super::TransferRecord;
|
||||
|
||||
// Format preferred by the Echo Client when using the Pick-List function.
|
||||
// Note that this does not export plate info!
|
||||
// Exports of this type should combine all transfers between the two actively selected plates.
|
||||
/// Format preferred by the Echo Client when using the Pick-List function.
|
||||
///
|
||||
/// Note that this does not export plate info!
|
||||
/// Exports of this type should combine all transfers between the two actively selected plates.
|
||||
#[derive(Serialize, Debug)]
|
||||
pub struct EchoClientTransferRecord {
|
||||
#[serde(rename = "SrcWell")]
|
||||
|
|
|
|||
|
|
@ -1,10 +1,17 @@
|
|||
//! Auto module for importing picklists without creating plates first
|
||||
//!
|
||||
//! Before the auto module, it was necessary for a user to create the plates
|
||||
//! used in an imported transfer before import.
|
||||
|
||||
use super::{string_well_to_pt, TransferRecord, read_csv};
|
||||
use crate::plate::{PlateFormat, PlateType};
|
||||
use crate::plate_instances::PlateInstance;
|
||||
use crate::transfer::Transfer;
|
||||
use crate::transfer_volume::{TransferVolume, VolumeMaps};
|
||||
use crate::Well;
|
||||
use crate::transfer_region::{CustomRegion, Region, TransferRegion};
|
||||
|
||||
use std::collections::HashSet;
|
||||
use std::collections::{HashSet, HashMap};
|
||||
|
||||
pub struct AutoOutput {
|
||||
pub sources: Vec<PlateInstance>,
|
||||
|
|
@ -12,6 +19,7 @@ pub struct AutoOutput {
|
|||
pub transfers: Vec<Transfer>,
|
||||
}
|
||||
|
||||
/// Two lists of plates that are guaranteed to be unique (no duplicate plates)
|
||||
struct UniquePlates {
|
||||
sources: Vec<PlateInstance>,
|
||||
destinations: Vec<PlateInstance>,
|
||||
|
|
@ -24,6 +32,12 @@ const W384_ROW_MAX: u8 = 16;
|
|||
const W1536_COL_MAX: u8 = 48;
|
||||
const W1536_ROW_MAX: u8 = 32;
|
||||
|
||||
/// Main function for the auto module
|
||||
/// Takes a list of pre-deserialized transfer records and generates output
|
||||
/// This output is 3 lists of:
|
||||
/// 1. The source plates used in the picklist
|
||||
/// 2. The destination plates used in the picklist
|
||||
/// 3. All of the transfers between those plates
|
||||
pub fn auto(records: &[TransferRecord]) -> AutoOutput {
|
||||
let unique_plates = find_unique_plates(records);
|
||||
let transfers = get_transfer_for_all_pairs(records, &unique_plates);
|
||||
|
|
@ -31,11 +45,18 @@ pub fn auto(records: &[TransferRecord]) -> AutoOutput {
|
|||
AutoOutput { sources: unique_plates.sources, destinations: unique_plates.destinations, transfers }
|
||||
}
|
||||
|
||||
/// Helper function that reads a CSV and immediately dumps the resulting transfer records
|
||||
/// into the auto function defined in this module.
|
||||
pub fn read_csv_auto(data: &str) -> AutoOutput {
|
||||
let transfer_records = read_csv(data);
|
||||
auto(&transfer_records)
|
||||
}
|
||||
|
||||
/// Looks through a list of transfer records and generates two lists
|
||||
/// of all of the unique plates found in those transfers.
|
||||
/// Worth noting that the Transfer struct requires two associated PlateInstances;
|
||||
/// these PlateInstance structs are generated here---they are not present in a TransferRecord.
|
||||
/// See notes on the UniquePlates struct
|
||||
fn find_unique_plates(records: &[TransferRecord]) -> UniquePlates {
|
||||
let mut source_names: HashSet<&str> = HashSet::new();
|
||||
let mut destination_names: HashSet<&str> = HashSet::new();
|
||||
|
|
@ -79,10 +100,16 @@ fn find_unique_plates(records: &[TransferRecord]) -> UniquePlates {
|
|||
}
|
||||
}
|
||||
|
||||
/// Tries to guess the format of a plate given the southeastern-est well used.
|
||||
/// A picklist does not necessarily contain plate format info; this method guesses
|
||||
/// based on the well furthest from A1 that exists in a transfer.
|
||||
/// It's possible for a 1536 well plate to be seen as a 384 well if all of the wells
|
||||
/// used could have fit in the top-left quadrant of a 384 well plate
|
||||
/// (i.e. all lower than P24 in this case)
|
||||
fn guess_plate_size(plate_filtered_records: &[&TransferRecord], which: PlateType) -> PlateFormat {
|
||||
let mut guess = PlateFormat::W96; // Never guess smaller than 96
|
||||
for record in plate_filtered_records {
|
||||
if let Some((row, col)) = string_well_to_pt(match which {
|
||||
if let Some(Well { row, col }) = string_well_to_pt(match which {
|
||||
PlateType::Source => &record.source_well,
|
||||
PlateType::Destination => &record.destination_well,
|
||||
}) {
|
||||
|
|
@ -116,6 +143,17 @@ fn get_transfer_for_all_pairs(
|
|||
transfers
|
||||
}
|
||||
|
||||
/// Given a source and destination plate, get all of the wells transferred
|
||||
/// from source to destination and turn this into a Transfer.
|
||||
///
|
||||
/// Note that even if you have what looks like two separate transfers,
|
||||
/// this will join all transfers for a given source-dest pair.
|
||||
/// For example:
|
||||
/// Consider expanding all of src:A1 to the column dst:A
|
||||
/// and src:B1 -> row dst:1
|
||||
/// If you were making this transfer in plate tool, it would be easiest
|
||||
/// to do this as two separate transfers.
|
||||
/// On import, this would be seen as one transfer.
|
||||
fn get_transfer_for_pair(
|
||||
records: &[TransferRecord],
|
||||
source: &PlateInstance,
|
||||
|
|
@ -129,12 +167,16 @@ fn get_transfer_for_pair(
|
|||
.filter(|x| x.source_plate == source_name && x.destination_plate == destination_name)
|
||||
.peekable();
|
||||
|
||||
if filtered_records.peek().is_none() {
|
||||
return None;
|
||||
}
|
||||
filtered_records.peek()?;
|
||||
|
||||
let mut source_wells: HashSet<Well> = HashSet::new();
|
||||
let mut destination_wells: HashSet<Well> = HashSet::new();
|
||||
|
||||
// Volume Hash Maps
|
||||
let mut source_only_volume_map: HashMap<Well, f32> = HashMap::new();
|
||||
let mut destination_only_volume_map: HashMap<Well, f32> = HashMap::new();
|
||||
let mut paired_volume_map: HashMap<(Well, Well), f32> = HashMap::new();
|
||||
|
||||
let mut source_wells: HashSet<(u8, u8)> = HashSet::new();
|
||||
let mut destination_wells: HashSet<(u8, u8)> = HashSet::new();
|
||||
for record in filtered_records {
|
||||
let source_point_opt = string_well_to_pt(&record.source_well);
|
||||
let destination_point_opt = string_well_to_pt(&record.destination_well);
|
||||
|
|
@ -145,10 +187,23 @@ fn get_transfer_for_pair(
|
|||
|
||||
source_wells.insert(source_point);
|
||||
destination_wells.insert(destination_point);
|
||||
|
||||
source_only_volume_map.entry(source_point).and_modify(|v| *v += record.volume)
|
||||
.or_insert(record.volume);
|
||||
destination_only_volume_map.entry(destination_point).and_modify(|v| *v += record.volume)
|
||||
.or_insert(record.volume);
|
||||
paired_volume_map.entry((source_point, destination_point)).and_modify(|v| *v += record.volume)
|
||||
.or_insert_with(|| record.volume); // No idea why this one needs to be different
|
||||
}
|
||||
}
|
||||
let source_wells_vec: Vec<(u8, u8)> = source_wells.into_iter().collect();
|
||||
let destination_wells_vec: Vec<(u8, u8)> = destination_wells.into_iter().collect();
|
||||
let source_wells_vec: Vec<Well> = source_wells.into_iter().collect();
|
||||
let destination_wells_vec: Vec<Well> = destination_wells.into_iter().collect();
|
||||
|
||||
let transfer_volume: TransferVolume = TransferVolume::WellMap(VolumeMaps {
|
||||
source_only: source_only_volume_map,
|
||||
destination_only: destination_only_volume_map,
|
||||
paired: paired_volume_map,
|
||||
});
|
||||
|
||||
let custom_region: Region =
|
||||
Region::Custom(CustomRegion::new(source_wells_vec, destination_wells_vec));
|
||||
|
|
@ -164,10 +219,13 @@ fn get_transfer_for_pair(
|
|||
|
||||
let transfer_name = format!("{} to {}", source.name, destination.name);
|
||||
|
||||
Some(Transfer::new(
|
||||
let mut transfer = Transfer::new(
|
||||
source.clone(),
|
||||
destination.clone(),
|
||||
transfer_region,
|
||||
transfer_name,
|
||||
))
|
||||
);
|
||||
transfer.volume = transfer_volume;
|
||||
|
||||
Some(transfer)
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,7 +1,11 @@
|
|||
use crate::transfer::Transfer;
|
||||
use crate::transfer_volume::TransferVolume;
|
||||
use crate::util::*;
|
||||
use crate::{transfer::Transfer, Well};
|
||||
|
||||
use super::{alternative_formats::EchoClientTransferRecord, mangle_headers::mangle_headers, transfer_record::TransferRecordDeserializeIntermediate, TransferRecord};
|
||||
use super::{
|
||||
alternative_formats::EchoClientTransferRecord, mangle_headers::mangle_headers,
|
||||
transfer_record::TransferRecordDeserializeIntermediate, TransferRecord,
|
||||
};
|
||||
use lazy_static::lazy_static;
|
||||
use regex::Regex;
|
||||
use std::error::Error;
|
||||
|
|
@ -15,17 +19,32 @@ pub fn transfer_to_records(
|
|||
let map = tr.transfer_region.calculate_map();
|
||||
|
||||
let mut records: Vec<TransferRecord> = vec![];
|
||||
if let TransferVolume::WellMap(wm) = &tr.volume {
|
||||
log::debug!("{:?}\n{}", wm.paired, wm.paired.len());
|
||||
}
|
||||
|
||||
for s_well in source_wells {
|
||||
let dest_wells = map(s_well);
|
||||
if let Some(dest_wells) = dest_wells {
|
||||
for d_well in dest_wells {
|
||||
// Get volume here:
|
||||
let volume: f32 = match &tr.volume {
|
||||
TransferVolume::Single(x) => *x, // If all have the same value, use it everywhere
|
||||
TransferVolume::WellMap(wm) => {
|
||||
*wm.paired.get(&(s_well, d_well)).unwrap_or(&2.5f32)
|
||||
}
|
||||
};
|
||||
|
||||
records.push(TransferRecord {
|
||||
source_plate: src_barcode.to_string(),
|
||||
source_well: format!("{}{}", num_to_letters(s_well.0).unwrap(), s_well.1),
|
||||
source_well: format!("{}{}", num_to_letters(s_well.row).unwrap(), s_well.col),
|
||||
destination_plate: dest_barcode.to_string(),
|
||||
destination_well: format!("{}{}", num_to_letters(d_well.0).unwrap(), d_well.1),
|
||||
volume: tr.volume,
|
||||
destination_well: format!(
|
||||
"{}{}",
|
||||
num_to_letters(d_well.row).unwrap(),
|
||||
d_well.col
|
||||
),
|
||||
volume,
|
||||
concentration: None,
|
||||
})
|
||||
}
|
||||
|
|
@ -52,16 +71,19 @@ pub fn records_to_echo_client_csv(trs: Vec<TransferRecord>) -> Result<String, Bo
|
|||
Ok(data)
|
||||
}
|
||||
|
||||
pub fn string_well_to_pt(input: &str) -> Option<(u8, u8)> {
|
||||
/// Converts "spreadsheet format" well identification to coordinates
|
||||
pub fn string_well_to_pt(input: &str) -> Option<Well> {
|
||||
lazy_static! {
|
||||
static ref REGEX: Regex = Regex::new(r"([A-Z,a-z]+)(\d+)").unwrap();
|
||||
|
||||
// Can this be removed?
|
||||
static ref REGEX_ALT: Regex = Regex::new(r"(\d+)").unwrap();
|
||||
}
|
||||
if let Some(c1) = REGEX.captures(input) {
|
||||
if let (Some(row), Some(col)) = (letters_to_num(&c1[1]), c1[2].parse::<u8>().ok()) {
|
||||
return Some((row, col))
|
||||
return Some(Well { row, col });
|
||||
} else {
|
||||
return None
|
||||
return None;
|
||||
}
|
||||
}
|
||||
None
|
||||
|
|
|
|||
|
|
@ -1,6 +1,15 @@
|
|||
//! This contains the `mangle_headers` function and its helpers
|
||||
//!
|
||||
//! Mangling headers is necessary to normalize CSV column names before
|
||||
//! deserialization can be done by Serde.
|
||||
//! Field detection occurs in `detect_field`.
|
||||
//!
|
||||
//! As of lib 0.4.0, unrecognized headers are ignored and left untouched by mangling.
|
||||
//! However, they are not passed through to any subsequent exports from plate-tool.
|
||||
|
||||
pub fn mangle_headers(data: &str) -> String {
|
||||
let (header, rows) = data.split_at(data.find('\n').unwrap());
|
||||
let fields = header.trim().split(",");
|
||||
let fields = header.trim().split(',');
|
||||
let mut modified_headers: Vec<String> = Vec::new();
|
||||
for field in fields {
|
||||
if let Some(f) = detect_field(field) {
|
||||
|
|
|
|||
|
|
@ -4,7 +4,6 @@ mod auto;
|
|||
mod mangle_headers;
|
||||
mod alternative_formats;
|
||||
|
||||
pub use transfer_record::volume_default;
|
||||
pub use transfer_record::TransferRecord;
|
||||
pub use conversion::*;
|
||||
|
||||
|
|
|
|||
|
|
@ -1,14 +1,18 @@
|
|||
use serde::{Deserialize, Serialize};
|
||||
|
||||
use crate::{plate::PlateFormat, transfer::Transfer, util::num_to_letters};
|
||||
use crate::{plate::PlateFormat, util::num_to_letters};
|
||||
|
||||
/// Represents a single line of a CSV picklist.
|
||||
/// In practice, this is generated from the deserialize intermediate.
|
||||
/// A list of `TransferRecord`s can be used to create a `transfer::Transfer` struct;
|
||||
/// see the `auto` module for this.
|
||||
#[derive(Serialize, Debug, Clone)]
|
||||
pub struct TransferRecord {
|
||||
#[serde(rename = "Source Plate")]
|
||||
#[serde(rename = "Source Barcode")]
|
||||
pub source_plate: String,
|
||||
#[serde(rename = "Source Well")]
|
||||
pub source_well: String,
|
||||
#[serde(rename = "Dest Plate")]
|
||||
#[serde(rename = "Dest Barcode")]
|
||||
pub destination_plate: String,
|
||||
#[serde(rename = "Destination Well")]
|
||||
pub destination_well: String,
|
||||
|
|
@ -18,6 +22,12 @@ pub struct TransferRecord {
|
|||
pub concentration: Option<f32>,
|
||||
}
|
||||
|
||||
/// The deserialization intermediate is generated from a mangled CSV s.t.
|
||||
/// the column headers are standardized to those given to the derive macro.
|
||||
///
|
||||
/// `TransferRecord` can *always* be generated from the intermediate.
|
||||
/// Currently there's no reason why the inverse couldn't be true,
|
||||
/// but there's no reason to convert back into the deserialize-only intermediate.
|
||||
#[derive(Deserialize, Debug, Clone)]
|
||||
pub struct TransferRecordDeserializeIntermediate {
|
||||
#[serde(rename = "sourceplate")]
|
||||
|
|
@ -64,7 +74,7 @@ impl From<TransferRecordDeserializeIntermediate> for TransferRecord {
|
|||
}
|
||||
}
|
||||
|
||||
let volume = value.volume.unwrap_or(volume_default());
|
||||
let volume = value.volume.unwrap_or(2.5f32);
|
||||
|
||||
TransferRecord {
|
||||
source_plate: value.source_plate,
|
||||
|
|
@ -78,6 +88,7 @@ impl From<TransferRecordDeserializeIntermediate> for TransferRecord {
|
|||
}
|
||||
|
||||
impl TransferRecordDeserializeIntermediate {
|
||||
/// Used to cull malformed picklist entries that lack required information
|
||||
pub fn is_empty(&self) -> bool {
|
||||
self.source_plate.is_empty()
|
||||
|| self.destination_plate.is_empty()
|
||||
|
|
@ -94,7 +105,3 @@ fn numeric_well_to_alphanumeric(input: u16, pformat: PlateFormat) -> Option<Stri
|
|||
|
||||
Some(format!("{}{}", row_str, column))
|
||||
}
|
||||
|
||||
pub fn volume_default() -> f32 {
|
||||
Transfer::default().volume
|
||||
}
|
||||
|
|
|
|||
|
|
@ -3,4 +3,8 @@ pub mod plate;
|
|||
pub mod plate_instances;
|
||||
pub mod transfer;
|
||||
pub mod transfer_region;
|
||||
pub mod transfer_volume;
|
||||
pub mod util;
|
||||
|
||||
mod well;
|
||||
pub use well::Well;
|
||||
|
|
|
|||
|
|
@ -1,5 +1,8 @@
|
|||
use crate::transfer_volume;
|
||||
|
||||
use super::plate_instances::*;
|
||||
use super::transfer_region::*;
|
||||
use super::transfer_volume::*;
|
||||
use serde::Deserialize;
|
||||
use serde::Serialize;
|
||||
use uuid::Uuid;
|
||||
|
|
@ -14,8 +17,7 @@ pub struct Transfer {
|
|||
#[serde(default = "Uuid::now_v7")]
|
||||
pub id: Uuid,
|
||||
pub transfer_region: TransferRegion,
|
||||
#[serde(default = "default_volume")]
|
||||
pub volume: f32,
|
||||
pub volume: TransferVolume,
|
||||
}
|
||||
|
||||
impl Default for Transfer {
|
||||
|
|
@ -26,15 +28,11 @@ impl Default for Transfer {
|
|||
name: "New Transfer".to_string(),
|
||||
id: Default::default(),
|
||||
transfer_region: Default::default(),
|
||||
volume: default_volume(),
|
||||
volume: Default::default(),
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
fn default_volume() -> f32 {
|
||||
2.5f32
|
||||
}
|
||||
|
||||
impl Transfer {
|
||||
pub fn new(
|
||||
source: PlateInstance,
|
||||
|
|
@ -48,7 +46,7 @@ impl Transfer {
|
|||
name,
|
||||
id: Uuid::now_v7(),
|
||||
transfer_region: tr,
|
||||
volume: 2.5,
|
||||
volume: transfer_volume::TransferVolume::Single(2.5),
|
||||
}
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,31 +1,32 @@
|
|||
use serde::{Deserialize, Serialize};
|
||||
|
||||
use super::plate::Plate;
|
||||
use crate::Well;
|
||||
|
||||
#[derive(Clone, PartialEq, Eq, Serialize, Deserialize, Debug)]
|
||||
pub struct CustomRegion {
|
||||
src: Vec<(u8, u8)>,
|
||||
dest: Vec<(u8, u8)>,
|
||||
src: Vec<Well>,
|
||||
dest: Vec<Well>,
|
||||
}
|
||||
|
||||
impl CustomRegion {
|
||||
pub fn new(src: Vec<(u8, u8)>, dest: Vec<(u8, u8)>) -> Self {
|
||||
pub fn new(src: Vec<Well>, dest: Vec<Well>) -> Self {
|
||||
CustomRegion { src, dest }
|
||||
}
|
||||
}
|
||||
|
||||
#[derive(Clone, PartialEq, Eq, Serialize, Deserialize, Debug)]
|
||||
pub enum Region {
|
||||
Rect((u8, u8), (u8, u8)),
|
||||
Point((u8, u8)),
|
||||
Rect(Well, Well),
|
||||
Point(Well),
|
||||
Custom(CustomRegion),
|
||||
}
|
||||
impl Default for Region {
|
||||
fn default() -> Self {
|
||||
Region::Point((1, 1))
|
||||
Region::Point(Well { row: 1, col: 1 })
|
||||
}
|
||||
}
|
||||
impl TryFrom<Region> for ((u8, u8), (u8, u8)) {
|
||||
impl TryFrom<Region> for (Well, Well) {
|
||||
type Error = &'static str;
|
||||
fn try_from(region: Region) -> Result<Self, Self::Error> {
|
||||
if let Region::Rect(c1, c2) = region {
|
||||
|
|
@ -37,12 +38,10 @@ impl TryFrom<Region> for ((u8, u8), (u8, u8)) {
|
|||
}
|
||||
}
|
||||
|
||||
type Corner = (u8, u8);
|
||||
type Rectangle = (Corner, Corner);
|
||||
impl Region {
|
||||
pub fn new_custom(transfers: &Vec<Rectangle>) -> Self {
|
||||
let mut src_pts: Vec<(u8, u8)> = Vec::with_capacity(transfers.len());
|
||||
let mut dest_pts: Vec<(u8, u8)> = Vec::with_capacity(transfers.len());
|
||||
pub fn new_custom(transfers: &Vec<(Well, Well)>) -> Self {
|
||||
let mut src_pts: Vec<Well> = Vec::with_capacity(transfers.len());
|
||||
let mut dest_pts: Vec<Well> = Vec::with_capacity(transfers.len());
|
||||
|
||||
for transfer in transfers {
|
||||
src_pts.push(transfer.0);
|
||||
|
|
@ -80,10 +79,10 @@ impl Default for TransferRegion {
|
|||
}
|
||||
|
||||
impl TransferRegion {
|
||||
pub fn get_source_wells(&self) -> Vec<(u8, u8)> {
|
||||
pub fn get_source_wells(&self) -> Vec<Well> {
|
||||
match &self.source_region {
|
||||
Region::Rect(c1, c2) => {
|
||||
let mut wells = Vec::<(u8, u8)>::new();
|
||||
let mut wells = Vec::<Well>::new();
|
||||
let (ul, br) = standardize_rectangle(c1, c2);
|
||||
let (interleave_i, interleave_j) = self.interleave_source;
|
||||
// NOTE: This will panic if either is 0!
|
||||
|
|
@ -93,12 +92,12 @@ impl TransferRegion {
|
|||
let (interleave_i, interleave_j) =
|
||||
(i8::max(interleave_i, 1), i8::max(interleave_j, 1));
|
||||
|
||||
for i in (ul.0..=br.0).step_by(i8::abs(interleave_i) as usize) {
|
||||
for j in (ul.1..=br.1).step_by(i8::abs(interleave_j) as usize) {
|
||||
for i in (ul.row..=br.row).step_by(i8::abs(interleave_i) as usize) {
|
||||
for j in (ul.col..=br.col).step_by(i8::abs(interleave_j) as usize) {
|
||||
// NOTE: It looks like we're ignoring negative interleaves,
|
||||
// because it wouldn't make a difference here---the same
|
||||
// wells will still be involved in the transfer.
|
||||
wells.push((i, j))
|
||||
wells.push(Well { row: i, col: j })
|
||||
}
|
||||
}
|
||||
wells
|
||||
|
|
@ -108,14 +107,14 @@ impl TransferRegion {
|
|||
}
|
||||
}
|
||||
|
||||
pub fn get_destination_wells(&self) -> Vec<(u8, u8)> {
|
||||
pub fn get_destination_wells(&self) -> Vec<Well> {
|
||||
match &self.source_region {
|
||||
Region::Custom(c) => c.dest.clone(),
|
||||
_ => {
|
||||
let map = self.calculate_map();
|
||||
let source_wells = self.get_source_wells();
|
||||
|
||||
let mut wells = Vec::<(u8, u8)>::new();
|
||||
let mut wells = Vec::<Well>::new();
|
||||
|
||||
for well in source_wells {
|
||||
if let Some(mut dest_wells) = map(well) {
|
||||
|
|
@ -129,14 +128,14 @@ impl TransferRegion {
|
|||
}
|
||||
|
||||
#[allow(clippy::type_complexity)] // Resolving gives inherent associated type error
|
||||
pub fn calculate_map(&self) -> Box<dyn Fn((u8, u8)) -> Option<Vec<(u8, u8)>> + '_> {
|
||||
pub fn calculate_map(&self) -> Box<dyn Fn(Well) -> Option<Vec<Well>> + '_> {
|
||||
// By validating first, we have a stronger guarantee that
|
||||
// this function will not panic. :)
|
||||
// log::debug!("Validating: {:?}", self.validate());
|
||||
if let Err(msg) = self.validate() {
|
||||
eprintln!("{}", msg);
|
||||
eprintln!("This transfer will be empty.");
|
||||
return Box::new(|(_, _)| None);
|
||||
return Box::new(|_| None);
|
||||
}
|
||||
|
||||
// log::debug!("What is ild? {:?}", self);
|
||||
|
|
@ -144,10 +143,10 @@ impl TransferRegion {
|
|||
let il_dest = self.interleave_dest;
|
||||
let il_source = self.interleave_source;
|
||||
|
||||
let source_corners: ((u8, u8), (u8, u8)) = match self.source_region {
|
||||
Region::Point((x, y)) => ((x, y), (x, y)),
|
||||
let source_corners: (Well, Well) = match self.source_region {
|
||||
Region::Point(w) => (w, w),
|
||||
Region::Rect(c1, c2) => (c1, c2),
|
||||
Region::Custom(_) => ((0, 0), (0, 0)),
|
||||
Region::Custom(_) => (Well { row: 0, col: 0 }, Well { row: 0, col: 0 }),
|
||||
};
|
||||
let (source_ul, _) = standardize_rectangle(&source_corners.0, &source_corners.1);
|
||||
// This map is not necessarily injective or surjective,
|
||||
|
|
@ -157,43 +156,44 @@ impl TransferRegion {
|
|||
|
||||
// Non-replicate transfers:
|
||||
match &self.dest_region {
|
||||
Region::Point((x, y)) => {
|
||||
Box::new(move |(i, j)| {
|
||||
if source_wells.contains(&(i, j)) {
|
||||
Region::Point(Well { row: x, col: y }) => {
|
||||
Box::new(move |Well { row: i, col: j }| {
|
||||
if source_wells.contains(&Well { row: i, col: j }) {
|
||||
// Validity here already checked by self.validate()
|
||||
Some(vec![(
|
||||
x + i
|
||||
.checked_sub(source_ul.0)
|
||||
Some(vec![Well {
|
||||
row: x + i
|
||||
.checked_sub(source_ul.row)
|
||||
.expect("Point cannot have been less than UL")
|
||||
.checked_div(il_source.0.unsigned_abs())
|
||||
.expect("Source interleave cannot be 0")
|
||||
.mul(il_dest.0.unsigned_abs()),
|
||||
y + j
|
||||
.checked_sub(source_ul.1)
|
||||
col: y + j
|
||||
.checked_sub(source_ul.col)
|
||||
.expect("Point cannot have been less than UL")
|
||||
.checked_div(il_source.1.unsigned_abs())
|
||||
.expect("Source interleave cannot be 0")
|
||||
.mul(il_dest.1.unsigned_abs()),
|
||||
)])
|
||||
}])
|
||||
} else {
|
||||
None
|
||||
}
|
||||
})
|
||||
}
|
||||
Region::Rect(c1, c2) => {
|
||||
Box::new(move |(i, j)| {
|
||||
if source_wells.contains(&(i, j)) {
|
||||
Box::new(move |w| {
|
||||
let Well { row: i, col: j } = w;
|
||||
if source_wells.contains(&w) {
|
||||
let possible_destination_wells = create_dense_rectangle(c1, c2);
|
||||
let (d_ul, d_br) = standardize_rectangle(c1, c2);
|
||||
let (s_ul, s_br) =
|
||||
standardize_rectangle(&source_corners.0, &source_corners.1);
|
||||
let s_dims = (
|
||||
s_br.0.checked_sub(s_ul.0).unwrap() + 1,
|
||||
s_br.1.checked_sub(s_ul.1).unwrap() + 1,
|
||||
s_br.row.checked_sub(s_ul.row).unwrap() + 1,
|
||||
s_br.col.checked_sub(s_ul.col).unwrap() + 1,
|
||||
);
|
||||
let d_dims = (
|
||||
d_br.0.checked_sub(d_ul.0).unwrap() + 1,
|
||||
d_br.1.checked_sub(d_ul.1).unwrap() + 1,
|
||||
d_br.row.checked_sub(d_ul.row).unwrap() + 1,
|
||||
d_br.col.checked_sub(d_ul.col).unwrap() + 1,
|
||||
);
|
||||
let number_used_src_wells = (
|
||||
// Number of used source wells
|
||||
|
|
@ -222,34 +222,34 @@ impl TransferRegion {
|
|||
.unwrap() as u8,
|
||||
);
|
||||
let i = i
|
||||
.saturating_sub(s_ul.0)
|
||||
.saturating_sub(s_ul.row)
|
||||
.saturating_div(il_source.0.unsigned_abs());
|
||||
let j = j
|
||||
.saturating_sub(s_ul.1)
|
||||
.saturating_sub(s_ul.col)
|
||||
.saturating_div(il_source.1.unsigned_abs());
|
||||
|
||||
Some(
|
||||
possible_destination_wells
|
||||
.into_iter()
|
||||
.filter(|(x, _)| {
|
||||
x.checked_sub(d_ul.0).unwrap()
|
||||
.filter(|Well { row: x , ..}| {
|
||||
x.checked_sub(d_ul.row).unwrap()
|
||||
% (number_used_src_wells.0 * il_dest.0.unsigned_abs()) // Counter along x
|
||||
== (il_dest.0.unsigned_abs() *i)
|
||||
% (number_used_src_wells.0 * il_dest.0.unsigned_abs())
|
||||
})
|
||||
.filter(|(_, y)| {
|
||||
y.checked_sub(d_ul.1).unwrap()
|
||||
.filter(|Well { col: y, .. }| {
|
||||
y.checked_sub(d_ul.col).unwrap()
|
||||
% (number_used_src_wells.1 * il_dest.1.unsigned_abs()) // Counter along u
|
||||
== (il_dest.1.unsigned_abs() *j)
|
||||
% (number_used_src_wells.1 * il_dest.1.unsigned_abs())
|
||||
})
|
||||
.filter(|(x, y)| {
|
||||
.filter(|Well { row: x, col: y }| {
|
||||
// How many times have we replicated? < How many are we allowed
|
||||
// to replicate?
|
||||
x.checked_sub(d_ul.0).unwrap().div_euclid(
|
||||
x.checked_sub(d_ul.row).unwrap().div_euclid(
|
||||
number_used_src_wells.0 * il_dest.0.unsigned_abs(),
|
||||
) < count.0
|
||||
&& y.checked_sub(d_ul.1).unwrap().div_euclid(
|
||||
&& y.checked_sub(d_ul.col).unwrap().div_euclid(
|
||||
number_used_src_wells.1 * il_dest.1.unsigned_abs(),
|
||||
) < count.1
|
||||
})
|
||||
|
|
@ -260,14 +260,14 @@ impl TransferRegion {
|
|||
}
|
||||
})
|
||||
}
|
||||
Region::Custom(c) => Box::new(move |(i, j)| {
|
||||
Region::Custom(c) => Box::new(move |Well { row: i, col: j }| {
|
||||
let src = c.src.clone();
|
||||
let dest = c.dest.clone();
|
||||
|
||||
let points: Vec<(u8, u8)> = src
|
||||
let points: Vec<Well> = src
|
||||
.iter()
|
||||
.enumerate()
|
||||
.filter(|(_index, (x, y))| *x == i && *y == j)
|
||||
.filter(|(_index, Well { row: x, col: y })| *x == i && *y == j)
|
||||
.map(|(index, _)| dest[index])
|
||||
.collect();
|
||||
if points.is_empty() {
|
||||
|
|
@ -296,15 +296,15 @@ impl TransferRegion {
|
|||
// later
|
||||
Region::Rect(s1, s2) => {
|
||||
// Check if all source wells exist:
|
||||
if s1.0 == 0 || s1.1 == 0 || s2.0 == 0 || s2.1 == 0 {
|
||||
if s1.row == 0 || s1.col == 0 || s2.row == 0 || s2.col == 0 {
|
||||
return Err("Source region is out-of-bounds! (Too small)");
|
||||
}
|
||||
// Sufficient to check if the corners are in-bounds
|
||||
let source_max = self.source_plate.size();
|
||||
if s1.0 > source_max.0 || s2.0 > source_max.0 {
|
||||
if s1.row > source_max.0 || s2.row > source_max.0 {
|
||||
return Err("Source region is out-of-bounds! (Too tall)");
|
||||
}
|
||||
if s1.1 > source_max.1 || s2.1 > source_max.1 {
|
||||
if s1.col > source_max.1 || s2.col > source_max.1 {
|
||||
// log::debug!("s1.1: {}, max.1: {}", s1.1, source_max.1);
|
||||
return Err("Source region is out-of-bounds! (Too wide)");
|
||||
}
|
||||
|
|
@ -325,28 +325,34 @@ impl TransferRegion {
|
|||
}
|
||||
}
|
||||
|
||||
fn create_dense_rectangle(c1: &(u8, u8), c2: &(u8, u8)) -> Vec<(u8, u8)> {
|
||||
fn create_dense_rectangle(c1: &Well, c2: &Well) -> Vec<Well> {
|
||||
// Creates a vector of every point between two corners
|
||||
let (c1, c2) = standardize_rectangle(c1, c2);
|
||||
|
||||
let mut points = Vec::<(u8, u8)>::new();
|
||||
for i in c1.0..=c2.0 {
|
||||
for j in c1.1..=c2.1 {
|
||||
points.push((i, j));
|
||||
let mut points = Vec::<Well>::new();
|
||||
for i in c1.row..=c2.row {
|
||||
for j in c1.col..=c2.col {
|
||||
points.push(Well { row: i, col: j });
|
||||
}
|
||||
}
|
||||
|
||||
points
|
||||
}
|
||||
|
||||
fn standardize_rectangle(c1: &(u8, u8), c2: &(u8, u8)) -> ((u8, u8), (u8, u8)) {
|
||||
let upper_left_i = u8::min(c1.0, c2.0);
|
||||
let upper_left_j = u8::min(c1.1, c2.1);
|
||||
let bottom_right_i = u8::max(c1.0, c2.0);
|
||||
let bottom_right_j = u8::max(c1.1, c2.1);
|
||||
fn standardize_rectangle(c1: &Well, c2: &Well) -> (Well, Well) {
|
||||
let upper_left_i = u8::min(c1.row, c2.row);
|
||||
let upper_left_j = u8::min(c1.col, c2.col);
|
||||
let bottom_right_i = u8::max(c1.row, c2.row);
|
||||
let bottom_right_j = u8::max(c1.col, c2.col);
|
||||
(
|
||||
(upper_left_i, upper_left_j),
|
||||
(bottom_right_i, bottom_right_j),
|
||||
Well {
|
||||
row: upper_left_i,
|
||||
col: upper_left_j,
|
||||
},
|
||||
Well {
|
||||
row: bottom_right_i,
|
||||
col: bottom_right_j,
|
||||
},
|
||||
)
|
||||
}
|
||||
|
||||
|
|
@ -363,7 +369,7 @@ impl fmt::Display for TransferRegion {
|
|||
let mut source_string = String::new();
|
||||
for i in 1..=source_dims.0 {
|
||||
for j in 1..=source_dims.1 {
|
||||
if source_wells.contains(&(i, j)) {
|
||||
if source_wells.contains(&Well { row: i, col: j }) {
|
||||
source_string.push('x')
|
||||
} else {
|
||||
source_string.push('.')
|
||||
|
|
@ -379,7 +385,7 @@ impl fmt::Display for TransferRegion {
|
|||
let mut dest_string = String::new();
|
||||
for i in 1..=dest_dims.0 {
|
||||
for j in 1..=dest_dims.1 {
|
||||
if dest_wells.contains(&(i, j)) {
|
||||
if dest_wells.contains(&Well { row: i, col: j }) {
|
||||
dest_string.push('x')
|
||||
} else {
|
||||
dest_string.push('.')
|
||||
|
|
@ -393,134 +399,130 @@ impl fmt::Display for TransferRegion {
|
|||
|
||||
#[cfg(test)]
|
||||
mod tests {
|
||||
use wasm_bindgen_test::*;
|
||||
|
||||
use crate::data::plate::*;
|
||||
use crate::data::transfer_region::*;
|
||||
use crate::plate::*;
|
||||
use crate::transfer_region::*;
|
||||
|
||||
#[test]
|
||||
#[wasm_bindgen_test]
|
||||
fn test_simple_transfer() {
|
||||
let source = Plate::new(PlateType::Source, PlateFormat::W96);
|
||||
let destination = Plate::new(PlateType::Destination, PlateFormat::W384);
|
||||
|
||||
let transfer1 = TransferRegion {
|
||||
source_plate: source,
|
||||
source_region: Region::Rect((1, 1), (3, 3)),
|
||||
source_region: Region::Rect(Well{ row: 1, col: 1}, Well { row: 1, col: 1 }),
|
||||
dest_plate: destination,
|
||||
dest_region: Region::Point((3, 3)),
|
||||
dest_region: Region::Point(Well {row: 3, col: 3}),
|
||||
interleave_source: (1, 1),
|
||||
interleave_dest: (1, 1),
|
||||
};
|
||||
let transfer1_map = transfer1.calculate_map();
|
||||
assert_eq!(
|
||||
transfer1_map((1, 1)),
|
||||
Some(vec! {(3,3)}),
|
||||
transfer1_map(Well {row: 1, col: 1}),
|
||||
Some(vec! {Well {row: 3, col: 3}}),
|
||||
"Failed basic shift transfer 1"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer1_map((1, 2)),
|
||||
Some(vec! {(3,4)}),
|
||||
transfer1_map(Well{ row: 1, col: 2}),
|
||||
Some(vec! {Well{ row: 3, col: 4}}),
|
||||
"Failed basic shift transfer 2"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer1_map((2, 2)),
|
||||
Some(vec! {(4,4)}),
|
||||
transfer1_map(Well{ row: 2, col: 2}),
|
||||
Some(vec! {Well{ row: 4, col: 4}}),
|
||||
"Failed basic shift transfer 3"
|
||||
);
|
||||
|
||||
let transfer2 = TransferRegion {
|
||||
source_plate: source,
|
||||
source_region: Region::Rect((1, 1), (3, 3)),
|
||||
source_region: Region::Rect(Well{ row: 1, col: 1}, Well{ row: 3, col: 3}),
|
||||
dest_plate: destination,
|
||||
dest_region: Region::Point((3, 3)),
|
||||
dest_region: Region::Point(Well{ row: 3, col: 3}),
|
||||
interleave_source: (2, 2),
|
||||
interleave_dest: (1, 1),
|
||||
};
|
||||
let transfer2_map = transfer2.calculate_map();
|
||||
assert_eq!(
|
||||
transfer2_map((1, 1)),
|
||||
Some(vec! {(3,3)}),
|
||||
transfer2_map(Well{ row: 1, col: 1}),
|
||||
Some(vec! {Well{ row: 3, col: 3}}),
|
||||
"Failed source interleave, type simple 1"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer2_map((1, 2)),
|
||||
transfer2_map(Well{ row: 1, col: 2}),
|
||||
None,
|
||||
"Failed source interleave, type simple 2"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer2_map((2, 2)),
|
||||
transfer2_map(Well{ row: 2, col: 2}),
|
||||
None,
|
||||
"Failed source interleave, type simple 3"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer2_map((3, 3)),
|
||||
Some(vec! {(4,4)}),
|
||||
transfer2_map(Well{ row: 3, col: 3}),
|
||||
Some(vec! {Well{ row: 4, col: 4}}),
|
||||
"Failed source interleave, type simple 4"
|
||||
);
|
||||
|
||||
let transfer3 = TransferRegion {
|
||||
source_plate: source,
|
||||
source_region: Region::Rect((1, 1), (3, 3)),
|
||||
source_region: Region::Rect(Well{ row: 1, col: 1}, Well{ row: 3, col: 3}),
|
||||
dest_plate: destination,
|
||||
dest_region: Region::Point((3, 3)),
|
||||
dest_region: Region::Point(Well{ row: 3, col: 3}),
|
||||
interleave_source: (1, 1),
|
||||
interleave_dest: (2, 3),
|
||||
};
|
||||
let transfer3_map = transfer3.calculate_map();
|
||||
assert_eq!(
|
||||
transfer3_map((1, 1)),
|
||||
Some(vec! {(3,3)}),
|
||||
transfer3_map(Well{ row: 1, col: 1}),
|
||||
Some(vec! {Well{ row: 3, col: 3}}),
|
||||
"Failed destination interleave, type simple 1"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer3_map((2, 1)),
|
||||
Some(vec! {(5,3)}),
|
||||
transfer3_map(Well{ row: 2, col: 1}),
|
||||
Some(vec! {Well{ row: 5, col: 3}}),
|
||||
"Failed destination interleave, type simple 2"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer3_map((1, 2)),
|
||||
Some(vec! {(3,6)}),
|
||||
transfer3_map(Well{ row: 1, col: 2}),
|
||||
Some(vec! {Well{ row: 3, col: 6}}),
|
||||
"Failed destination interleave, type simple 3"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer3_map((2, 2)),
|
||||
Some(vec! {(5,6)}),
|
||||
transfer3_map(Well{ row: 2, col: 2}),
|
||||
Some(vec! {Well{ row: 5, col: 6}}),
|
||||
"Failed destination interleave, type simple 4"
|
||||
);
|
||||
}
|
||||
|
||||
#[test]
|
||||
#[wasm_bindgen_test]
|
||||
fn test_replicate_transfer() {
|
||||
let source = Plate::new(PlateType::Source, PlateFormat::W96);
|
||||
let destination = Plate::new(PlateType::Destination, PlateFormat::W384);
|
||||
|
||||
let transfer1 = TransferRegion {
|
||||
source_plate: source,
|
||||
source_region: Region::Rect((1, 1), (2, 2)),
|
||||
source_region: Region::Rect(Well{ row: 1, col: 1}, Well{ row: 2, col: 2}),
|
||||
dest_plate: destination,
|
||||
dest_region: Region::Rect((2, 2), (11, 11)),
|
||||
dest_region: Region::Rect(Well{ row: 2, col: 2}, Well{row:11, col:11}),
|
||||
interleave_source: (1, 1),
|
||||
interleave_dest: (3, 3),
|
||||
};
|
||||
let transfer1_map = transfer1.calculate_map();
|
||||
assert_eq!(
|
||||
transfer1_map((1, 1)),
|
||||
Some(vec! {(2, 2), (2, 8), (8, 2), (8, 8)}),
|
||||
transfer1_map(Well{ row: 1, col: 1}),
|
||||
Some(vec! {Well{ row: 2, col: 2}, Well{ row: 2, col: 8}, Well{ row: 8, col: 2}, Well{ row: 8, col: 8}}),
|
||||
"Failed type replicate 1"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer1_map((2, 1)),
|
||||
Some(vec! {(5, 2), (5, 8), (11, 2), (11, 8)}),
|
||||
transfer1_map(Well{ row: 2, col: 1}),
|
||||
Some(vec! {Well{ row: 5, col: 2}, Well{ row: 5, col: 8}, Well{ row: 11, col: 2}, Well{ row: 11, col: 8}}),
|
||||
"Failed type replicate 1"
|
||||
);
|
||||
|
||||
let transfer2 = TransferRegion {
|
||||
source_plate: Plate::new(PlateType::Source, PlateFormat::W384),
|
||||
dest_plate: Plate::new(PlateType::Destination, PlateFormat::W384),
|
||||
source_region: Region::Rect((1, 1), (2, 3)),
|
||||
dest_region: Region::Rect((2, 2), (11, 16)),
|
||||
source_region: Region::Rect(Well{ row: 1, col: 1}, Well{ row: 2, col: 3}),
|
||||
dest_region: Region::Rect(Well{ row: 2, col: 2}, Well{ row: 11, col: 16}),
|
||||
interleave_source: (1, 1),
|
||||
interleave_dest: (2, 2),
|
||||
};
|
||||
|
|
@ -528,71 +530,69 @@ mod tests {
|
|||
let transfer2_dest = transfer2.get_destination_wells();
|
||||
assert_eq!(
|
||||
transfer2_source,
|
||||
vec![(1, 1), (1, 2), (1, 3), (2, 1), (2, 2), (2, 3)],
|
||||
vec![Well{ row: 1, col: 1}, Well{ row: 1, col: 2}, Well{ row: 1, col: 3}, Well{ row: 2, col: 1}, Well{ row: 2, col: 2}, Well{ row: 2, col: 3}],
|
||||
"Failed type replicate 2 source"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer2_dest,
|
||||
vec![
|
||||
(2, 2),
|
||||
(2, 8),
|
||||
(6, 2),
|
||||
(6, 8),
|
||||
(2, 4),
|
||||
(2, 10),
|
||||
(6, 4),
|
||||
(6, 10),
|
||||
(2, 6),
|
||||
(2, 12),
|
||||
(6, 6),
|
||||
(6, 12),
|
||||
(4, 2),
|
||||
(4, 8),
|
||||
(8, 2),
|
||||
(8, 8),
|
||||
(4, 4),
|
||||
(4, 10),
|
||||
(8, 4),
|
||||
(8, 10),
|
||||
(4, 6),
|
||||
(4, 12),
|
||||
(8, 6),
|
||||
(8, 12)
|
||||
Well{ row: 2, col: 2},
|
||||
Well{ row: 2, col: 8},
|
||||
Well{ row: 6, col: 2},
|
||||
Well{ row: 6, col: 8},
|
||||
Well{ row: 2, col: 4},
|
||||
Well{ row: 2, col: 10},
|
||||
Well{ row: 6, col: 4},
|
||||
Well{ row: 6, col: 10},
|
||||
Well{ row: 2, col: 6},
|
||||
Well{ row: 2, col: 12},
|
||||
Well{ row: 6, col: 6},
|
||||
Well{ row: 6, col: 12},
|
||||
Well{ row: 4, col: 2},
|
||||
Well{ row: 4, col: 8},
|
||||
Well{ row: 8, col: 2},
|
||||
Well{ row: 8, col: 8},
|
||||
Well{ row: 4, col: 4},
|
||||
Well{ row: 4, col: 10},
|
||||
Well{ row: 8, col: 4},
|
||||
Well{ row: 8, col: 10},
|
||||
Well{ row: 4, col: 6},
|
||||
Well{ row: 4, col: 12},
|
||||
Well{ row: 8, col: 6},
|
||||
Well{ row: 8, col: 12}
|
||||
],
|
||||
"Failed type replicate 2 destination"
|
||||
);
|
||||
}
|
||||
|
||||
#[test]
|
||||
#[wasm_bindgen_test]
|
||||
fn test_pooling_transfer() {
|
||||
use std::collections::HashSet;
|
||||
let transfer1 = TransferRegion {
|
||||
source_plate: Plate::new(PlateType::Source, PlateFormat::W384),
|
||||
dest_plate: Plate::new(PlateType::Destination, PlateFormat::W384),
|
||||
source_region: Region::Rect((1, 4), (3, 7)),
|
||||
dest_region: Region::Point((1, 9)),
|
||||
source_region: Region::Rect(Well{ row: 1, col: 4}, Well{ row: 3, col: 7}),
|
||||
dest_region: Region::Point(Well{ row: 1, col: 9}),
|
||||
interleave_source: (1, 1),
|
||||
interleave_dest: (0, 2),
|
||||
};
|
||||
//let transfer1_source = transfer1.get_source_wells();
|
||||
let mut transfer1_dest = transfer1.get_destination_wells();
|
||||
transfer1_dest.sort();
|
||||
transfer1_dest.dedup(); // Makes our check easier, otherwise we have repeated wells
|
||||
let transfer1_dest: HashSet<Well> = transfer1.get_destination_wells().into_iter().collect();
|
||||
let transfer1_map = transfer1.calculate_map();
|
||||
// Skipping source check---it's just 12 wells.
|
||||
assert_eq!(
|
||||
transfer1_dest,
|
||||
vec![(1, 9), (1, 11), (1, 13), (1, 15)],
|
||||
vec![Well{ row: 1, col: 9}, Well{ row: 1, col: 11}, Well{ row: 1, col: 13}, Well{ row: 1, col: 15}].into_iter().collect(),
|
||||
"Failed type pool 1 dest"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer1_map((2, 6)),
|
||||
Some(vec![(1, 13)]),
|
||||
transfer1_map(Well{ row: 2, col: 6}),
|
||||
Some(vec![Well{ row: 1, col: 13}]),
|
||||
"Failed type pool 1 map 1"
|
||||
);
|
||||
assert_eq!(
|
||||
transfer1_map((3, 7)),
|
||||
Some(vec![(1, 15)]),
|
||||
transfer1_map(Well{ row: 3, col: 7}),
|
||||
Some(vec![Well{ row: 1, col: 15}]),
|
||||
"Failed type pool 1 map 2"
|
||||
);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -0,0 +1,30 @@
|
|||
use serde::{Deserialize, Serialize};
|
||||
use std::collections::HashMap;
|
||||
|
||||
use crate::Well;
|
||||
|
||||
type WellPair = (Well, Well);
|
||||
|
||||
#[non_exhaustive]
|
||||
#[derive(Debug, PartialEq, Deserialize, Serialize, Clone)]
|
||||
pub enum TransferVolume {
|
||||
Single(f32),
|
||||
WellMap(VolumeMaps),
|
||||
}
|
||||
|
||||
#[serde_with::serde_as]
|
||||
#[derive(Debug, PartialEq, Deserialize, Serialize, Clone)]
|
||||
pub struct VolumeMaps {
|
||||
#[serde_as(as = "HashMap<serde_with::json::JsonString, _>")]
|
||||
pub source_only: HashMap<Well, f32>,
|
||||
#[serde_as(as = "HashMap<serde_with::json::JsonString, _>")]
|
||||
pub destination_only: HashMap<Well, f32>,
|
||||
#[serde_as(as = "HashMap<serde_with::json::JsonString, _>")]
|
||||
pub paired: HashMap<WellPair, f32>,
|
||||
}
|
||||
|
||||
impl Default for TransferVolume {
|
||||
fn default() -> Self {
|
||||
TransferVolume::Single(2.5f32)
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,9 @@
|
|||
use serde::{Deserialize, Serialize};
|
||||
|
||||
#[derive(Clone, Copy, PartialEq, Eq, Deserialize, Serialize, Debug, Hash)]
|
||||
pub struct Well {
|
||||
/// Top to bottom assuming landscape, i.e. lettered
|
||||
pub row: u8,
|
||||
/// Left to right assuming landscape, i.e. numbered
|
||||
pub col: u8,
|
||||
}
|
||||
|
|
@ -1,6 +1,6 @@
|
|||
[package]
|
||||
name = "plate-tool-web"
|
||||
version = "0.4.0"
|
||||
version = "0.5.0"
|
||||
edition = "2021"
|
||||
|
||||
# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
|
||||
|
|
|
|||
|
|
@ -0,0 +1,27 @@
|
|||
@use "sass:color";
|
||||
@use "./variables" as *;
|
||||
|
||||
$selection-border-width: 2px;
|
||||
|
||||
@mixin standard_button {
|
||||
color: inherit;
|
||||
|
||||
display: inline;
|
||||
margin-left: 3px;
|
||||
border: 2px solid rgba(1,1,1,0.2);
|
||||
background: transparent;
|
||||
|
||||
user-select: none;
|
||||
list-style: none;
|
||||
line-height: 1em;
|
||||
|
||||
&::before {
|
||||
text-align: center;
|
||||
vertical-align: middle;
|
||||
}
|
||||
&:hover {
|
||||
background: color.change($color-light, $alpha: 0.08);
|
||||
transition: background 0.1s;
|
||||
border: $selection-border-width solid color.change($color-light, $alpha:0.3);
|
||||
}
|
||||
}
|
||||
|
|
@ -2,6 +2,8 @@
|
|||
@use "../variables" as *;
|
||||
|
||||
div.plate_container {
|
||||
position: relative;
|
||||
|
||||
display: flex;
|
||||
flex-direction: column;
|
||||
justify-content: space-evenly;
|
||||
|
|
@ -38,4 +40,22 @@ div.plate_container {
|
|||
grid-row: 2;
|
||||
}
|
||||
}
|
||||
|
||||
div.plate_container--heatmap-notice {
|
||||
position: absolute;
|
||||
top: 0.5em;
|
||||
left: 0.5em;
|
||||
|
||||
animation: 1s 1 attention_on_load;
|
||||
}
|
||||
}
|
||||
|
||||
@keyframes attention_on_load {
|
||||
from{
|
||||
color: $color-light;
|
||||
transform: scale(1.05);
|
||||
}
|
||||
to {
|
||||
color: inherit;
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
@use "sass:color";
|
||||
@use "../variables" as *;
|
||||
@use "../button" as *;
|
||||
|
||||
div.transfer_menu {
|
||||
position: relative;
|
||||
|
|
@ -40,6 +41,11 @@ div.transfer_menu {
|
|||
}
|
||||
}
|
||||
|
||||
div.transfer_menu input[type="button"] {
|
||||
@include standard_button;
|
||||
}
|
||||
|
||||
|
||||
input {
|
||||
text-align: center;
|
||||
margin-left: 0.5em;
|
||||
|
|
@ -50,10 +56,10 @@ input {
|
|||
padding: 0;
|
||||
|
||||
&[type="text"] {
|
||||
width: 4em;
|
||||
width: 6em;
|
||||
}
|
||||
&[name="name"] {
|
||||
width: 6em; // Override above
|
||||
width: calc(100% - 6em); // Override above
|
||||
}
|
||||
&[type="number"] {
|
||||
width: 2em;
|
||||
|
|
|
|||
|
|
@ -1,5 +1,6 @@
|
|||
@use "sass:color";
|
||||
@use "../variables" as *;
|
||||
@use "../button" as *;
|
||||
|
||||
$selection-border-width: 2px;
|
||||
|
||||
|
|
@ -53,3 +54,17 @@ div.tree li {
|
|||
background: color.change($color-light, $alpha: 0.2);
|
||||
}
|
||||
}
|
||||
|
||||
div.tree--header {
|
||||
margin-top: 1%;
|
||||
display: flex;
|
||||
align-items: center;
|
||||
}
|
||||
|
||||
div.tree--header button {
|
||||
@include standard_button;
|
||||
|
||||
&::before {
|
||||
content: "Add";
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -12,6 +12,7 @@ use crate::components::states::MainState;
|
|||
|
||||
use plate_tool_lib::transfer::Transfer;
|
||||
use plate_tool_lib::transfer_region::{Region, TransferRegion};
|
||||
use plate_tool_lib::Well;
|
||||
|
||||
use plate_tool_lib::csv::{auto, string_well_to_pt, TransferRecord};
|
||||
|
||||
|
|
@ -238,7 +239,7 @@ pub fn import_transfer_csv_submit_callback(
|
|||
let from_dest = from_dest.value();
|
||||
let to_dest = to_dest.value();
|
||||
|
||||
let records: Vec<((u8, u8), (u8, u8))> = records
|
||||
let records: Vec<(Well, Well)> = records
|
||||
.iter()
|
||||
.filter(|record| record.source_plate == from_source)
|
||||
.filter(|record| record.destination_plate == from_dest)
|
||||
|
|
@ -295,11 +296,11 @@ fn auto_callback(
|
|||
Closure::<dyn FnMut(_)>::new(move |_| {
|
||||
let res = auto(&records);
|
||||
main_dispatch.reduce_mut(|state| {
|
||||
state.source_plates.extend(res.sources.into_iter());
|
||||
state.source_plates.extend(res.sources);
|
||||
state
|
||||
.destination_plates
|
||||
.extend(res.destinations.into_iter());
|
||||
state.transfers.extend(res.transfers.into_iter());
|
||||
.extend(res.destinations);
|
||||
state.transfers.extend(res.transfers);
|
||||
});
|
||||
})
|
||||
}
|
||||
|
|
|
|||
|
|
@ -9,8 +9,6 @@ use crate::components::states::MainState;
|
|||
|
||||
use super::create_close_button;
|
||||
|
||||
type NoParamsCallback = Box<dyn Fn(())>;
|
||||
|
||||
pub fn input_json_input_callback(
|
||||
main_dispatch: Dispatch<MainState>,
|
||||
modal: HtmlDialogElement,
|
||||
|
|
|
|||
|
|
@ -1,35 +1,27 @@
|
|||
#![allow(non_snake_case)]
|
||||
|
||||
use js_sys::Array;
|
||||
|
||||
use wasm_bindgen::{prelude::*, JsCast, JsValue};
|
||||
use web_sys::{
|
||||
Blob, HtmlAnchorElement, HtmlDialogElement, HtmlElement, HtmlFormElement, HtmlInputElement, Url,
|
||||
};
|
||||
use yew::prelude::*;
|
||||
use yewdux::prelude::*;
|
||||
|
||||
use crate::components::states::{CurrentTransfer, MainState};
|
||||
|
||||
use crate::state_to_csv;
|
||||
use crate::components::{new_plate_dialog::{NewPlateDialogType}, states::{CurrentTransfer, MainState}};
|
||||
|
||||
type NoParamsCallback = Box<dyn Fn(())>;
|
||||
|
||||
pub fn new_plate_dialog_callback(
|
||||
new_plate_dialog_is_open: UseStateHandle<bool>,
|
||||
new_plate_dialog_is_open: UseStateHandle<Option<NewPlateDialogType>>,
|
||||
) -> NoParamsCallback {
|
||||
let new_plate_dialog_is_open = new_plate_dialog_is_open.clone();
|
||||
Box::new(move |_| {
|
||||
new_plate_dialog_is_open.set(false);
|
||||
new_plate_dialog_is_open.set(None);
|
||||
})
|
||||
}
|
||||
|
||||
pub fn open_new_plate_dialog_callback(
|
||||
new_plate_dialog_is_open: UseStateHandle<bool>,
|
||||
) -> NoParamsCallback {
|
||||
new_plate_dialog_is_open: UseStateHandle<Option<NewPlateDialogType>>
|
||||
) -> Box<dyn Fn(NewPlateDialogType)> {
|
||||
let new_plate_dialog_is_open = new_plate_dialog_is_open.clone();
|
||||
Box::new(move |_| {
|
||||
new_plate_dialog_is_open.set(true);
|
||||
Box::new(move |dt| {
|
||||
new_plate_dialog_is_open.set(Some(dt));
|
||||
})
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -1,10 +1,9 @@
|
|||
#![allow(non_snake_case)]
|
||||
|
||||
use js_sys::Function;
|
||||
|
||||
use wasm_bindgen::{prelude::*, JsCast};
|
||||
use web_sys::{
|
||||
FileReader, HtmlButtonElement, HtmlDialogElement, HtmlElement, HtmlFormElement,
|
||||
HtmlInputElement, HtmlOptionElement, HtmlSelectElement,
|
||||
HtmlDialogElement, HtmlFormElement, HtmlOptionElement, HtmlSelectElement,
|
||||
};
|
||||
|
||||
use yew::prelude::*;
|
||||
|
|
@ -14,8 +13,6 @@ use crate::components::states::{CsvExportType, MainState};
|
|||
|
||||
use super::create_close_button;
|
||||
|
||||
type NoParamsCallback = Box<dyn Fn(())>;
|
||||
|
||||
pub fn toggle_in_transfer_hashes_callback(
|
||||
main_dispatch: Dispatch<MainState>,
|
||||
) -> Callback<web_sys::MouseEvent> {
|
||||
|
|
|
|||
|
|
@ -4,8 +4,6 @@ use wasm_bindgen::{prelude::*, JsCast};
|
|||
use web_sys::HtmlElement;
|
||||
use yew::prelude::*;
|
||||
|
||||
type NoParamsCallback = Box<dyn Fn(())>;
|
||||
|
||||
pub fn create_close_button(close: &Closure<dyn FnMut(Event)>) -> HtmlElement {
|
||||
let document = web_sys::window().unwrap().document().unwrap();
|
||||
let close_button = document
|
||||
|
|
|
|||
|
|
@ -6,7 +6,7 @@ use yew::prelude::*;
|
|||
use yewdux::prelude::*;
|
||||
|
||||
use crate::components::transfer_menu::RegionDisplay;
|
||||
use plate_tool_lib::{transfer::Transfer, transfer_region::Region};
|
||||
use plate_tool_lib::{transfer::Transfer, transfer_region::Region, transfer_volume::TransferVolume};
|
||||
|
||||
use crate::components::states::{CurrentTransfer, MainState};
|
||||
|
||||
|
|
@ -142,7 +142,7 @@ pub fn on_volume_change_callback(ct_dispatch: Dispatch<CurrentTransfer>) -> Call
|
|||
.expect("Must have been emitted by input");
|
||||
if let Ok(num) = input.value().parse::<f32>() {
|
||||
ct_dispatch.reduce_mut(|state| {
|
||||
state.transfer.volume = num;
|
||||
state.transfer.volume = TransferVolume::Single(num);
|
||||
});
|
||||
}
|
||||
})
|
||||
|
|
@ -184,12 +184,18 @@ pub fn save_transfer_button_callback_callback(
|
|||
.iter()
|
||||
.find(|dpi| dpi.get_uuid() == main_state.selected_dest_plate)
|
||||
{
|
||||
let new_transfer = Transfer::new(
|
||||
// Only mutable for volume assignment!
|
||||
let mut new_transfer = Transfer::new(
|
||||
spi.clone(),
|
||||
dpi.clone(),
|
||||
ct_state.transfer.transfer_region.clone(),
|
||||
ct_state.transfer.name.clone(),
|
||||
);
|
||||
|
||||
// This clone is cheap - we know this is just a single value
|
||||
// so cloning f32 will be fast.
|
||||
new_transfer.volume = ct_state.transfer.volume.clone();
|
||||
|
||||
main_dispatch.reduce_mut(|state| {
|
||||
state.transfers.push(new_transfer);
|
||||
state.selected_transfer = state
|
||||
|
|
|
|||
|
|
@ -1,8 +1,8 @@
|
|||
use plate_tool_lib::{plate::PlateType, plate_instances::PlateInstance};
|
||||
use plate_tool_lib::{plate::PlateType};
|
||||
use uuid::Uuid;
|
||||
use wasm_bindgen::{prelude::*, JsCast};
|
||||
use web_sys::{
|
||||
HtmlDialogElement, HtmlElement, HtmlFormElement, HtmlInputElement, HtmlOptionElement,
|
||||
HtmlDialogElement, HtmlElement, HtmlOptionElement,
|
||||
HtmlSelectElement,
|
||||
};
|
||||
|
||||
|
|
@ -203,7 +203,7 @@ fn find_plate_type(main_dispatch: Dispatch<MainState>, id: Uuid) -> Option<Plate
|
|||
.iter()
|
||||
.any(|x| x.get_uuid() == id)
|
||||
{
|
||||
return Some(PlateType::Source);
|
||||
Some(PlateType::Source)
|
||||
} else if main_dispatch
|
||||
.get()
|
||||
.destination_plates
|
||||
|
|
|
|||
|
|
@ -2,7 +2,7 @@
|
|||
use yew::prelude::*;
|
||||
use yewdux::prelude::*;
|
||||
|
||||
use crate::components::new_plate_dialog::NewPlateDialog;
|
||||
use crate::components::new_plate_dialog::{NewPlateDialog, NewPlateDialogType};
|
||||
use crate::components::plates::plate_container::PlateContainer;
|
||||
use crate::components::states::{CurrentTransfer, MainState};
|
||||
use crate::components::transfer_menu::TransferMenu;
|
||||
|
|
@ -53,7 +53,7 @@ pub fn MainWindow() -> Html {
|
|||
main_window_callbacks::change_csv_export_type_callback(main_dispatch)
|
||||
};
|
||||
|
||||
let new_plate_dialog_is_open = use_state_eq(|| false);
|
||||
let new_plate_dialog_is_open: UseStateHandle<Option<NewPlateDialogType>> = use_state_eq(|| None);
|
||||
let new_plate_dialog_callback =
|
||||
main_window_callbacks::new_plate_dialog_callback(new_plate_dialog_is_open.clone());
|
||||
|
||||
|
|
@ -124,8 +124,8 @@ pub fn MainWindow() -> Html {
|
|||
<TransferMenu />
|
||||
<PlateContainer source_dims={source_plate_instance}
|
||||
destination_dims={destination_plate_instance}/>
|
||||
if {*new_plate_dialog_is_open} {
|
||||
<NewPlateDialog close_callback={new_plate_dialog_callback}/>
|
||||
if {new_plate_dialog_is_open.is_some()} {
|
||||
<NewPlateDialog close_callback={new_plate_dialog_callback} dialog_type={new_plate_dialog_is_open.unwrap()}/>
|
||||
}
|
||||
</div>
|
||||
</>
|
||||
|
|
|
|||
|
|
@ -10,6 +10,16 @@ use crate::components::callbacks::new_plate_dialog_callbacks;
|
|||
#[derive(PartialEq, Properties)]
|
||||
pub struct NewPlateDialogProps {
|
||||
pub close_callback: Callback<()>,
|
||||
pub dialog_type: NewPlateDialogType,
|
||||
}
|
||||
|
||||
#[derive(PartialEq, Clone, Copy, Debug)]
|
||||
pub enum NewPlateDialogType {
|
||||
SourceOnly,
|
||||
DestinationOnly,
|
||||
|
||||
#[allow(dead_code)]
|
||||
Both, // Retained old functionality
|
||||
}
|
||||
|
||||
#[function_component]
|
||||
|
|
@ -43,9 +53,15 @@ pub fn NewPlateDialog(props: &NewPlateDialogProps) -> Html {
|
|||
);
|
||||
}
|
||||
|
||||
let header_interior_text = match props.dialog_type {
|
||||
NewPlateDialogType::Both => "",
|
||||
NewPlateDialogType::SourceOnly => " source",
|
||||
NewPlateDialogType::DestinationOnly => " destination",
|
||||
};
|
||||
|
||||
html! {
|
||||
<dialog ref={dialog_ref} class="dialog new_plate_dialog" onclose={onclose}>
|
||||
<h2>{"Create a plate:"}</h2>
|
||||
<h2>{format!("Create a{} plate:", header_interior_text)}</h2>
|
||||
<form onsubmit={new_plate_callback}>
|
||||
<input type="text" name="new_plate_name" placeholder="Name"/>
|
||||
<select name="plate_format">
|
||||
|
|
@ -58,13 +74,35 @@ pub fn NewPlateDialog(props: &NewPlateDialogProps) -> Html {
|
|||
<option value="1536">{"1536"}</option>
|
||||
<option value="3456">{"3456"}</option>
|
||||
</select>
|
||||
<input type="radio" name="new_plate_type" id="npt_src" value="src" />
|
||||
<label for="npt_src">{"Source"}</label>
|
||||
<input type="radio" name="new_plate_type" id="npt_dest" value="dest" />
|
||||
<label for="npt_dest">{"Destination"}</label>
|
||||
{ plate_type_selector(props.dialog_type) }
|
||||
<input type="submit" name="new_plate_button" value="Create" />
|
||||
</form>
|
||||
<form class="modal_close" method="dialog"><button /></form>
|
||||
</dialog>
|
||||
}
|
||||
}
|
||||
|
||||
fn plate_type_selector(t: NewPlateDialogType) -> Html {
|
||||
match t {
|
||||
NewPlateDialogType::Both => {
|
||||
html! {
|
||||
<>
|
||||
<input type="radio" name="new_plate_type" id="npt_src" value="src" />
|
||||
<label for="npt_src">{"Source"}</label>
|
||||
<input type="radio" name="new_plate_type" id="npt_dest" value="dest" />
|
||||
<label for="npt_dest">{"Destination"}</label>
|
||||
</>
|
||||
}
|
||||
},
|
||||
NewPlateDialogType::SourceOnly => {
|
||||
html! {
|
||||
<input type="hidden" name="new_plate_type" id="npt_src" value="src" />
|
||||
}
|
||||
},
|
||||
NewPlateDialogType::DestinationOnly => {
|
||||
html! {
|
||||
<input type="hidden" name="new_plate_type" id="npt_dest" value="dest" />
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -1,6 +1,9 @@
|
|||
#![allow(non_snake_case)]
|
||||
|
||||
use std::collections::HashMap;
|
||||
|
||||
|
||||
use plate_tool_lib::transfer_volume::TransferVolume;
|
||||
use yew::prelude::*;
|
||||
use yewdux::prelude::*;
|
||||
|
||||
|
|
@ -8,6 +11,7 @@ use crate::components::states::{CurrentTransfer, MainState};
|
|||
use plate_tool_lib::plate::PlateType;
|
||||
use plate_tool_lib::transfer::Transfer;
|
||||
use plate_tool_lib::transfer_region::Region;
|
||||
use plate_tool_lib::Well;
|
||||
|
||||
// Color Palette for the Source Plates, can be changed here
|
||||
use crate::components::plates::util::Palettes;
|
||||
|
|
@ -32,24 +36,24 @@ pub fn Plate(props: &PlateProps) -> Html {
|
|||
PlateType::Destination => ct_state.transfer.transfer_region.dest_region.clone(),
|
||||
};
|
||||
let (pt1, pt2) = match region {
|
||||
Region::Point((x, y)) => ((x, y), (x, y)),
|
||||
Region::Rect(c1, c2) => (c1, c2),
|
||||
Region::Point(Well {row: x, col: y }) => ((x, y), (x, y)),
|
||||
Region::Rect(c1, c2) => ((c1.row, c1.col ), (c2.row, c2.col)),
|
||||
Region::Custom(_) => ((0, 0), (0, 0)),
|
||||
};
|
||||
m_start_handle.set(Some(pt1));
|
||||
m_end_handle.set(Some(pt2));
|
||||
}
|
||||
|
||||
let tooltip_map: HashMap<(u8, u8), Vec<&Transfer>>;
|
||||
let volume_map: HashMap<(u8, u8), f32>;
|
||||
let tooltip_map: HashMap<Well, Vec<&Transfer>>;
|
||||
let volume_map: HashMap<Well, f32>;
|
||||
let volume_max: f32;
|
||||
{
|
||||
let transfers = main_state.transfers.iter().filter(|t| match props.ptype {
|
||||
PlateType::Source => t.source_id == props.source_plate.get_uuid(),
|
||||
PlateType::Destination => t.dest_id == props.destination_plate.get_uuid(),
|
||||
});
|
||||
let mut tooltip_map_temp: HashMap<(u8, u8), Vec<&Transfer>> = HashMap::new();
|
||||
let mut volume_map_temp: HashMap<(u8,u8), f32> = HashMap::new();
|
||||
let mut tooltip_map_temp: HashMap<Well, Vec<&Transfer>> = HashMap::new();
|
||||
let mut volume_map_temp: HashMap<Well, f32> = HashMap::new();
|
||||
let mut volume_max_temp: f32 = f32::NEG_INFINITY;
|
||||
for transfer in transfers {
|
||||
let wells = match props.ptype {
|
||||
|
|
@ -62,12 +66,27 @@ pub fn Plate(props: &PlateProps) -> Html {
|
|||
} else {
|
||||
tooltip_map_temp.insert(well, vec![transfer]);
|
||||
}
|
||||
let temp_volume: f32 = match &transfer.volume {
|
||||
TransferVolume::Single(x) => *x,
|
||||
TransferVolume::WellMap(wm) => {
|
||||
*match props.ptype {
|
||||
PlateType::Source => wm.source_only.get(&well),
|
||||
PlateType::Destination => wm.destination_only.get(&well)
|
||||
}.unwrap_or(&2.5f32)
|
||||
},
|
||||
_ => unreachable!(),
|
||||
};
|
||||
// Usage to be used as a volume multiplier; should be in [1, U32_MAX]
|
||||
// First convert to f64 (u32 can not fit in f32 directly) and then cast
|
||||
// to round into the closest f32.
|
||||
let usage: f32 = Into::<f64>::into(count_plate_usage(transfer, &well).unwrap_or(1u32).max(1u32)) as f32;
|
||||
|
||||
if let Some(val) = volume_map_temp.get_mut(&well) {
|
||||
*val += transfer.volume;
|
||||
*val += temp_volume * usage;
|
||||
} else {
|
||||
volume_map_temp.insert(well, transfer.volume);
|
||||
volume_map_temp.insert(well, temp_volume * usage);
|
||||
}
|
||||
volume_max_temp = f32::max(volume_max_temp, transfer.volume);
|
||||
volume_max_temp = f32::max(volume_max_temp, *volume_map_temp.get(&well).expect("Just added"));
|
||||
}
|
||||
}
|
||||
tooltip_map = tooltip_map_temp;
|
||||
|
|
@ -135,22 +154,22 @@ pub fn Plate(props: &PlateProps) -> Html {
|
|||
.map(|j| {
|
||||
let color = {
|
||||
if !main_state.preferences.volume_heatmap {
|
||||
tooltip_map.get(&(i,j))
|
||||
tooltip_map.get(&Well { row: i, col: j })
|
||||
.and_then(|t| t.last())
|
||||
.map(|t| PALETTE.get_ordered(t.get_uuid(), &ordered_ids))
|
||||
} else {
|
||||
volume_map.get(&(i,j))
|
||||
volume_map.get(&Well { row: i, col: j })
|
||||
.map(|t| PALETTE.get_linear(*t as f64, volume_max as f64))
|
||||
}
|
||||
};
|
||||
let title = {
|
||||
let mut out = String::new();
|
||||
let used_by = tooltip_map.get(&(i,j)).map(|transfers| format!("Used by: {}", transfers.iter().map(|t| t.name.clone())
|
||||
let used_by = tooltip_map.get(&Well { row: i, col: j }).map(|transfers| format!("Used by: {}", transfers.iter().map(|t| t.name.clone())
|
||||
.collect::<Vec<_>>().join(", ")));
|
||||
if let Some(val) = used_by {
|
||||
out += &val;
|
||||
}
|
||||
let volume_sum = volume_map.get(&(i,j))
|
||||
let volume_sum = volume_map.get(&Well { row: i, col: j })
|
||||
.map(|t| format!("Volume: {}", t));
|
||||
if let Some(val) = volume_sum {
|
||||
if !out.is_empty() { out += "\n" }
|
||||
|
|
@ -162,7 +181,7 @@ pub fn Plate(props: &PlateProps) -> Html {
|
|||
<PlateCell i={i} j={j}
|
||||
selected={in_rect(*m_start_handle.clone(), *m_end_handle.clone(), (i,j))}
|
||||
mouse={mouse_callback.clone()}
|
||||
in_transfer={wells.contains(&(i,j)) && main_state.preferences.in_transfer_hashes}
|
||||
in_transfer={wells.contains(&Well { row: i, col: j }) && main_state.preferences.in_transfer_hashes}
|
||||
color={ color }
|
||||
cell_height={props.cell_height}
|
||||
title={title}
|
||||
|
|
@ -256,6 +275,15 @@ pub fn in_rect(corner1: Option<(u8, u8)>, corner2: Option<(u8, u8)>, pt: (u8, u8
|
|||
}
|
||||
}
|
||||
|
||||
fn count_plate_usage(transfer: &Transfer, well: &Well) -> Option<u32> {
|
||||
if let Region::Custom(_) = transfer.transfer_region.source_region {
|
||||
return None;
|
||||
}
|
||||
|
||||
let map = transfer.transfer_region.calculate_map();
|
||||
map(*well).map(|list| list.len() as u32)
|
||||
}
|
||||
|
||||
#[cfg(test)]
|
||||
mod tests {
|
||||
use wasm_bindgen_test::*;
|
||||
|
|
|
|||
|
|
@ -41,7 +41,7 @@ pub fn mouseup_callback(
|
|||
m_stat_handle.set(false);
|
||||
if let Some(ul) = *m_start_handle {
|
||||
if let Some(br) = *m_end_handle {
|
||||
if let Ok(rd) = RegionDisplay::try_from((ul.0, ul.1, br.0, br.1)) {
|
||||
if let Ok(rd) = RegionDisplay::try_from((ul.1, ul.0, br.1, br.0)) {
|
||||
ct_dispatch.reduce_mut(|state| {
|
||||
match ptype {
|
||||
PlateType::Source => state.transfer.transfer_region.source_region = Region::from(&rd),
|
||||
|
|
|
|||
|
|
@ -5,10 +5,12 @@ use yew::prelude::*;
|
|||
|
||||
use plate_tool_lib::plate::PlateType;
|
||||
use plate_tool_lib::plate_instances::PlateInstance;
|
||||
use yewdux::functional::use_store;
|
||||
|
||||
// use super::destination_plate::DestinationPlate;
|
||||
// use super::source_plate::SourcePlate;
|
||||
use super::plate::Plate;
|
||||
use crate::components::states::MainState;
|
||||
|
||||
#[derive(Properties, PartialEq)]
|
||||
pub struct PlateContainerProps {
|
||||
|
|
@ -18,6 +20,8 @@ pub struct PlateContainerProps {
|
|||
|
||||
#[function_component]
|
||||
pub fn PlateContainer(props: &PlateContainerProps) -> Html {
|
||||
let (main_state, _) = use_store::<MainState>();
|
||||
|
||||
let cell_height = {
|
||||
let height = web_sys::window()
|
||||
.unwrap()
|
||||
|
|
@ -49,8 +53,15 @@ pub fn PlateContainer(props: &PlateContainerProps) -> Html {
|
|||
.set_onresize(Some(onresize.as_ref().unchecked_ref()));
|
||||
onresize.forget(); // Magic!
|
||||
|
||||
let heatmap_enabled = main_state.preferences.volume_heatmap;
|
||||
|
||||
html! {
|
||||
<div class="plate_container">
|
||||
if heatmap_enabled {
|
||||
<div class="plate_container--heatmap-notice" >
|
||||
<h3>{"Volume Heatmap Enabled"}</h3>
|
||||
</div>
|
||||
}
|
||||
if let Some(spi) = props.source_dims.clone() {
|
||||
if let Some(dpi) = props.destination_dims.clone() {
|
||||
<div class="plate_container--source">
|
||||
|
|
|
|||
|
|
@ -26,6 +26,7 @@ impl ColorPalette {
|
|||
]
|
||||
}
|
||||
|
||||
#[allow(dead_code)] // Preserve old implementation for reference
|
||||
fn get_u8(&self, t: u8) -> [f64; 3] {
|
||||
assert!(t > 0, "t must be greater than zero!");
|
||||
self.get((2f64.powi(-(t.ilog2() as i32))) * (t as f64 + 0.5f64) - 1.0f64)
|
||||
|
|
|
|||
|
|
@ -1,6 +1,7 @@
|
|||
#![allow(non_snake_case)]
|
||||
|
||||
use lazy_static::lazy_static;
|
||||
use plate_tool_lib::Well;
|
||||
use regex::Regex;
|
||||
use serde::{Deserialize, Serialize};
|
||||
use yew::prelude::*;
|
||||
|
|
@ -8,6 +9,7 @@ use yewdux::prelude::*;
|
|||
|
||||
use crate::components::callbacks::transfer_menu_callbacks;
|
||||
use plate_tool_lib::transfer_region::Region;
|
||||
use plate_tool_lib::transfer_volume::TransferVolume;
|
||||
use plate_tool_lib::util::{letters_to_num, num_to_letters};
|
||||
|
||||
use super::states::{CurrentTransfer, MainState};
|
||||
|
|
@ -143,7 +145,10 @@ pub fn TransferMenu() -> Html {
|
|||
<input type="number" name="volume" class="volume_input"
|
||||
min="0" step="0.1"
|
||||
onchange={on_volume_change}
|
||||
value={ct_state.transfer.volume.to_string()}/>
|
||||
value={match ct_state.transfer.volume {
|
||||
TransferVolume::Single(x) => x.to_string(),
|
||||
_ => unreachable!(),
|
||||
}}/>
|
||||
</div>
|
||||
}
|
||||
<div id="controls">
|
||||
|
|
@ -233,10 +238,10 @@ impl TryFrom<&str> for RegionDisplay {
|
|||
impl From<&Region> for RegionDisplay {
|
||||
fn from(value: &Region) -> Self {
|
||||
match *value {
|
||||
Region::Point((col, row)) => {
|
||||
Region::Point(Well { row, col }) => {
|
||||
RegionDisplay::try_from((col, row, col, row)).ok().unwrap()
|
||||
}
|
||||
Region::Rect(c1, c2) => RegionDisplay::try_from((c1.0, c1.1, c2.0, c2.1))
|
||||
Region::Rect(c1, c2) => RegionDisplay::try_from((c1.row, c1.col, c2.row, c2.col))
|
||||
.ok()
|
||||
.unwrap(),
|
||||
Region::Custom(_) => RegionDisplay {
|
||||
|
|
@ -252,11 +257,11 @@ impl From<&Region> for RegionDisplay {
|
|||
impl From<&RegionDisplay> for Region {
|
||||
fn from(value: &RegionDisplay) -> Self {
|
||||
if value.col_start == value.col_end && value.row_start == value.row_end {
|
||||
Region::Point((value.col_start, value.row_start))
|
||||
Region::Point(Well { row: value.row_start, col: value.col_start })
|
||||
} else {
|
||||
Region::Rect(
|
||||
(value.col_start, value.row_start),
|
||||
(value.col_end, value.row_end),
|
||||
Well { row: value.row_start, col: value.col_start },
|
||||
Well { row: value.row_end, col: value.col_end },
|
||||
)
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -2,17 +2,18 @@
|
|||
|
||||
use plate_tool_lib::plate::PlateFormat;
|
||||
use uuid::Uuid;
|
||||
use wasm_bindgen::JsCast;
|
||||
use web_sys::{HtmlDialogElement, HtmlInputElement};
|
||||
|
||||
use web_sys::{HtmlDialogElement};
|
||||
use yew::prelude::*;
|
||||
use yewdux::prelude::*;
|
||||
|
||||
use crate::components::callbacks::tree_callbacks;
|
||||
use crate::components::callbacks::{tree_callbacks};
|
||||
use crate::components::new_plate_dialog::NewPlateDialogType;
|
||||
use crate::components::states::{CurrentTransfer, MainState};
|
||||
|
||||
#[derive(PartialEq, Properties)]
|
||||
pub struct TreeProps {
|
||||
pub open_new_plate_callback: Callback<()>,
|
||||
pub open_new_plate_callback: Callback<NewPlateDialogType>,
|
||||
}
|
||||
|
||||
#[function_component]
|
||||
|
|
@ -98,13 +99,25 @@ pub fn Tree(props: &TreeProps) -> Html {
|
|||
html! {
|
||||
<div class="tree">
|
||||
<div id="source-plates">
|
||||
<div class="tree--header">
|
||||
<h3>{"Source Plates:"}</h3>
|
||||
<button onclick={
|
||||
let open_new_plate_callback = props.open_new_plate_callback.clone();
|
||||
move |_| {open_new_plate_callback.emit(NewPlateDialogType::SourceOnly)}
|
||||
} />
|
||||
</div>
|
||||
<ul>
|
||||
{source_plates}
|
||||
</ul>
|
||||
</div>
|
||||
<div id="destination-plates">
|
||||
<div class="tree--header">
|
||||
<h3>{"Destination Plates:"}</h3>
|
||||
<button onclick={
|
||||
let open_new_plate_callback = props.open_new_plate_callback.clone();
|
||||
move |_| {open_new_plate_callback.emit(NewPlateDialogType::DestinationOnly)}
|
||||
} />
|
||||
</div>
|
||||
<ul>
|
||||
{dest_plates}
|
||||
</ul>
|
||||
|
|
@ -120,14 +133,6 @@ pub fn Tree(props: &TreeProps) -> Html {
|
|||
delete_button_callback={plate_info_delete_callback}/>
|
||||
}
|
||||
|
||||
<div id="controls">
|
||||
<button type="button"
|
||||
onclick={
|
||||
let open_new_plate_callback = props.open_new_plate_callback.clone();
|
||||
move |_| {open_new_plate_callback.emit(())}
|
||||
}>
|
||||
{"New Plate"}</button>
|
||||
</div>
|
||||
</div>
|
||||
}
|
||||
}
|
||||
|
|
@ -159,19 +164,17 @@ fn PlateInfoModal(props: &PlateInfoModalProps) -> Html {
|
|||
None => "Not Found".to_string(),
|
||||
};
|
||||
let plate_format = plate.map(|p| p.plate.plate_format);
|
||||
let plate_formats = vec![
|
||||
PlateFormat::W6,
|
||||
let plate_formats = [PlateFormat::W6,
|
||||
PlateFormat::W12,
|
||||
PlateFormat::W24,
|
||||
PlateFormat::W48,
|
||||
PlateFormat::W96,
|
||||
PlateFormat::W384,
|
||||
PlateFormat::W1536,
|
||||
PlateFormat::W3456,
|
||||
];
|
||||
PlateFormat::W3456];
|
||||
let plate_format_options = plate_formats.iter().map(|v| {
|
||||
let selected = Some(v) == plate_format.as_ref();
|
||||
html!{
|
||||
html! {
|
||||
<option value={v.to_string()} selected={selected}>{ v.to_string() }</option>
|
||||
}
|
||||
});
|
||||
|
|
|
|||
|
|
@ -25,9 +25,9 @@ pub fn plate_test() {
|
|||
|
||||
let transfer = transfer_region::TransferRegion {
|
||||
source_plate: source,
|
||||
source_region: transfer_region::Region::Rect((1, 1), (2, 2)),
|
||||
source_region: transfer_region::Region::Rect(Well { row: 1, col: 1 }, Well { row: 2, col: 2 }),
|
||||
dest_plate: destination,
|
||||
dest_region: transfer_region::Region::Rect((2, 2), (11, 11)),
|
||||
dest_region: transfer_region::Region::Rect(Well { row: 2, col: 2 }, Well { row: 11, col: 11 }),
|
||||
interleave_source: (1, 1),
|
||||
interleave_dest: (3, 3),
|
||||
};
|
||||
|
|
|
|||
Loading…
Reference in New Issue