implement correct status handling and add snakemake profile

Cargo.lock

@@ -223,6 +223,43 @@ dependencies = [
  "alloc-no-stdlib",
 ]
 
+[[package]]
+name = "android_system_properties"
+version = "0.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "819e7219dbd41043ac279b19830f2efc897156490d7fd6ea916720117ee66311"
+dependencies = [
+ "libc",
+]
+
+[[package]]
+name = "anyhow"
+version = "1.0.65"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "98161a4e3e2184da77bb14f02184cdd111e83bbbcc9979dfee3c44b9a85f5602"
+
+[[package]]
+name = "async-trait"
+version = "0.1.57"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "76464446b8bc32758d7e88ee1a804d9914cd9b1cb264c029899680b0be29826f"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
+[[package]]
+name = "atty"
+version = "0.2.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d9b39be18770d11421cdb1b9947a45dd3f37e93092cbf377614828a319d5fee8"
+dependencies = [
+ "hermit-abi",
+ "libc",
+ "winapi",
+]
+
 [[package]]
 name = "autocfg"
 version = "1.1.0"
@@ -307,6 +344,42 @@ version = "1.0.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "baf1de4339761588bc0619e3cbc0120ee582ebb74b53b4efbf79117bd2da40fd"
 
+[[package]]
+name = "chrono"
+version = "0.4.22"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bfd4d1b31faaa3a89d7934dbded3111da0d2ef28e3ebccdb4f0179f5929d1ef1"
+dependencies = [
+ "iana-time-zone",
+ "num-integer",
+ "num-traits",
+ "winapi",
+]
+
+[[package]]
+name = "clap"
+version = "3.2.22"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "86447ad904c7fb335a790c9d7fe3d0d971dc523b8ccd1561a520de9a85302750"
+dependencies = [
+ "atty",
+ "bitflags",
+ "clap_lex",
+ "indexmap",
+ "strsim",
+ "termcolor",
+ "textwrap",
+]
+
+[[package]]
+name = "clap_lex"
+version = "0.2.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2850f2f5a82cbf437dd5af4d49848fbdfc27c157c3d010345776f952765261c5"
+dependencies = [
+ "os_str_bytes",
+]
+
 [[package]]
 name = "convert_case"
 version = "0.4.0"
@@ -455,6 +528,21 @@ dependencies = [
  "percent-encoding",
 ]
 
+[[package]]
+name = "futures"
+version = "0.3.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7f21eda599937fba36daeb58a22e8f5cee2d14c4a17b5b7739c7c8e5e3b8230c"
+dependencies = [
+ "futures-channel",
+ "futures-core",
+ "futures-executor",
+ "futures-io",
+ "futures-sink",
+ "futures-task",
+ "futures-util",
+]
+
 [[package]]
 name = "futures-channel"
 version = "0.3.24"
@@ -462,6 +550,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "30bdd20c28fadd505d0fd6712cdfcb0d4b5648baf45faef7f852afb2399bb050"
 dependencies = [
  "futures-core",
+ "futures-sink",
 ]
 
 [[package]]
@@ -470,12 +559,34 @@ version = "0.3.24"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "4e5aa3de05362c3fb88de6531e6296e85cde7739cccad4b9dfeeb7f6ebce56bf"
 
+[[package]]
+name = "futures-executor"
+version = "0.3.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ff63c23854bee61b6e9cd331d523909f238fc7636290b96826e9cfa5faa00ab"
+dependencies = [
+ "futures-core",
+ "futures-task",
+ "futures-util",
+]
+
 [[package]]
 name = "futures-io"
 version = "0.3.24"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bbf4d2a7a308fd4578637c0b17c7e1c7ba127b8f6ba00b29f717e9655d85eb68"
 
+[[package]]
+name = "futures-macro"
+version = "0.3.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "42cd15d1c7456c04dbdf7e88bcd69760d74f3a798d6444e16974b505b0e62f17"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "futures-sink"
 version = "0.3.24"
@@ -494,8 +605,11 @@ version = "0.3.24"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "44fb6cb1be61cc1d2e43b262516aafcf63b241cffdb1d3fa115f91d9c7b09c90"
 dependencies = [
+ "futures-channel",
  "futures-core",
  "futures-io",
+ "futures-macro",
+ "futures-sink",
  "futures-task",
  "memchr",
  "pin-project-lite",
@@ -629,6 +743,20 @@ dependencies = [
  "tokio-native-tls",
 ]
 
+[[package]]
+name = "iana-time-zone"
+version = "0.1.48"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "237a0714f28b1ee39ccec0770ccb544eb02c9ef2c82bb096230eefcffa6468b0"
+dependencies = [
+ "android_system_properties",
+ "core-foundation-sys",
+ "js-sys",
+ "once_cell",
+ "wasm-bindgen",
+ "winapi",
+]
+
 [[package]]
 name = "idna"
 version = "0.3.0"
@@ -755,6 +883,16 @@ version = "0.3.16"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2a60c7ce501c71e03a9c9c0d35b861413ae925bd979cc7a4e30d060069aaac8d"
 
+[[package]]
+name = "mime_guess"
+version = "2.0.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4192263c238a5f0d0c6bfd21f336a313a4ce1c450542449ca191bb657b4642ef"
+dependencies = [
+ "mime",
+ "unicase",
+]
+
 [[package]]
 name = "miniz_oxide"
 version = "0.5.4"
@@ -794,6 +932,25 @@ dependencies = [
  "tempfile",
 ]
 
+[[package]]
+name = "num-integer"
+version = "0.1.45"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "225d3389fb3509a24c93f5c29eb6bde2586b98d9f016636dff58d7c6f7569cd9"
+dependencies = [
+ "autocfg",
+ "num-traits",
+]
+
+[[package]]
+name = "num-traits"
+version = "0.2.15"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "578ede34cf02f8924ab9447f50c28075b4d3e5b269972345e7e0372b38c6cdcd"
+dependencies = [
+ "autocfg",
+]
+
 [[package]]
 name = "num_cpus"
 version = "1.13.1"
@@ -864,6 +1021,12 @@ dependencies = [
  "vcpkg",
 ]
 
+[[package]]
+name = "os_str_bytes"
+version = "6.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9ff7415e9ae3fff1225851df9e0d9e4e5479f947619774677a63572e55e80eff"
+
 [[package]]
 name = "parking_lot"
 version = "0.12.1"
@@ -1027,6 +1190,7 @@ dependencies = [
  "lazy_static",
  "log",
  "mime",
+ "mime_guess",
  "native-tls",
  "percent-encoding",
  "pin-project-lite",
@@ -1043,6 +1207,62 @@ dependencies = [
  "winreg",
 ]
 
+[[package]]
+name = "reqwest-middleware"
+version = "0.1.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "69539cea4148dce683bec9dc95be3f0397a9bb2c248a49c8296a9d21659a8cdd"
+dependencies = [
+ "anyhow",
+ "async-trait",
+ "futures",
+ "http",
+ "reqwest",
+ "serde",
+ "task-local-extensions",
+ "thiserror",
+]
+
+[[package]]
+name = "reqwest-retry"
+version = "0.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ce246a729eaa6aff5e215aee42845bf5fed9893cc6cd51aeeb712f34e04dd9f3"
+dependencies = [
+ "anyhow",
+ "async-trait",
+ "chrono",
+ "futures",
+ "http",
+ "hyper",
+ "reqwest",
+ "reqwest-middleware",
+ "retry-policies",
+ "task-local-extensions",
+ "tokio",
+ "tracing",
+]
+
+[[package]]
+name = "retry"
+version = "2.0.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9166d72162de3575f950507683fac47e30f6f2c3836b71b7fbc61aa517c9c5f4"
+dependencies = [
+ "rand",
+]
+
+[[package]]
+name = "retry-policies"
+version = "0.1.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "47f9e19b18c6cdd796cc70aea8a9ea5ee7b813be611c6589e3624fcdbfd05f9d"
+dependencies = [
+ "anyhow",
+ "chrono",
+ "rand",
+]
+
 [[package]]
 name = "rustc_version"
 version = "0.4.0"
@@ -1191,6 +1411,12 @@ dependencies = [
  "winapi",
 ]
 
+[[package]]
+name = "strsim"
+version = "0.10.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623"
+
 [[package]]
 name = "syn"
 version = "1.0.99"
@@ -1202,6 +1428,15 @@ dependencies = [
  "unicode-ident",
 ]
 
+[[package]]
+name = "task-local-extensions"
+version = "0.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4167afbec18ae012de40f8cf1b9bf48420abb390678c34821caa07d924941cc4"
+dependencies = [
+ "tokio",
+]
+
 [[package]]
 name = "tempfile"
 version = "3.3.0"
@@ -1216,6 +1451,41 @@ dependencies = [
  "winapi",
 ]
 
+[[package]]
+name = "termcolor"
+version = "1.1.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bab24d30b911b2376f3a13cc2cd443142f0c81dda04c118693e35b3835757755"
+dependencies = [
+ "winapi-util",
+]
+
+[[package]]
+name = "textwrap"
+version = "0.15.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "949517c0cf1bf4ee812e2e07e08ab448e3ae0d23472aee8a06c985f0c8815b16"
+
+[[package]]
+name = "thiserror"
+version = "1.0.35"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "c53f98874615aea268107765aa1ed8f6116782501d18e53d08b471733bea6c85"
+dependencies = [
+ "thiserror-impl",
+]
+
+[[package]]
+name = "thiserror-impl"
+version = "1.0.35"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f8b463991b4eab2d801e724172285ec4195c650e8ec79b149e6c2a8e6dd3f783"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "time"
 version = "0.3.14"
@@ -1266,9 +1536,21 @@ dependencies = [
  "pin-project-lite",
  "signal-hook-registry",
  "socket2",
+ "tokio-macros",
  "winapi",
 ]
 
+[[package]]
+name = "tokio-macros"
+version = "1.8.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9724f9a975fb987ef7a3cd9be0350edcbe130698af5b8f7a631e23d42d052484"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "tokio-native-tls"
 version = "0.3.0"
@@ -1308,9 +1590,21 @@ dependencies = [
  "cfg-if",
  "log",
  "pin-project-lite",
+ "tracing-attributes",
  "tracing-core",
 ]
 
+[[package]]
+name = "tracing-attributes"
+version = "0.1.22"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "11c75893af559bc8e10716548bdef5cb2b983f8e637db9d0e15126b61b484ee2"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn",
+]
+
 [[package]]
 name = "tracing-core"
 version = "0.1.29"
@@ -1332,6 +1626,15 @@ version = "1.15.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "dcf81ac59edc17cc8697ff311e8f5ef2d99fcbd9817b34cec66f90b6c3dfd987"
 
+[[package]]
+name = "unicase"
+version = "2.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "50f37be617794602aabbeee0be4f259dc1778fabe05e2d67ee8f79326d5cb4f6"
+dependencies = [
+ "version_check",
+]
+
 [[package]]
 name = "unicode-bidi"
 version = "0.3.8"
@@ -1484,6 +1787,15 @@ version = "0.4.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6"
 
+[[package]]
+name = "winapi-util"
+version = "0.1.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "70ec6ce85bb158151cae5e5c87f95a8e97d2c0c4b001223f33a334e3ce5de178"
+dependencies = [
+ "winapi",
+]
+
 [[package]]
 name = "winapi-x86_64-pc-windows-gnu"
 version = "0.4.0"
@@ -1546,7 +1858,13 @@ dependencies = [
 name = "zoidberg_client"
 version = "0.1.0"
 dependencies = [
+ "clap",
  "reqwest",
+ "reqwest-middleware",
+ "reqwest-retry",
+ "retry",
+ "serde_json",
+ "tokio",
  "zoidberg_lib",
 ]
 
@@ -1562,6 +1880,8 @@ name = "zoidberg_server"
 version = "0.1.0"
 dependencies = [
  "actix-web",
+ "clap",
+ "serde_json",
  "zoidberg_lib",
 ]