From b3b58d2ced21ce73c5ba0fec01822d5f2611dae2 Mon Sep 17 00:00:00 2001
From: Andrew Sparkes <as28@sanger.ac.uk>
Date: Wed, 16 Mar 2022 15:39:27 +0000
Subject: [PATCH 01/12] Added additional failure types and renamed Beckman
 specific one to be generic

---
 lighthouse/config/defaults.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/lighthouse/config/defaults.py b/lighthouse/config/defaults.py
index 10ca114f..cbb4dff0 100644
--- a/lighthouse/config/defaults.py
+++ b/lighthouse/config/defaults.py
@@ -217,11 +217,13 @@
 }
 # TODO: make these the generic failure types
 BECKMAN_FAILURE_TYPES = {
+    "plate_too_low_empty": "Plate too low/empty",
+    "general_software_error": "General software error",
     "robot_crashed": "The robot crashed",
     "sample_contamination": "Sample contamination occurred",
     "power_failure": "Power loss to instrument",
     "network_failure": "Cannot retrieve sample data",
-    "SILAS_error": "Internal communication error in Beckman system",
+    "SILAS_error": "Internal communication error in robot system",
     "instrument_loaded_incorrectly": "Labware has been incorrectly loaded onto instrument",
     "other": "Any other failure",
 }

From eb13e0b6e12f0fe8b90d776493085a0ef219fa79 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 21 Mar 2022 07:16:07 +0000
Subject: [PATCH 02/12] Bump flake8-bugbear from 22.1.11 to 22.3.20

Bumps [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) from 22.1.11 to 22.3.20.
- [Release notes](https://github.com/PyCQA/flake8-bugbear/releases)
- [Commits](https://github.com/PyCQA/flake8-bugbear/compare/22.1.11...22.3.20)

---
updated-dependencies:
- dependency-name: flake8-bugbear
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Pipfile.lock | 137 ++++++++++++++++++++++++++-------------------------
 1 file changed, 69 insertions(+), 68 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 7ce93374..8fd15c1e 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -368,11 +368,11 @@
         },
         "itsdangerous": {
             "hashes": [
-                "sha256:29285842166554469a56d427addc0843914172343784cb909695fdbe90a3e129",
-                "sha256:d848fcb8bc7d507c4546b448574e8a44fc4ea2ba84ebf8d783290d53e81992f5"
+                "sha256:7b7d3023cd35d9cb0c1fd91392f8c95c6fa02c59bf8ad64b8849be3401b95afb",
+                "sha256:935642cd4b987cdbee7210080004033af76306757ff8b4c0a506a4b6e06f02cf"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==2.1.0"
+            "version": "==2.1.1"
         },
         "jinja2": {
             "hashes": [
@@ -384,49 +384,49 @@
         },
         "markupsafe": {
             "hashes": [
-                "sha256:023af8c54fe63530545f70dd2a2a7eed18d07a9a77b94e8bf1e2ff7f252db9a3",
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-                "sha256:b8811d48078d1cf2a6863dafb896e68406c5f513048451cd2ded0473133473c7",
-                "sha256:c532d5ab79be0199fa2658e24a02fce8542df196e60665dd322409a03db6a52c",
-                "sha256:d3b64c65328cb4cd252c94f83e66e3d7acf8891e60ebf588d7b493a55a1dbf26",
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-                "sha256:e67ec74fada3841b8c5f4c4f197bea916025cb9aa3fe5abf7d52b655d042f956",
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-                "sha256:fc3150f85e2dbcf99e65238c842d1cfe69d3e7649b19864c1cc043213d9cd730"
+                "sha256:0212a68688482dc52b2d45013df70d169f542b7394fc744c02a57374a4207003",
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+                "sha256:4a33dea2b688b3190ee12bd7cfa29d39c9ed176bda40bfa11099a3ce5d3a7ac6",
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+                "sha256:56442863ed2b06d19c37f94d999035e15ee982988920e12a5b4ba29b62ad1f77",
+                "sha256:671cd1187ed5e62818414afe79ed29da836dde67166a9fac6d435873c44fdd02",
+                "sha256:694deca8d702d5db21ec83983ce0bb4b26a578e71fbdbd4fdcd387daa90e4d5e",
+                "sha256:6a074d34ee7a5ce3effbc526b7083ec9731bb3cbf921bbe1d3005d4d2bdb3a63",
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+                "sha256:7f91197cc9e48f989d12e4e6fbc46495c446636dfc81b9ccf50bb0ec74b91d4b",
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+                "sha256:97a68e6ada378df82bc9f16b800ab77cbf4b2fada0081794318520138c088e4a",
+                "sha256:99a2a507ed3ac881b975a2976d59f38c19386d128e7a9a18b7df6fff1fd4c1d6",
+                "sha256:a49907dd8420c5685cfa064a1335b6754b74541bbb3706c259c02ed65b644b3e",
+                "sha256:b09bf97215625a311f669476f44b8b318b075847b49316d3e28c08e41a7a573f",
+                "sha256:b7bd98b796e2b6553da7225aeb61f447f80a1ca64f41d83612e6139ca5213aa4",
+                "sha256:b87db4360013327109564f0e591bd2a3b318547bcef31b468a92ee504d07ae4f",
+                "sha256:bcb3ed405ed3222f9904899563d6fc492ff75cce56cba05e32eff40e6acbeaa3",
+                "sha256:d4306c36ca495956b6d568d276ac11fdd9c30a36f1b6eb928070dc5360b22e1c",
+                "sha256:d5ee4f386140395a2c818d149221149c54849dfcfcb9f1debfe07a8b8bd63f9a",
+                "sha256:dda30ba7e87fbbb7eab1ec9f58678558fd9a6b8b853530e176eabd064da81417",
+                "sha256:e04e26803c9c3851c931eac40c695602c6295b8d432cbe78609649ad9bd2da8a",
+                "sha256:e1c0b87e09fa55a220f058d1d49d3fb8df88fbfab58558f1198e08c1e1de842a",
+                "sha256:e72591e9ecd94d7feb70c1cbd7be7b3ebea3f548870aa91e2732960fa4d57a37",
+                "sha256:e8c843bbcda3a2f1e3c2ab25913c80a3c5376cd00c6e8c4a86a89a28c8dc5452",
+                "sha256:efc1913fd2ca4f334418481c7e595c00aad186563bbc1ec76067848c7ca0a933",
+                "sha256:f121a1420d4e173a5d96e47e9a0c0dcff965afdf1626d28de1460815f7c4ee7a",
+                "sha256:fc7b548b17d238737688817ab67deebb30e8073c95749d55538ed473130ec0c7"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==2.1.0"
+            "version": "==2.1.1"
         },
         "multidict": {
             "hashes": [
@@ -512,6 +512,7 @@
                 "sha256:dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18",
                 "sha256:e7927a589df200c5e23c57970bafbd0cd322459aa7b1ff73b7c2e84d6e3eae62",
                 "sha256:f8c1f39caad2c896bc0018f699882b345b2a63708008be29b1f355ebf6f933fe",
+                "sha256:f950f8845b480cffe522913d35567e29dd381b0dc7e4ce6a4a9f9156417d2430",
                 "sha256:fade0d4f4d292b6f39951b6836d7a3c7ef5b2347f3c420cd9820a1d90d794802",
                 "sha256:fdf3c08bce27132395d3c3ba1503cac12e17282358cb4bddc25cc46b0aca07aa"
             ],
@@ -719,10 +720,10 @@
         },
         "pytz": {
             "hashes": [
-                "sha256:3672058bc3453457b622aab7a1c3bfd5ab0bdae451512f6cf25f64ed37f5b87c",
-                "sha256:acad2d8b20a1af07d4e4c9d2e9285c5ed9104354062f275f3fcd88dcef4f1326"
+                "sha256:1e760e2fe6a8163bc0b3d9a19c4f84342afa0a2affebfaa84b01b978a02ecaa7",
+                "sha256:e68985985296d9a66a881eb3193b0906246245294a881e7c8afe623866ac6a5c"
             ],
-            "version": "==2021.3"
+            "version": "==2022.1"
         },
         "pytz-deprecation-shim": {
             "hashes": [
@@ -742,11 +743,11 @@
         },
         "setuptools": {
             "hashes": [
-                "sha256:2347b2b432c891a863acadca2da9ac101eae6169b1d3dfee2ec605ecd50dbfe5",
-                "sha256:e4f30b9f84e5ab3decf945113119649fec09c1fc3507c6ebffec75646c56e62b"
+                "sha256:6599055eeb23bfef457d5605d33a4d68804266e6cb430b0fb12417c5efeae36c",
+                "sha256:782ef48d58982ddb49920c11a0c5c9c0b02e7d7d1c2ad0aa44e1a1e133051c96"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==60.9.3"
+            "version": "==60.10.0"
         },
         "simplejson": {
             "hashes": [
@@ -874,11 +875,11 @@
         },
         "tzdata": {
             "hashes": [
-                "sha256:3eee491e22ebfe1e5cfcc97a4137cd70f092ce59144d81f8924a844de05ba8f5",
-                "sha256:68dbe41afd01b867894bbdfd54fa03f468cfa4f0086bfb4adcd8de8f24f3ee21"
+                "sha256:238e70234214138ed7b4e8a0fab0e5e13872edab3be586ab8198c407620e2ab9",
+                "sha256:8b536a8ec63dc0751342b3984193a3118f8fca2afe25752bb9b7fffd398552d3"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==2021.5"
+            "version": "==2022.1"
         },
         "tzlocal": {
             "hashes": [
@@ -890,11 +891,11 @@
         },
         "urllib3": {
             "hashes": [
-                "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed",
-                "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"
+                "sha256:44ece4d53fb1706f667c9bd1c648f5469a2ec925fcf3a776667042d645472c14",
+                "sha256:aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.8"
+            "version": "==1.26.9"
         },
         "werkzeug": {
             "hashes": [
@@ -1104,19 +1105,19 @@
         },
         "flake8-bugbear": {
             "hashes": [
-                "sha256:4c2a4136bd4ecb8bf02d5159af302ffc067642784c9d0488b33ce4610da825ee",
-                "sha256:ce7ae44aaaf67ef192b8a6de94a5ac617144e1675ad0654fdea556f48dc18d9b"
+                "sha256:152e64a86f6bff6e295d630ccc993f62434c1fd2b20d2fae47547cb1c1b868e0",
+                "sha256:19fe179ee3286e16198603c438788e2949e79f31d653f0bdb56d53fb69217bd0"
             ],
             "index": "pypi",
-            "version": "==22.1.11"
+            "version": "==22.3.20"
         },
         "freezegun": {
             "hashes": [
-                "sha256:93e90676da387a241a7c2ae7ae68af7b95bfe80e952d0bbf3e088342de90a38d",
-                "sha256:e19563d0b05dcab6dc8ad21c05269004a96998ce2b6b1b8131f1297ae20dd038"
+                "sha256:15103a67dfa868ad809a8f508146e396be2995172d25f927e48ce51c0bf5cb09",
+                "sha256:b4c64efb275e6bc68dc6e771b17ffe0ff0f90b81a2a5189043550b6519926ba4"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==1.2.0"
+            "version": "==1.2.1"
         },
         "idna": {
             "hashes": [
@@ -1310,10 +1311,10 @@
         },
         "types-urllib3": {
             "hashes": [
-                "sha256:a26898f530e6c3f43f25b907f2b884486868ffd56a9faa94cbf9b3eb6e165d6a",
-                "sha256:d755278d5ecd7a7a6479a190e54230f241f1a99c19b81518b756b19dc69e518c"
+                "sha256:24d64e441168851eb05f1d022de18ae31558f5649c8f1117e384c2e85e31315b",
+                "sha256:bd0abc01e9fb963e4fddd561a56d21cc371b988d1245662195c90379077139cd"
             ],
-            "version": "==1.26.10"
+            "version": "==1.26.11"
         },
         "typing-extensions": {
             "hashes": [
@@ -1325,11 +1326,11 @@
         },
         "urllib3": {
             "hashes": [
-                "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed",
-                "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"
+                "sha256:44ece4d53fb1706f667c9bd1c648f5469a2ec925fcf3a776667042d645472c14",
+                "sha256:aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.8"
+            "version": "==1.26.9"
         }
     }
 }

From 08c8408c4149b608443975498aeb60a49878b954 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 21 Mar 2022 07:19:22 +0000
Subject: [PATCH 03/12] Bump responses from 0.19.0 to 0.20.0

Bumps [responses](https://github.com/getsentry/responses) from 0.19.0 to 0.20.0.
- [Release notes](https://github.com/getsentry/responses/releases)
- [Changelog](https://github.com/getsentry/responses/blob/master/CHANGES)
- [Commits](https://github.com/getsentry/responses/compare/0.19.0...0.20.0)

---
updated-dependencies:
- dependency-name: responses
  dependency-type: direct:development
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Pipfile.lock | 137 ++++++++++++++++++++++++++-------------------------
 1 file changed, 69 insertions(+), 68 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 7ce93374..f61acc0e 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -368,11 +368,11 @@
         },
         "itsdangerous": {
             "hashes": [
-                "sha256:29285842166554469a56d427addc0843914172343784cb909695fdbe90a3e129",
-                "sha256:d848fcb8bc7d507c4546b448574e8a44fc4ea2ba84ebf8d783290d53e81992f5"
+                "sha256:7b7d3023cd35d9cb0c1fd91392f8c95c6fa02c59bf8ad64b8849be3401b95afb",
+                "sha256:935642cd4b987cdbee7210080004033af76306757ff8b4c0a506a4b6e06f02cf"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==2.1.0"
+            "version": "==2.1.1"
         },
         "jinja2": {
             "hashes": [
@@ -384,49 +384,49 @@
         },
         "markupsafe": {
             "hashes": [
-                "sha256:023af8c54fe63530545f70dd2a2a7eed18d07a9a77b94e8bf1e2ff7f252db9a3",
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+                "sha256:56442863ed2b06d19c37f94d999035e15ee982988920e12a5b4ba29b62ad1f77",
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+                "sha256:6a074d34ee7a5ce3effbc526b7083ec9731bb3cbf921bbe1d3005d4d2bdb3a63",
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+                "sha256:86b1f75c4e7c2ac2ccdaec2b9022845dbb81880ca318bb7a0a01fbf7813e3812",
+                "sha256:8dc1c72a69aa7e082593c4a203dcf94ddb74bb5c8a731e4e1eb68d031e8498ff",
+                "sha256:8e3dcf21f367459434c18e71b2a9532d96547aef8a871872a5bd69a715c15f96",
+                "sha256:8e576a51ad59e4bfaac456023a78f6b5e6e7651dcd383bcc3e18d06f9b55d6d1",
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+                "sha256:99a2a507ed3ac881b975a2976d59f38c19386d128e7a9a18b7df6fff1fd4c1d6",
+                "sha256:a49907dd8420c5685cfa064a1335b6754b74541bbb3706c259c02ed65b644b3e",
+                "sha256:b09bf97215625a311f669476f44b8b318b075847b49316d3e28c08e41a7a573f",
+                "sha256:b7bd98b796e2b6553da7225aeb61f447f80a1ca64f41d83612e6139ca5213aa4",
+                "sha256:b87db4360013327109564f0e591bd2a3b318547bcef31b468a92ee504d07ae4f",
+                "sha256:bcb3ed405ed3222f9904899563d6fc492ff75cce56cba05e32eff40e6acbeaa3",
+                "sha256:d4306c36ca495956b6d568d276ac11fdd9c30a36f1b6eb928070dc5360b22e1c",
+                "sha256:d5ee4f386140395a2c818d149221149c54849dfcfcb9f1debfe07a8b8bd63f9a",
+                "sha256:dda30ba7e87fbbb7eab1ec9f58678558fd9a6b8b853530e176eabd064da81417",
+                "sha256:e04e26803c9c3851c931eac40c695602c6295b8d432cbe78609649ad9bd2da8a",
+                "sha256:e1c0b87e09fa55a220f058d1d49d3fb8df88fbfab58558f1198e08c1e1de842a",
+                "sha256:e72591e9ecd94d7feb70c1cbd7be7b3ebea3f548870aa91e2732960fa4d57a37",
+                "sha256:e8c843bbcda3a2f1e3c2ab25913c80a3c5376cd00c6e8c4a86a89a28c8dc5452",
+                "sha256:efc1913fd2ca4f334418481c7e595c00aad186563bbc1ec76067848c7ca0a933",
+                "sha256:f121a1420d4e173a5d96e47e9a0c0dcff965afdf1626d28de1460815f7c4ee7a",
+                "sha256:fc7b548b17d238737688817ab67deebb30e8073c95749d55538ed473130ec0c7"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==2.1.0"
+            "version": "==2.1.1"
         },
         "multidict": {
             "hashes": [
@@ -512,6 +512,7 @@
                 "sha256:dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18",
                 "sha256:e7927a589df200c5e23c57970bafbd0cd322459aa7b1ff73b7c2e84d6e3eae62",
                 "sha256:f8c1f39caad2c896bc0018f699882b345b2a63708008be29b1f355ebf6f933fe",
+                "sha256:f950f8845b480cffe522913d35567e29dd381b0dc7e4ce6a4a9f9156417d2430",
                 "sha256:fade0d4f4d292b6f39951b6836d7a3c7ef5b2347f3c420cd9820a1d90d794802",
                 "sha256:fdf3c08bce27132395d3c3ba1503cac12e17282358cb4bddc25cc46b0aca07aa"
             ],
@@ -719,10 +720,10 @@
         },
         "pytz": {
             "hashes": [
-                "sha256:3672058bc3453457b622aab7a1c3bfd5ab0bdae451512f6cf25f64ed37f5b87c",
-                "sha256:acad2d8b20a1af07d4e4c9d2e9285c5ed9104354062f275f3fcd88dcef4f1326"
+                "sha256:1e760e2fe6a8163bc0b3d9a19c4f84342afa0a2affebfaa84b01b978a02ecaa7",
+                "sha256:e68985985296d9a66a881eb3193b0906246245294a881e7c8afe623866ac6a5c"
             ],
-            "version": "==2021.3"
+            "version": "==2022.1"
         },
         "pytz-deprecation-shim": {
             "hashes": [
@@ -742,11 +743,11 @@
         },
         "setuptools": {
             "hashes": [
-                "sha256:2347b2b432c891a863acadca2da9ac101eae6169b1d3dfee2ec605ecd50dbfe5",
-                "sha256:e4f30b9f84e5ab3decf945113119649fec09c1fc3507c6ebffec75646c56e62b"
+                "sha256:6599055eeb23bfef457d5605d33a4d68804266e6cb430b0fb12417c5efeae36c",
+                "sha256:782ef48d58982ddb49920c11a0c5c9c0b02e7d7d1c2ad0aa44e1a1e133051c96"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==60.9.3"
+            "version": "==60.10.0"
         },
         "simplejson": {
             "hashes": [
@@ -874,11 +875,11 @@
         },
         "tzdata": {
             "hashes": [
-                "sha256:3eee491e22ebfe1e5cfcc97a4137cd70f092ce59144d81f8924a844de05ba8f5",
-                "sha256:68dbe41afd01b867894bbdfd54fa03f468cfa4f0086bfb4adcd8de8f24f3ee21"
+                "sha256:238e70234214138ed7b4e8a0fab0e5e13872edab3be586ab8198c407620e2ab9",
+                "sha256:8b536a8ec63dc0751342b3984193a3118f8fca2afe25752bb9b7fffd398552d3"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==2021.5"
+            "version": "==2022.1"
         },
         "tzlocal": {
             "hashes": [
@@ -890,11 +891,11 @@
         },
         "urllib3": {
             "hashes": [
-                "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed",
-                "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"
+                "sha256:44ece4d53fb1706f667c9bd1c648f5469a2ec925fcf3a776667042d645472c14",
+                "sha256:aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.8"
+            "version": "==1.26.9"
         },
         "werkzeug": {
             "hashes": [
@@ -1112,11 +1113,11 @@
         },
         "freezegun": {
             "hashes": [
-                "sha256:93e90676da387a241a7c2ae7ae68af7b95bfe80e952d0bbf3e088342de90a38d",
-                "sha256:e19563d0b05dcab6dc8ad21c05269004a96998ce2b6b1b8131f1297ae20dd038"
+                "sha256:15103a67dfa868ad809a8f508146e396be2995172d25f927e48ce51c0bf5cb09",
+                "sha256:b4c64efb275e6bc68dc6e771b17ffe0ff0f90b81a2a5189043550b6519926ba4"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==1.2.0"
+            "version": "==1.2.1"
         },
         "idna": {
             "hashes": [
@@ -1278,11 +1279,11 @@
         },
         "responses": {
             "hashes": [
-                "sha256:3fc29c3117e14136b833a0a6d4e7f1217c6301bf08b6086db468e12f1e3290e2",
-                "sha256:53354b5de163aa2074312c71d8ebccb8bd1ab336cff7053abb75e84dc5637abe"
+                "sha256:18831bc2d72443b67664d98038374a6fa1f27eaaff4dd9a7d7613723416fea3c",
+                "sha256:644905bc4fb8a18fa37e3882b2ac05e610fe8c2f967d327eed669e314d94a541"
             ],
             "index": "pypi",
-            "version": "==0.19.0"
+            "version": "==0.20.0"
         },
         "six": {
             "hashes": [
@@ -1310,10 +1311,10 @@
         },
         "types-urllib3": {
             "hashes": [
-                "sha256:a26898f530e6c3f43f25b907f2b884486868ffd56a9faa94cbf9b3eb6e165d6a",
-                "sha256:d755278d5ecd7a7a6479a190e54230f241f1a99c19b81518b756b19dc69e518c"
+                "sha256:24d64e441168851eb05f1d022de18ae31558f5649c8f1117e384c2e85e31315b",
+                "sha256:bd0abc01e9fb963e4fddd561a56d21cc371b988d1245662195c90379077139cd"
             ],
-            "version": "==1.26.10"
+            "version": "==1.26.11"
         },
         "typing-extensions": {
             "hashes": [
@@ -1325,11 +1326,11 @@
         },
         "urllib3": {
             "hashes": [
-                "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed",
-                "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"
+                "sha256:44ece4d53fb1706f667c9bd1c648f5469a2ec925fcf3a776667042d645472c14",
+                "sha256:aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.8"
+            "version": "==1.26.9"
         }
     }
 }

From dee57147ef0912737975adffec11eea3e2d509df Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Mon, 21 Mar 2022 10:54:50 +0000
Subject: [PATCH 04/12] Bump types-requests from 2.27.11 to 2.27.14

Bumps [types-requests](https://github.com/python/typeshed) from 2.27.11 to 2.27.14.
- [Release notes](https://github.com/python/typeshed/releases)
- [Commits](https://github.com/python/typeshed/commits)

---
updated-dependencies:
- dependency-name: types-requests
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Pipfile.lock | 20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index ae23691e..a4c16d2e 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -720,10 +720,10 @@
         },
         "pytz": {
             "hashes": [
-                "sha256:3672058bc3453457b622aab7a1c3bfd5ab0bdae451512f6cf25f64ed37f5b87c",
-                "sha256:acad2d8b20a1af07d4e4c9d2e9285c5ed9104354062f275f3fcd88dcef4f1326"
+                "sha256:1e760e2fe6a8163bc0b3d9a19c4f84342afa0a2affebfaa84b01b978a02ecaa7",
+                "sha256:e68985985296d9a66a881eb3193b0906246245294a881e7c8afe623866ac6a5c"
             ],
-            "version": "==2021.3"
+            "version": "==2022.1"
         },
         "pytz-deprecation-shim": {
             "hashes": [
@@ -1113,11 +1113,11 @@
         },
         "freezegun": {
             "hashes": [
-                "sha256:93e90676da387a241a7c2ae7ae68af7b95bfe80e952d0bbf3e088342de90a38d",
-                "sha256:e19563d0b05dcab6dc8ad21c05269004a96998ce2b6b1b8131f1297ae20dd038"
+                "sha256:15103a67dfa868ad809a8f508146e396be2995172d25f927e48ce51c0bf5cb09",
+                "sha256:b4c64efb275e6bc68dc6e771b17ffe0ff0f90b81a2a5189043550b6519926ba4"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==1.2.0"
+            "version": "==1.2.1"
         },
         "idna": {
             "hashes": [
@@ -1306,11 +1306,11 @@
         },
         "types-requests": {
             "hashes": [
-                "sha256:506279bad570c7b4b19ac1f22e50146538befbe0c133b2cea66a9b04a533a859",
-                "sha256:6a7ed24b21780af4a5b5e24c310b2cd885fb612df5fd95584d03d87e5f2a195a"
+                "sha256:04579ee164f7c2659be46950e3c2f8d51a081ad252ef1b01d4b12faba5c3810b",
+                "sha256:c01838abfe3e8a83ba68346cd373afff97594c19c15c922ddee4a0e80ba7e329"
             ],
             "index": "pypi",
-            "version": "==2.27.11"
+            "version": "==2.27.14"
         },
         "types-urllib3": {
             "hashes": [
@@ -1324,7 +1324,7 @@
                 "sha256:1a9462dcc3347a79b1f1c0271fbe79e844580bb598bafa1ed208b94da3cdcd42",
                 "sha256:21c85e0fe4b9a155d0799430b0ad741cdce7e359660ccbd8b530613e8df88ce2"
             ],
-            "markers": "python_version >= '3.6'",
+            "markers": "python_version < '3.10'",
             "version": "==4.1.1"
         },
         "urllib3": {

From 60a21f73307b2aba8b84d5716740c01dccb6effd Mon Sep 17 00:00:00 2001
From: Andrew Sparkes <as28@sanger.ac.uk>
Date: Mon, 21 Mar 2022 17:00:29 +0000
Subject: [PATCH 05/12] Added note to readme to remind to re-build docker image
 if needed

---
 README.md | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 7fdb312a..92d488e0 100644
--- a/README.md
+++ b/README.md
@@ -85,9 +85,11 @@ Various environment variables are set in the docker-compose file.
 ### Running
 
 1. Start the Lighthouse service specified in the `docker-compose.yml` from the
-   root of the repository:
+   root of the repository (this builds the docker image if it does not exist, then starts it up i.e. take care to delete old images or add --build):
 
         docker-compose up
+        or
+        docker-compose up --build
 
    This will keep running continuously in your terminal window, so to execute further commands you'll need
    to open a new terminal window or tab.

From 4339b2a50c5954b480411ec80414e69e41fd2a3b Mon Sep 17 00:00:00 2001
From: Andrew Sparkes <as28@sanger.ac.uk>
Date: Mon, 21 Mar 2022 17:01:26 +0000
Subject: [PATCH 06/12] Added cryptography as now seems to be required

---
 Pipfile      |   1 +
 Pipfile.lock | 494 ++++++++++++++++++++++++++++++---------------------
 2 files changed, 294 insertions(+), 201 deletions(-)

diff --git a/Pipfile b/Pipfile
index af94354d..ad527c01 100644
--- a/Pipfile
+++ b/Pipfile
@@ -31,6 +31,7 @@ requests = "~=2.27"
 slackclient = "~=2.5"
 sqlalchemy = "~=1.4"
 pymongo = "~=3.12.1"
+cryptography = "*"
 
 [requires]
 python_version = "3.8"
diff --git a/Pipfile.lock b/Pipfile.lock
index 7ce93374..bc94cc14 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "50de8689f93240b910f0b5a4ca1d2a12240dcb915a5871d9a9cfe95f93b4abdb"
+            "sha256": "4857141b5d8f3df25e840ecd14581925bcc1af3a493cc40b2727bee111ad92e3"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -162,6 +162,61 @@
             ],
             "version": "==2021.10.8"
         },
+        "cffi": {
+            "hashes": [
+                "sha256:00c878c90cb53ccfaae6b8bc18ad05d2036553e6d9d1d9dbcf323bbe83854ca3",
+                "sha256:0104fb5ae2391d46a4cb082abdd5c69ea4eab79d8d44eaaf79f1b1fd806ee4c2",
+                "sha256:06c48159c1abed75c2e721b1715c379fa3200c7784271b3c46df01383b593636",
+                "sha256:0808014eb713677ec1292301ea4c81ad277b6cdf2fdd90fd540af98c0b101d20",
+                "sha256:10dffb601ccfb65262a27233ac273d552ddc4d8ae1bf93b21c94b8511bffe728",
+                "sha256:14cd121ea63ecdae71efa69c15c5543a4b5fbcd0bbe2aad864baca0063cecf27",
+                "sha256:17771976e82e9f94976180f76468546834d22a7cc404b17c22df2a2c81db0c66",
+                "sha256:181dee03b1170ff1969489acf1c26533710231c58f95534e3edac87fff06c443",
+                "sha256:23cfe892bd5dd8941608f93348c0737e369e51c100d03718f108bf1add7bd6d0",
+                "sha256:263cc3d821c4ab2213cbe8cd8b355a7f72a8324577dc865ef98487c1aeee2bc7",
+                "sha256:2756c88cbb94231c7a147402476be2c4df2f6078099a6f4a480d239a8817ae39",
+                "sha256:27c219baf94952ae9d50ec19651a687b826792055353d07648a5695413e0c605",
+                "sha256:2a23af14f408d53d5e6cd4e3d9a24ff9e05906ad574822a10563efcef137979a",
+                "sha256:31fb708d9d7c3f49a60f04cf5b119aeefe5644daba1cd2a0fe389b674fd1de37",
+                "sha256:3415c89f9204ee60cd09b235810be700e993e343a408693e80ce7f6a40108029",
+                "sha256:3773c4d81e6e818df2efbc7dd77325ca0dcb688116050fb2b3011218eda36139",
+                "sha256:3b96a311ac60a3f6be21d2572e46ce67f09abcf4d09344c49274eb9e0bf345fc",
+                "sha256:3f7d084648d77af029acb79a0ff49a0ad7e9d09057a9bf46596dac9514dc07df",
+                "sha256:41d45de54cd277a7878919867c0f08b0cf817605e4eb94093e7516505d3c8d14",
+                "sha256:4238e6dab5d6a8ba812de994bbb0a79bddbdf80994e4ce802b6f6f3142fcc880",
+                "sha256:45db3a33139e9c8f7c09234b5784a5e33d31fd6907800b316decad50af323ff2",
+                "sha256:45e8636704eacc432a206ac7345a5d3d2c62d95a507ec70d62f23cd91770482a",
+                "sha256:4958391dbd6249d7ad855b9ca88fae690783a6be9e86df65865058ed81fc860e",
+                "sha256:4a306fa632e8f0928956a41fa8e1d6243c71e7eb59ffbd165fc0b41e316b2474",
+                "sha256:57e9ac9ccc3101fac9d6014fba037473e4358ef4e89f8e181f8951a2c0162024",
+                "sha256:59888172256cac5629e60e72e86598027aca6bf01fa2465bdb676d37636573e8",
+                "sha256:5e069f72d497312b24fcc02073d70cb989045d1c91cbd53979366077959933e0",
+                "sha256:64d4ec9f448dfe041705426000cc13e34e6e5bb13736e9fd62e34a0b0c41566e",
+                "sha256:6dc2737a3674b3e344847c8686cf29e500584ccad76204efea14f451d4cc669a",
+                "sha256:74fdfdbfdc48d3f47148976f49fab3251e550a8720bebc99bf1483f5bfb5db3e",
+                "sha256:75e4024375654472cc27e91cbe9eaa08567f7fbdf822638be2814ce059f58032",
+                "sha256:786902fb9ba7433aae840e0ed609f45c7bcd4e225ebb9c753aa39725bb3e6ad6",
+                "sha256:8b6c2ea03845c9f501ed1313e78de148cd3f6cad741a75d43a29b43da27f2e1e",
+                "sha256:91d77d2a782be4274da750752bb1650a97bfd8f291022b379bb8e01c66b4e96b",
+                "sha256:91ec59c33514b7c7559a6acda53bbfe1b283949c34fe7440bcf917f96ac0723e",
+                "sha256:920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954",
+                "sha256:a5263e363c27b653a90078143adb3d076c1a748ec9ecc78ea2fb916f9b861962",
+                "sha256:abb9a20a72ac4e0fdb50dae135ba5e77880518e742077ced47eb1499e29a443c",
+                "sha256:c2051981a968d7de9dd2d7b87bcb9c939c74a34626a6e2f8181455dd49ed69e4",
+                "sha256:c21c9e3896c23007803a875460fb786118f0cdd4434359577ea25eb556e34c55",
+                "sha256:c2502a1a03b6312837279c8c1bd3ebedf6c12c4228ddbad40912d671ccc8a962",
+                "sha256:d4d692a89c5cf08a8557fdeb329b82e7bf609aadfaed6c0d79f5a449a3c7c023",
+                "sha256:da5db4e883f1ce37f55c667e5c0de439df76ac4cb55964655906306918e7363c",
+                "sha256:e7022a66d9b55e93e1a845d8c9eba2a1bebd4966cd8bfc25d9cd07d515b33fa6",
+                "sha256:ef1f279350da2c586a69d32fc8733092fd32cc8ac95139a00377841f59a3f8d8",
+                "sha256:f54a64f8b0c8ff0b64d18aa76675262e1700f3995182267998c31ae974fbc382",
+                "sha256:f5c7150ad32ba43a07c4479f40241756145a1f03b43480e058cfd862bf5041c7",
+                "sha256:f6f824dc3bce0edab5f427efcfb1d63ee75b6fcb7282900ccaf925be84efb0fc",
+                "sha256:fd8a250edc26254fe5b33be00402e6d287f562b6a5b2152dec302fa15bb3e997",
+                "sha256:ffaa5c925128e29efbde7301d8ecaf35c8c60ffbcd6a1ffd3a552177c8e5e796"
+            ],
+            "version": "==1.15.0"
+        },
         "charset-normalizer": {
             "hashes": [
                 "sha256:2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597",
@@ -186,6 +241,32 @@
             "index": "pypi",
             "version": "==6.6.0"
         },
+        "cryptography": {
+            "hashes": [
+                "sha256:0a3bf09bb0b7a2c93ce7b98cb107e9170a90c51a0162a20af1c61c765b90e60b",
+                "sha256:1f64a62b3b75e4005df19d3b5235abd43fa6358d5516cfc43d87aeba8d08dd51",
+                "sha256:32db5cc49c73f39aac27574522cecd0a4bb7384e71198bc65a0d23f901e89bb7",
+                "sha256:4881d09298cd0b669bb15b9cfe6166f16fc1277b4ed0d04a22f3d6430cb30f1d",
+                "sha256:4e2dddd38a5ba733be6a025a1475a9f45e4e41139d1321f412c6b360b19070b6",
+                "sha256:53e0285b49fd0ab6e604f4c5d9c5ddd98de77018542e88366923f152dbeb3c29",
+                "sha256:70f8f4f7bb2ac9f340655cbac89d68c527af5bb4387522a8413e841e3e6628c9",
+                "sha256:7b2d54e787a884ffc6e187262823b6feb06c338084bbe80d45166a1cb1c6c5bf",
+                "sha256:7be666cc4599b415f320839e36367b273db8501127b38316f3b9f22f17a0b815",
+                "sha256:8241cac0aae90b82d6b5c443b853723bcc66963970c67e56e71a2609dc4b5eaf",
+                "sha256:82740818f2f240a5da8dfb8943b360e4f24022b093207160c77cadade47d7c85",
+                "sha256:8897b7b7ec077c819187a123174b645eb680c13df68354ed99f9b40a50898f77",
+                "sha256:c2c5250ff0d36fd58550252f54915776940e4e866f38f3a7866d92b32a654b86",
+                "sha256:ca9f686517ec2c4a4ce930207f75c00bf03d94e5063cbc00a1dc42531511b7eb",
+                "sha256:d2b3d199647468d410994dbeb8cec5816fb74feb9368aedf300af709ef507e3e",
+                "sha256:da73d095f8590ad437cd5e9faf6628a218aa7c387e1fdf67b888b47ba56a17f0",
+                "sha256:e167b6b710c7f7bc54e67ef593f8731e1f45aa35f8a8a7b72d6e42ec76afd4b3",
+                "sha256:ea634401ca02367c1567f012317502ef3437522e2fc44a3ea1844de028fa4b84",
+                "sha256:ec6597aa85ce03f3e507566b8bcdf9da2227ec86c4266bd5e6ab4d9e0cc8dab2",
+                "sha256:f64b232348ee82f13aac22856515ce0195837f6968aeaa94a3d0353ea2ec06a6"
+            ],
+            "index": "pypi",
+            "version": "==36.0.2"
+        },
         "et-xmlfile": {
             "hashes": [
                 "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c",
@@ -368,11 +449,11 @@
         },
         "itsdangerous": {
             "hashes": [
-                "sha256:29285842166554469a56d427addc0843914172343784cb909695fdbe90a3e129",
-                "sha256:d848fcb8bc7d507c4546b448574e8a44fc4ea2ba84ebf8d783290d53e81992f5"
+                "sha256:7b7d3023cd35d9cb0c1fd91392f8c95c6fa02c59bf8ad64b8849be3401b95afb",
+                "sha256:935642cd4b987cdbee7210080004033af76306757ff8b4c0a506a4b6e06f02cf"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==2.1.0"
+            "version": "==2.1.1"
         },
         "jinja2": {
             "hashes": [
@@ -384,49 +465,49 @@
         },
         "markupsafe": {
             "hashes": [
-                "sha256:023af8c54fe63530545f70dd2a2a7eed18d07a9a77b94e8bf1e2ff7f252db9a3",
-                "sha256:09c86c9643cceb1d87ca08cdc30160d1b7ab49a8a21564868921959bd16441b8",
-                "sha256:142119fb14a1ef6d758912b25c4e803c3ff66920635c44078666fe7cc3f8f759",
-                "sha256:1d1fb9b2eec3c9714dd936860850300b51dbaa37404209c8d4cb66547884b7ed",
-                "sha256:204730fd5fe2fe3b1e9ccadb2bd18ba8712b111dcabce185af0b3b5285a7c989",
-                "sha256:24c3be29abb6b34052fd26fc7a8e0a49b1ee9d282e3665e8ad09a0a68faee5b3",
-                "sha256:290b02bab3c9e216da57c1d11d2ba73a9f73a614bbdcc027d299a60cdfabb11a",
-                "sha256:3028252424c72b2602a323f70fbf50aa80a5d3aa616ea6add4ba21ae9cc9da4c",
-                "sha256:30c653fde75a6e5eb814d2a0a89378f83d1d3f502ab710904ee585c38888816c",
-                "sha256:3cace1837bc84e63b3fd2dfce37f08f8c18aeb81ef5cf6bb9b51f625cb4e6cd8",
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-                "sha256:fc3150f85e2dbcf99e65238c842d1cfe69d3e7649b19864c1cc043213d9cd730"
+                "sha256:0212a68688482dc52b2d45013df70d169f542b7394fc744c02a57374a4207003",
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+                "sha256:43093fb83d8343aac0b1baa75516da6092f58f41200907ef92448ecab8825135",
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+                "sha256:a49907dd8420c5685cfa064a1335b6754b74541bbb3706c259c02ed65b644b3e",
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+                "sha256:b87db4360013327109564f0e591bd2a3b318547bcef31b468a92ee504d07ae4f",
+                "sha256:bcb3ed405ed3222f9904899563d6fc492ff75cce56cba05e32eff40e6acbeaa3",
+                "sha256:d4306c36ca495956b6d568d276ac11fdd9c30a36f1b6eb928070dc5360b22e1c",
+                "sha256:d5ee4f386140395a2c818d149221149c54849dfcfcb9f1debfe07a8b8bd63f9a",
+                "sha256:dda30ba7e87fbbb7eab1ec9f58678558fd9a6b8b853530e176eabd064da81417",
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+                "sha256:fc7b548b17d238737688817ab67deebb30e8073c95749d55538ed473130ec0c7"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==2.1.0"
+            "version": "==2.1.1"
         },
         "multidict": {
             "hashes": [
@@ -512,6 +593,7 @@
                 "sha256:dbc7601a3b7472d559dc7b933b18b4b66f9aa7452c120e87dfb33d02008c8a18",
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                 "sha256:f8c1f39caad2c896bc0018f699882b345b2a63708008be29b1f355ebf6f933fe",
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                 "sha256:fdf3c08bce27132395d3c3ba1503cac12e17282358cb4bddc25cc46b0aca07aa"
             ],
@@ -561,118 +643,125 @@
             "index": "pypi",
             "version": "==1.2.0"
         },
+        "pycparser": {
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+            "version": "==2.21"
+        },
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+                "sha256:e1fc4d3985868860b6585376e511bb32403c5ffb58b0ed913496c27fd791deea",
+                "sha256:e2b4c95c47fb81b19ea77dc1c50d23af3eba87c9628fcc2e03d44124a3d336ea",
+                "sha256:e4e5d163e6644c2bc84dd9f67bfa89288c23af26983d08fefcc2cbc22f6e57e6",
+                "sha256:e66b3c9f8b89d4fd58a59c04fdbf10602a17c914fbaaa5e6ea593f1d54b06362",
+                "sha256:ed7d11330e443aeecab23866055e08a5a536c95d2c25333aeb441af2dbac38d2",
+                "sha256:f340a2a908644ea6cccd399be0fb308c66e05d2800107345f9f0f0d59e1731c4",
+                "sha256:f38b35ecd2628bf0267761ed659e48af7e620a7fcccfccf5774e7308fb18325c",
+                "sha256:f6d5443104f89a840250087863c91484a72f254574848e951d1bdd7d8b2ce7c9",
+                "sha256:fc2048d13ff427605fea328cbe5369dce549b8c7657b0e22051a5b8831170af6"
             ],
             "index": "pypi",
-            "version": "==3.12.1"
+            "version": "==3.12.3"
         },
         "pymysql": {
             "hashes": [
@@ -742,11 +831,11 @@
         },
         "setuptools": {
             "hashes": [
-                "sha256:2347b2b432c891a863acadca2da9ac101eae6169b1d3dfee2ec605ecd50dbfe5",
-                "sha256:e4f30b9f84e5ab3decf945113119649fec09c1fc3507c6ebffec75646c56e62b"
+                "sha256:6599055eeb23bfef457d5605d33a4d68804266e6cb430b0fb12417c5efeae36c",
+                "sha256:782ef48d58982ddb49920c11a0c5c9c0b02e7d7d1c2ad0aa44e1a1e133051c96"
             ],
             "markers": "python_version >= '3.7'",
-            "version": "==60.9.3"
+            "version": "==60.10.0"
         },
         "simplejson": {
             "hashes": [
@@ -874,11 +963,11 @@
         },
         "tzdata": {
             "hashes": [
-                "sha256:3eee491e22ebfe1e5cfcc97a4137cd70f092ce59144d81f8924a844de05ba8f5",
-                "sha256:68dbe41afd01b867894bbdfd54fa03f468cfa4f0086bfb4adcd8de8f24f3ee21"
+                "sha256:238e70234214138ed7b4e8a0fab0e5e13872edab3be586ab8198c407620e2ab9",
+                "sha256:8b536a8ec63dc0751342b3984193a3118f8fca2afe25752bb9b7fffd398552d3"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==2021.5"
+            "version": "==2022.1"
         },
         "tzlocal": {
             "hashes": [
@@ -890,11 +979,11 @@
         },
         "urllib3": {
             "hashes": [
-                "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed",
-                "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"
+                "sha256:44ece4d53fb1706f667c9bd1c648f5469a2ec925fcf3a776667042d645472c14",
+                "sha256:aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.8"
+            "version": "==1.26.9"
         },
         "werkzeug": {
             "hashes": [
@@ -1112,11 +1201,11 @@
         },
         "freezegun": {
             "hashes": [
-                "sha256:93e90676da387a241a7c2ae7ae68af7b95bfe80e952d0bbf3e088342de90a38d",
-                "sha256:e19563d0b05dcab6dc8ad21c05269004a96998ce2b6b1b8131f1297ae20dd038"
+                "sha256:15103a67dfa868ad809a8f508146e396be2995172d25f927e48ce51c0bf5cb09",
+                "sha256:b4c64efb275e6bc68dc6e771b17ffe0ff0f90b81a2a5189043550b6519926ba4"
             ],
             "markers": "python_version >= '3.6'",
-            "version": "==1.2.0"
+            "version": "==1.2.1"
         },
         "idna": {
             "hashes": [
@@ -1142,29 +1231,32 @@
         },
         "mypy": {
             "hashes": [
-                "sha256:0038b21890867793581e4cb0d810829f5fd4441aa75796b53033af3aa30430ce",
-                "sha256:1171f2e0859cfff2d366da2c7092b06130f232c636a3f7301e3feb8b41f6377d",
-                "sha256:1b06268df7eb53a8feea99cbfff77a6e2b205e70bf31743e786678ef87ee8069",
-                "sha256:1b65714dc296a7991000b6ee59a35b3f550e0073411ac9d3202f6516621ba66c",
-                "sha256:1bf752559797c897cdd2c65f7b60c2b6969ffe458417b8d947b8340cc9cec08d",
-                "sha256:300717a07ad09525401a508ef5d105e6b56646f7942eb92715a1c8d610149714",
-                "sha256:3c5b42d0815e15518b1f0990cff7a705805961613e701db60387e6fb663fe78a",
-                "sha256:4365c60266b95a3f216a3047f1d8e3f895da6c7402e9e1ddfab96393122cc58d",
-                "sha256:50c7346a46dc76a4ed88f3277d4959de8a2bd0a0fa47fa87a4cde36fe247ac05",
-                "sha256:5b56154f8c09427bae082b32275a21f500b24d93c88d69a5e82f3978018a0266",
-                "sha256:74f7eccbfd436abe9c352ad9fb65872cc0f1f0a868e9d9c44db0893440f0c697",
-                "sha256:7b3f6f557ba4afc7f2ce6d3215d5db279bcf120b3cfd0add20a5d4f4abdae5bc",
-                "sha256:8c11003aaeaf7cc2d0f1bc101c1cc9454ec4cc9cb825aef3cafff8a5fdf4c799",
-                "sha256:8ca7f8c4b1584d63c9a0f827c37ba7a47226c19a23a753d52e5b5eddb201afcd",
-                "sha256:c89702cac5b302f0c5d33b172d2b55b5df2bede3344a2fbed99ff96bddb2cf00",
-                "sha256:d8f1ff62f7a879c9fe5917b3f9eb93a79b78aad47b533911b853a757223f72e7",
-                "sha256:d9d2b84b2007cea426e327d2483238f040c49405a6bf4074f605f0156c91a47a",
-                "sha256:e839191b8da5b4e5d805f940537efcaa13ea5dd98418f06dc585d2891d228cf0",
-                "sha256:f9fe20d0872b26c4bba1c1be02c5340de1019530302cf2dcc85c7f9fc3252ae0",
-                "sha256:ff3bf387c14c805ab1388185dd22d6b210824e164d4bb324b195ff34e322d166"
+                "sha256:080097eee5393fd740f32c63f9343580aaa0fb1cda0128fd859dfcf081321c3d",
+                "sha256:0d3bcbe146247997e03bf030122000998b076b3ac6925b0b6563f46d1ce39b50",
+                "sha256:0dd441fbacf48e19dc0c5c42fafa72b8e1a0ba0a39309c1af9c84b9397d9b15a",
+                "sha256:108f3c7e14a038cf097d2444fa0155462362c6316e3ecb2d70f6dd99cd36084d",
+                "sha256:3bada0cf7b6965627954b3a128903a87cac79a79ccd83b6104912e723ef16c7b",
+                "sha256:3cf77f138efb31727ee7197bc824c9d6d7039204ed96756cc0f9ca7d8e8fc2a4",
+                "sha256:42c216a33d2bdba08098acaf5bae65b0c8196afeb535ef4b870919a788a27259",
+                "sha256:465a6ce9ca6268cadfbc27a2a94ddf0412568a6b27640ced229270be4f5d394d",
+                "sha256:6a8e1f63357851444940351e98fb3252956a15f2cabe3d698316d7a2d1f1f896",
+                "sha256:745071762f32f65e77de6df699366d707fad6c132a660d1342077cbf671ef589",
+                "sha256:818cfc51c25a5dbfd0705f3ac1919fff6971eb0c02e6f1a1f6a017a42405a7c0",
+                "sha256:8e5974583a77d630a5868eee18f85ac3093caf76e018c510aeb802b9973304ce",
+                "sha256:8eaf55fdf99242a1c8c792247c455565447353914023878beadb79600aac4a2a",
+                "sha256:98f61aad0bb54f797b17da5b82f419e6ce214de0aa7e92211ebee9e40eb04276",
+                "sha256:b2ce2788df0c066c2ff4ba7190fa84f18937527c477247e926abeb9b1168b8cc",
+                "sha256:b30d29251dff4c59b2e5a1fa1bab91ff3e117b4658cb90f76d97702b7a2ae699",
+                "sha256:bf446223b2e0e4f0a4792938e8d885e8a896834aded5f51be5c3c69566495540",
+                "sha256:cbcc691d8b507d54cb2b8521f0a2a3d4daa477f62fe77f0abba41e5febb377b7",
+                "sha256:d051ce0946521eba48e19b25f27f98e5ce4dbc91fff296de76240c46b4464df0",
+                "sha256:d61b73c01fc1de799226963f2639af831307fe1556b04b7c25e2b6c267a3bc76",
+                "sha256:eea10982b798ff0ccc3b9e7e42628f932f552c5845066970e67cd6858655d52c",
+                "sha256:f79137d012ff3227866222049af534f25354c07a0d6b9a171dba9f1d6a1fdef4",
+                "sha256:fc5ecff5a3bbfbe20091b1cad82815507f5ae9c380a3a9bf40f740c70ce30a9b"
             ],
             "index": "pypi",
-            "version": "==0.931"
+            "version": "==0.941"
         },
         "mypy-extensions": {
             "hashes": [
@@ -1238,11 +1330,11 @@
         },
         "pytest": {
             "hashes": [
-                "sha256:9ce3ff477af913ecf6321fe337b93a2c0dcf2a0a1439c43f5452112c1e4280db",
-                "sha256:e30905a0c131d3d94b89624a1cc5afec3e0ba2fbdb151867d8e0ebd49850f171"
+                "sha256:841132caef6b1ad17a9afde46dc4f6cfa59a05f9555aae5151f73bdf2820ca63",
+                "sha256:92f723789a8fdd7180b6b06483874feca4c48a5c76968e03bb3e7f806a1869ea"
             ],
             "index": "pypi",
-            "version": "==7.0.1"
+            "version": "==7.1.1"
         },
         "pytest-cov": {
             "hashes": [
@@ -1278,11 +1370,11 @@
         },
         "responses": {
             "hashes": [
-                "sha256:3fc29c3117e14136b833a0a6d4e7f1217c6301bf08b6086db468e12f1e3290e2",
-                "sha256:53354b5de163aa2074312c71d8ebccb8bd1ab336cff7053abb75e84dc5637abe"
+                "sha256:18831bc2d72443b67664d98038374a6fa1f27eaaff4dd9a7d7613723416fea3c",
+                "sha256:644905bc4fb8a18fa37e3882b2ac05e610fe8c2f967d327eed669e314d94a541"
             ],
             "index": "pypi",
-            "version": "==0.19.0"
+            "version": "==0.20.0"
         },
         "six": {
             "hashes": [
@@ -1302,18 +1394,18 @@
         },
         "types-requests": {
             "hashes": [
-                "sha256:506279bad570c7b4b19ac1f22e50146538befbe0c133b2cea66a9b04a533a859",
-                "sha256:6a7ed24b21780af4a5b5e24c310b2cd885fb612df5fd95584d03d87e5f2a195a"
+                "sha256:5d6f77f3c7565659bdb7b7bce1d33d1abb7d0b056138cac714860e13da2f19df",
+                "sha256:cf0646031dd6307113b37814f743c04f0707a3357378c2bb1326f848412f5ba9"
             ],
             "index": "pypi",
-            "version": "==2.27.11"
+            "version": "==2.27.13"
         },
         "types-urllib3": {
             "hashes": [
-                "sha256:a26898f530e6c3f43f25b907f2b884486868ffd56a9faa94cbf9b3eb6e165d6a",
-                "sha256:d755278d5ecd7a7a6479a190e54230f241f1a99c19b81518b756b19dc69e518c"
+                "sha256:24d64e441168851eb05f1d022de18ae31558f5649c8f1117e384c2e85e31315b",
+                "sha256:bd0abc01e9fb963e4fddd561a56d21cc371b988d1245662195c90379077139cd"
             ],
-            "version": "==1.26.10"
+            "version": "==1.26.11"
         },
         "typing-extensions": {
             "hashes": [
@@ -1325,11 +1417,11 @@
         },
         "urllib3": {
             "hashes": [
-                "sha256:000ca7f471a233c2251c6c7023ee85305721bfdf18621ebff4fd17a8653427ed",
-                "sha256:0e7c33d9a63e7ddfcb86780aac87befc2fbddf46c58dbb487e0855f7ceec283c"
+                "sha256:44ece4d53fb1706f667c9bd1c648f5469a2ec925fcf3a776667042d645472c14",
+                "sha256:aabaf16477806a5e1dd19aa41f8c2b7950dd3c746362d7e3223dbe6de6ac448e"
             ],
             "markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4' and python_version < '4'",
-            "version": "==1.26.8"
+            "version": "==1.26.9"
         }
     }
 }

From 4e52999f31d8b3dcfc4fb647014a513e8b83dec3 Mon Sep 17 00:00:00 2001
From: Andrew Sparkes <as28@sanger.ac.uk>
Date: Wed, 23 Mar 2022 14:45:43 +0000
Subject: [PATCH 07/12] Removing cryptography package

---
 Pipfile      |   1 -
 Pipfile.lock | 100 ++-------------------------------------------------
 2 files changed, 2 insertions(+), 99 deletions(-)

diff --git a/Pipfile b/Pipfile
index ad527c01..af94354d 100644
--- a/Pipfile
+++ b/Pipfile
@@ -31,7 +31,6 @@ requests = "~=2.27"
 slackclient = "~=2.5"
 sqlalchemy = "~=1.4"
 pymongo = "~=3.12.1"
-cryptography = "*"
 
 [requires]
 python_version = "3.8"
diff --git a/Pipfile.lock b/Pipfile.lock
index 08a067fd..0d1f1241 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1,7 +1,7 @@
 {
     "_meta": {
         "hash": {
-            "sha256": "4857141b5d8f3df25e840ecd14581925bcc1af3a493cc40b2727bee111ad92e3"
+            "sha256": "50de8689f93240b910f0b5a4ca1d2a12240dcb915a5871d9a9cfe95f93b4abdb"
         },
         "pipfile-spec": 6,
         "requires": {
@@ -145,7 +145,7 @@
                 "sha256:f04e857b59d9d1ccc39ce2da1021d196e47234873820cbeaad210724b1ee28ac",
                 "sha256:fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2"
             ],
-            "markers": "python_version < '3.9'",
+            "markers": "python_version >= '3.6' and python_version < '3.9'",
             "version": "==0.2.1"
         },
         "cerberus": {
@@ -162,61 +162,6 @@
             ],
             "version": "==2021.10.8"
         },
-        "cffi": {
-            "hashes": [
-                "sha256:00c878c90cb53ccfaae6b8bc18ad05d2036553e6d9d1d9dbcf323bbe83854ca3",
-                "sha256:0104fb5ae2391d46a4cb082abdd5c69ea4eab79d8d44eaaf79f1b1fd806ee4c2",
-                "sha256:06c48159c1abed75c2e721b1715c379fa3200c7784271b3c46df01383b593636",
-                "sha256:0808014eb713677ec1292301ea4c81ad277b6cdf2fdd90fd540af98c0b101d20",
-                "sha256:10dffb601ccfb65262a27233ac273d552ddc4d8ae1bf93b21c94b8511bffe728",
-                "sha256:14cd121ea63ecdae71efa69c15c5543a4b5fbcd0bbe2aad864baca0063cecf27",
-                "sha256:17771976e82e9f94976180f76468546834d22a7cc404b17c22df2a2c81db0c66",
-                "sha256:181dee03b1170ff1969489acf1c26533710231c58f95534e3edac87fff06c443",
-                "sha256:23cfe892bd5dd8941608f93348c0737e369e51c100d03718f108bf1add7bd6d0",
-                "sha256:263cc3d821c4ab2213cbe8cd8b355a7f72a8324577dc865ef98487c1aeee2bc7",
-                "sha256:2756c88cbb94231c7a147402476be2c4df2f6078099a6f4a480d239a8817ae39",
-                "sha256:27c219baf94952ae9d50ec19651a687b826792055353d07648a5695413e0c605",
-                "sha256:2a23af14f408d53d5e6cd4e3d9a24ff9e05906ad574822a10563efcef137979a",
-                "sha256:31fb708d9d7c3f49a60f04cf5b119aeefe5644daba1cd2a0fe389b674fd1de37",
-                "sha256:3415c89f9204ee60cd09b235810be700e993e343a408693e80ce7f6a40108029",
-                "sha256:3773c4d81e6e818df2efbc7dd77325ca0dcb688116050fb2b3011218eda36139",
-                "sha256:3b96a311ac60a3f6be21d2572e46ce67f09abcf4d09344c49274eb9e0bf345fc",
-                "sha256:3f7d084648d77af029acb79a0ff49a0ad7e9d09057a9bf46596dac9514dc07df",
-                "sha256:41d45de54cd277a7878919867c0f08b0cf817605e4eb94093e7516505d3c8d14",
-                "sha256:4238e6dab5d6a8ba812de994bbb0a79bddbdf80994e4ce802b6f6f3142fcc880",
-                "sha256:45db3a33139e9c8f7c09234b5784a5e33d31fd6907800b316decad50af323ff2",
-                "sha256:45e8636704eacc432a206ac7345a5d3d2c62d95a507ec70d62f23cd91770482a",
-                "sha256:4958391dbd6249d7ad855b9ca88fae690783a6be9e86df65865058ed81fc860e",
-                "sha256:4a306fa632e8f0928956a41fa8e1d6243c71e7eb59ffbd165fc0b41e316b2474",
-                "sha256:57e9ac9ccc3101fac9d6014fba037473e4358ef4e89f8e181f8951a2c0162024",
-                "sha256:59888172256cac5629e60e72e86598027aca6bf01fa2465bdb676d37636573e8",
-                "sha256:5e069f72d497312b24fcc02073d70cb989045d1c91cbd53979366077959933e0",
-                "sha256:64d4ec9f448dfe041705426000cc13e34e6e5bb13736e9fd62e34a0b0c41566e",
-                "sha256:6dc2737a3674b3e344847c8686cf29e500584ccad76204efea14f451d4cc669a",
-                "sha256:74fdfdbfdc48d3f47148976f49fab3251e550a8720bebc99bf1483f5bfb5db3e",
-                "sha256:75e4024375654472cc27e91cbe9eaa08567f7fbdf822638be2814ce059f58032",
-                "sha256:786902fb9ba7433aae840e0ed609f45c7bcd4e225ebb9c753aa39725bb3e6ad6",
-                "sha256:8b6c2ea03845c9f501ed1313e78de148cd3f6cad741a75d43a29b43da27f2e1e",
-                "sha256:91d77d2a782be4274da750752bb1650a97bfd8f291022b379bb8e01c66b4e96b",
-                "sha256:91ec59c33514b7c7559a6acda53bbfe1b283949c34fe7440bcf917f96ac0723e",
-                "sha256:920f0d66a896c2d99f0adbb391f990a84091179542c205fa53ce5787aff87954",
-                "sha256:a5263e363c27b653a90078143adb3d076c1a748ec9ecc78ea2fb916f9b861962",
-                "sha256:abb9a20a72ac4e0fdb50dae135ba5e77880518e742077ced47eb1499e29a443c",
-                "sha256:c2051981a968d7de9dd2d7b87bcb9c939c74a34626a6e2f8181455dd49ed69e4",
-                "sha256:c21c9e3896c23007803a875460fb786118f0cdd4434359577ea25eb556e34c55",
-                "sha256:c2502a1a03b6312837279c8c1bd3ebedf6c12c4228ddbad40912d671ccc8a962",
-                "sha256:d4d692a89c5cf08a8557fdeb329b82e7bf609aadfaed6c0d79f5a449a3c7c023",
-                "sha256:da5db4e883f1ce37f55c667e5c0de439df76ac4cb55964655906306918e7363c",
-                "sha256:e7022a66d9b55e93e1a845d8c9eba2a1bebd4966cd8bfc25d9cd07d515b33fa6",
-                "sha256:ef1f279350da2c586a69d32fc8733092fd32cc8ac95139a00377841f59a3f8d8",
-                "sha256:f54a64f8b0c8ff0b64d18aa76675262e1700f3995182267998c31ae974fbc382",
-                "sha256:f5c7150ad32ba43a07c4479f40241756145a1f03b43480e058cfd862bf5041c7",
-                "sha256:f6f824dc3bce0edab5f427efcfb1d63ee75b6fcb7282900ccaf925be84efb0fc",
-                "sha256:fd8a250edc26254fe5b33be00402e6d287f562b6a5b2152dec302fa15bb3e997",
-                "sha256:ffaa5c925128e29efbde7301d8ecaf35c8c60ffbcd6a1ffd3a552177c8e5e796"
-            ],
-            "version": "==1.15.0"
-        },
         "charset-normalizer": {
             "hashes": [
                 "sha256:2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597",
@@ -241,32 +186,6 @@
             "index": "pypi",
             "version": "==6.6.0"
         },
-        "cryptography": {
-            "hashes": [
-                "sha256:0a3bf09bb0b7a2c93ce7b98cb107e9170a90c51a0162a20af1c61c765b90e60b",
-                "sha256:1f64a62b3b75e4005df19d3b5235abd43fa6358d5516cfc43d87aeba8d08dd51",
-                "sha256:32db5cc49c73f39aac27574522cecd0a4bb7384e71198bc65a0d23f901e89bb7",
-                "sha256:4881d09298cd0b669bb15b9cfe6166f16fc1277b4ed0d04a22f3d6430cb30f1d",
-                "sha256:4e2dddd38a5ba733be6a025a1475a9f45e4e41139d1321f412c6b360b19070b6",
-                "sha256:53e0285b49fd0ab6e604f4c5d9c5ddd98de77018542e88366923f152dbeb3c29",
-                "sha256:70f8f4f7bb2ac9f340655cbac89d68c527af5bb4387522a8413e841e3e6628c9",
-                "sha256:7b2d54e787a884ffc6e187262823b6feb06c338084bbe80d45166a1cb1c6c5bf",
-                "sha256:7be666cc4599b415f320839e36367b273db8501127b38316f3b9f22f17a0b815",
-                "sha256:8241cac0aae90b82d6b5c443b853723bcc66963970c67e56e71a2609dc4b5eaf",
-                "sha256:82740818f2f240a5da8dfb8943b360e4f24022b093207160c77cadade47d7c85",
-                "sha256:8897b7b7ec077c819187a123174b645eb680c13df68354ed99f9b40a50898f77",
-                "sha256:c2c5250ff0d36fd58550252f54915776940e4e866f38f3a7866d92b32a654b86",
-                "sha256:ca9f686517ec2c4a4ce930207f75c00bf03d94e5063cbc00a1dc42531511b7eb",
-                "sha256:d2b3d199647468d410994dbeb8cec5816fb74feb9368aedf300af709ef507e3e",
-                "sha256:da73d095f8590ad437cd5e9faf6628a218aa7c387e1fdf67b888b47ba56a17f0",
-                "sha256:e167b6b710c7f7bc54e67ef593f8731e1f45aa35f8a8a7b72d6e42ec76afd4b3",
-                "sha256:ea634401ca02367c1567f012317502ef3437522e2fc44a3ea1844de028fa4b84",
-                "sha256:ec6597aa85ce03f3e507566b8bcdf9da2227ec86c4266bd5e6ab4d9e0cc8dab2",
-                "sha256:f64b232348ee82f13aac22856515ce0195837f6968aeaa94a3d0353ea2ec06a6"
-            ],
-            "index": "pypi",
-            "version": "==36.0.2"
-        },
         "et-xmlfile": {
             "hashes": [
                 "sha256:8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c",
@@ -643,13 +562,6 @@
             "index": "pypi",
             "version": "==1.2.0"
         },
-        "pycparser": {
-            "hashes": [
-                "sha256:8ee45429555515e1f6b185e78100aea234072576aa43ab53aefcae078162fca9",
-                "sha256:e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206"
-            ],
-            "version": "==2.21"
-        },
         "pymongo": {
             "hashes": [
                 "sha256:06b64cdf5121f86b78a84e61b8f899b6988732a8d304b503ea1f94a676221c06",
@@ -829,14 +741,6 @@
             "index": "pypi",
             "version": "==2.27.1"
         },
-        "setuptools": {
-            "hashes": [
-                "sha256:6599055eeb23bfef457d5605d33a4d68804266e6cb430b0fb12417c5efeae36c",
-                "sha256:782ef48d58982ddb49920c11a0c5c9c0b02e7d7d1c2ad0aa44e1a1e133051c96"
-            ],
-            "markers": "python_version >= '3.7'",
-            "version": "==60.10.0"
-        },
         "simplejson": {
             "hashes": [
                 "sha256:04e31fa6ac8e326480703fb6ded1488bfa6f1d3f760d32e29dbf66d0838982ce",

From af1651a5bd12f4d21a484951771ecc9217d42546 Mon Sep 17 00:00:00 2001
From: Andrew Sparkes <as28@sanger.ac.uk>
Date: Wed, 23 Mar 2022 14:54:01 +0000
Subject: [PATCH 08/12] Renamed BECKMAN_FAILURE_TYPES list to be generic as
 shared with Biosero

---
 lighthouse/classes/beckman.py                   | 2 +-
 lighthouse/config/defaults.py                   | 4 ++--
 lighthouse/config/test.py                       | 4 ++--
 lighthouse/routes/common/cherrypicked_plates.py | 2 +-
 tests/helpers/test_plates_helpers.py            | 2 +-
 tests/routes/v1/test_beckman.py                 | 4 ++--
 6 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/lighthouse/classes/beckman.py b/lighthouse/classes/beckman.py
index f6bd4296..fc6834df 100644
--- a/lighthouse/classes/beckman.py
+++ b/lighthouse/classes/beckman.py
@@ -76,7 +76,7 @@ def get_robots() -> Optional[List[Dict[str, str]]]:
     def get_failure_types() -> List[Dict[str, str]]:
         logger.debug("Getting Beckman failure types information from config...")
 
-        failure_types_config = app.config.get("BECKMAN_FAILURE_TYPES")
+        failure_types_config = app.config.get("ROBOT_FAILURE_TYPES")
 
         if failure_types_config is None or not isinstance(failure_types_config, dict):
             message = "no config found or unreadable"
diff --git a/lighthouse/config/defaults.py b/lighthouse/config/defaults.py
index cd9b3fa9..c2c460e6 100644
--- a/lighthouse/config/defaults.py
+++ b/lighthouse/config/defaults.py
@@ -213,8 +213,8 @@
     "BKRB0003": {"name": "Robot 3", "uuid": "90d8bc7a-2f6e-4a5f-8bea-1e8d27a1ac89"},
     "BKRB0004": {"name": "Robot 4", "uuid": "675002fe-f364-47e4-b71f-4fe1bb7b5091"},
 }
-# TODO: make these the generic failure types
-BECKMAN_FAILURE_TYPES = {
+# failure types (shared by Beckman and Biosero fail screens in Lighthouse-UI)
+ROBOT_FAILURE_TYPES = {
     "plate_too_low_empty": "Plate too low/empty",
     "general_software_error": "General software error",
     "robot_crashed": "The robot crashed",
diff --git a/lighthouse/config/test.py b/lighthouse/config/test.py
index 47a07344..522c7e6c 100644
--- a/lighthouse/config/test.py
+++ b/lighthouse/config/test.py
@@ -80,9 +80,9 @@
 RMQ_LIMS_ID = "LH_TEST"
 
 ###
-# Beckman config
+# Robot config
 ###
-BECKMAN_FAILURE_TYPES = {key: BECKMAN_FAILURE_TYPES[key] for key in ("robot_crashed", "sample_contamination", "other")}
+ROBOT_FAILURE_TYPES = {key: ROBOT_FAILURE_TYPES[key] for key in ("robot_crashed", "sample_contamination", "other")}
 
 ###
 # SS plate creation config (UUID for the plate purpose and study of the plate created)
diff --git a/lighthouse/routes/common/cherrypicked_plates.py b/lighthouse/routes/common/cherrypicked_plates.py
index 46ec7083..a4c66171 100644
--- a/lighthouse/routes/common/cherrypicked_plates.py
+++ b/lighthouse/routes/common/cherrypicked_plates.py
@@ -153,7 +153,7 @@ def fail_plate_from_barcode() -> FlaskResponse:
 
         return bad_request(str(e))
     try:
-        if failure_type not in app.config["BECKMAN_FAILURE_TYPES"]:
+        if failure_type not in app.config["ROBOT_FAILURE_TYPES"]:
             logger.error(f"{ERROR_CHERRYPICKED_FAILURE_RECORD} unknown failure type")
 
             return bad_request(f"'{failure_type}' is not a known cherrypicked plate failure type")
diff --git a/tests/helpers/test_plates_helpers.py b/tests/helpers/test_plates_helpers.py
index 961e0ef6..df4de65a 100644
--- a/tests/helpers/test_plates_helpers.py
+++ b/tests/helpers/test_plates_helpers.py
@@ -103,7 +103,7 @@ def mock_event_helpers():
 
 
 def any_failure_type(app):
-    return list(app.config["BECKMAN_FAILURE_TYPES"].keys())[0]
+    return list(app.config["ROBOT_FAILURE_TYPES"].keys())[0]
 
 
 # ---------- tests ----------
diff --git a/tests/routes/v1/test_beckman.py b/tests/routes/v1/test_beckman.py
index a2f62cf3..25fae924 100644
--- a/tests/routes/v1/test_beckman.py
+++ b/tests/routes/v1/test_beckman.py
@@ -70,7 +70,7 @@ def test_get_failure_types_returns_expected_failure_types(app, client, base_url)
 @pytest.mark.parametrize("base_url", FAILURE_TYPES_BASE_URLS)
 def test_get_failure_types_internal_server_error_no_failure_types_config_exists(app, client, base_url):
     with app.app_context():
-        del app.config["BECKMAN_FAILURE_TYPES"]
+        del app.config["ROBOT_FAILURE_TYPES"]
         response = client.get(base_url)
 
         assert response.status_code == HTTPStatus.INTERNAL_SERVER_ERROR
@@ -81,7 +81,7 @@ def test_get_failure_types_internal_server_error_no_failure_types_config_exists(
 @pytest.mark.parametrize("base_url", FAILURE_TYPES_BASE_URLS)
 def test_get_failure_types_internal_server_error_incorrect_format_config(app, client, base_url):
     with app.app_context():
-        app.config["BECKMAN_FAILURE_TYPES"] = ["not the expected dictionary"]
+        app.config["ROBOT_FAILURE_TYPES"] = ["not the expected dictionary"]
         response = client.get(base_url)
 
         assert response.status_code == HTTPStatus.INTERNAL_SERVER_ERROR

From a2e096503c85829d3919371706219a42993560ed Mon Sep 17 00:00:00 2001
From: Andrew Sparkes <as28@sanger.ac.uk>
Date: Wed, 23 Mar 2022 15:01:09 +0000
Subject: [PATCH 09/12] Adjusted failure type message to remove slash

---
 lighthouse/config/defaults.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lighthouse/config/defaults.py b/lighthouse/config/defaults.py
index c2c460e6..b90b579c 100644
--- a/lighthouse/config/defaults.py
+++ b/lighthouse/config/defaults.py
@@ -215,7 +215,7 @@
 }
 # failure types (shared by Beckman and Biosero fail screens in Lighthouse-UI)
 ROBOT_FAILURE_TYPES = {
-    "plate_too_low_empty": "Plate too low/empty",
+    "plate_too_low_empty": "Plate volumes too low or empty",
     "general_software_error": "General software error",
     "robot_crashed": "The robot crashed",
     "sample_contamination": "Sample contamination occurred",

From 2e91430198acc674580cbc7ed847e1255abb1b07 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Thu, 24 Mar 2022 07:14:16 +0000
Subject: [PATCH 10/12] Bump flake8-bugbear from 22.3.20 to 22.3.23

Bumps [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) from 22.3.20 to 22.3.23.
- [Release notes](https://github.com/PyCQA/flake8-bugbear/releases)
- [Commits](https://github.com/PyCQA/flake8-bugbear/compare/22.3.20...22.3.23)

---
updated-dependencies:
- dependency-name: flake8-bugbear
  dependency-type: direct:development
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 Pipfile.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/Pipfile.lock b/Pipfile.lock
index 4337b163..2bbb3941 100644
--- a/Pipfile.lock
+++ b/Pipfile.lock
@@ -1105,11 +1105,11 @@
         },
         "flake8-bugbear": {
             "hashes": [
-                "sha256:152e64a86f6bff6e295d630ccc993f62434c1fd2b20d2fae47547cb1c1b868e0",
-                "sha256:19fe179ee3286e16198603c438788e2949e79f31d653f0bdb56d53fb69217bd0"
+                "sha256:e0dc2a36474490d5b1a2d57f9e4ef570abc09f07cbb712b29802e28a2367ff19",
+                "sha256:ec5ec92195720cee1589315416b844ffa5e82f73a78e65329e8055322df1e939"
             ],
             "index": "pypi",
-            "version": "==22.3.20"
+            "version": "==22.3.23"
         },
         "freezegun": {
             "hashes": [

From 9c031cf883c0836cbc1992fec9a85c370ba223c0 Mon Sep 17 00:00:00 2001
From: Andrew Sparkes <as28@sanger.ac.uk>
Date: Thu, 24 Mar 2022 09:35:01 +0000
Subject: [PATCH 11/12] Minor failure type text change

---
 lighthouse/config/defaults.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lighthouse/config/defaults.py b/lighthouse/config/defaults.py
index b90b579c..bdde4fbd 100644
--- a/lighthouse/config/defaults.py
+++ b/lighthouse/config/defaults.py
@@ -215,7 +215,7 @@
 }
 # failure types (shared by Beckman and Biosero fail screens in Lighthouse-UI)
 ROBOT_FAILURE_TYPES = {
-    "plate_too_low_empty": "Plate volumes too low or empty",
+    "plate_too_low_empty": "Plate volumes are too low or empty",
     "general_software_error": "General software error",
     "robot_crashed": "The robot crashed",
     "sample_contamination": "Sample contamination occurred",

From d6380b4fac3ed51985edf4a92cf4bfbf37877ce4 Mon Sep 17 00:00:00 2001
From: Andrew Sparkes <as28@sanger.ac.uk>
Date: Thu, 24 Mar 2022 09:55:01 +0000
Subject: [PATCH 12/12] bump release version

---
 .release-version | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.release-version b/.release-version
index ad226192..5c18f919 100644
--- a/.release-version
+++ b/.release-version
@@ -1 +1 @@
-2.24.0
+2.25.0