From 41770229b814b4a4c5a854d1cd037e86927735b8 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 25 Oct 2023 19:48:12 +0000 Subject: [PATCH 01/38] Bump werkzeug from 2.3.6 to 3.0.1 Bumps [werkzeug](https://github.com/pallets/werkzeug) from 2.3.6 to 3.0.1. - [Release notes](https://github.com/pallets/werkzeug/releases) - [Changelog](https://github.com/pallets/werkzeug/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/werkzeug/compare/2.3.6...3.0.1) --- updated-dependencies: - dependency-name: werkzeug dependency-type: indirect ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 1046 ++++++++++++++++++++++++++------------------------ 1 file changed, 547 insertions(+), 499 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 21b503e0..a636886f 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -18,96 +18,85 @@ "default": { "aiohttp": { "hashes": [ - "sha256:00ad4b6f185ec67f3e6562e8a1d2b69660be43070bd0ef6fcec5211154c7df67", - "sha256:0175d745d9e85c40dcc51c8f88c74bfbaef9e7afeeeb9d03c37977270303064c", - "sha256:01d4c0c874aa4ddfb8098e85d10b5e875a70adc63db91f1ae65a4b04d3344cda", - "sha256:043d2299f6dfdc92f0ac5e995dfc56668e1587cea7f9aa9d8a78a1b6554e5755", - "sha256:0c413c633d0512df4dc7fd2373ec06cc6a815b7b6d6c2f208ada7e9e93a5061d", - "sha256:0d21c684808288a98914e5aaf2a7c6a3179d4df11d249799c32d1808e79503b5", - "sha256:0e584a10f204a617d71d359fe383406305a4b595b333721fa50b867b4a0a1548", - "sha256:1274477e4c71ce8cfe6c1ec2f806d57c015ebf84d83373676036e256bc55d690", - 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"sha256:a461508f3096d1d5810ec5ab95d7eeecb651f3a15b71959999988942063bf01d" + "sha256:334373d392fde0fdf95af5c3f1661885fa10c52167b14593eb856289e1855062", + "sha256:c05bc6c158facb0676674b7f11fe3960db4f389718e19e62bd2b84d6205cfd24" ], - "version": "==6.0.12.11" + "version": "==6.0.12.12" }, "typing-extensions": { "hashes": [ - "sha256:440d5dd3af93b060174bf433bccd69b0babc3b15b1a8dca43789fd7f61514b36", - "sha256:b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2" + "sha256:8f92fc8806f9a6b641eaa5318da32b44d401efaac0f6678c9bc448ba3605faa0", + "sha256:df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef" ], - "markers": "python_version >= '3.7'", - "version": "==4.7.1" + "markers": "python_version >= '3.8'", + "version": "==4.8.0" }, "urllib3": { "hashes": [ - "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11", - "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4" + "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84", + "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e" ], "markers": "python_version >= '3.7'", - "version": "==2.0.4" + "version": "==2.0.7" } } } From 250fa2f81671ba61ff55546b58a0ec3308a9e6db Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 8 Dec 2023 15:13:31 +0000 Subject: [PATCH 02/38] Bump aiohttp from 3.9.0b0 to 3.9.0 Bumps [aiohttp](https://github.com/aio-libs/aiohttp) from 3.9.0b0 to 3.9.0. - [Release notes](https://github.com/aio-libs/aiohttp/releases) - [Changelog](https://github.com/aio-libs/aiohttp/blob/master/CHANGES.rst) - [Commits](https://github.com/aio-libs/aiohttp/compare/v3.9.0b0...v3.9.0) --- updated-dependencies: - dependency-name: aiohttp dependency-type: indirect ... 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dependency-name: cryptography dependency-type: indirect ... 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Signed-off-by: dependabot[bot] --- Pipfile.lock | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 371c6408..003cc1a6 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1556,11 +1556,11 @@ }, "exceptiongroup": { "hashes": [ - "sha256:097acd85d473d75af5bb98e41b61ff7fe35efe6675e4f9370ec6ec5126d160e9", - "sha256:343280667a4585d195ca1cf9cef84a4e178c4b6cf2274caef9859782b567d5e3" + "sha256:4bfd3996ac73b41e9b9628b04e079f193850720ea5945fc96a08633c66912f14", + "sha256:91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68" ], "markers": "python_version < '3.11'", - "version": "==1.1.3" + "version": "==1.2.0" }, "flake8": { "hashes": [ @@ -1711,12 +1711,12 @@ }, "pytest": { "hashes": [ - "sha256:78bf16451a2eb8c7a2ea98e32dc119fd2aa758f1d5d66dbf0a59d69a3969df32", - "sha256:b4bf8c45bd59934ed84001ad51e11b4ee40d40a1229d2c79f9c592b0a3f6bd8a" + "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac", + "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5" ], "index": "pypi", "markers": "python_version >= '3.7'", - "version": "==7.4.0" + "version": "==7.4.3" }, "pytest-cov": { "hashes": [ From da3df1ee3908b7b78ef52d3926a091dbbe743163 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 11 Dec 2023 07:37:30 +0000 Subject: [PATCH 05/38] Bump pymongo from 4.4.1 to 4.6.1 Bumps [pymongo](https://github.com/mongodb/mongo-python-driver) from 4.4.1 to 4.6.1. - [Release notes](https://github.com/mongodb/mongo-python-driver/releases) - [Changelog](https://github.com/mongodb/mongo-python-driver/blob/master/doc/changelog.rst) - [Commits](https://github.com/mongodb/mongo-python-driver/compare/4.4.1...4.6.1) --- updated-dependencies: - dependency-name: pymongo dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Pipfile | 2 +- Pipfile.lock | 159 +++++++++++++++++++++++++++------------------------ 2 files changed, 84 insertions(+), 77 deletions(-) diff --git a/Pipfile b/Pipfile index b8eb3df8..9bb04cbf 100644 --- a/Pipfile +++ b/Pipfile @@ -25,7 +25,7 @@ more-itertools = "~=10.0" mysql-connector-python = "~=8.1" pandas = "~=2.0" pika = "~=1.3" -pymongo = "~=4.4" +pymongo = "~=4.6" pymysql = "~=1.1" pyodbc = "~=4.0" pysftp = "~=0.2" diff --git a/Pipfile.lock b/Pipfile.lock index 003cc1a6..bbcabdec 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "f29c7cb8de27441531a1dcfb43bba75b5190815be28b5a9f5432de886eb0deb3" + "sha256": "325332baeb13c762030635aef109abb92442519e470e17b7452f3027ed836973" }, "pipfile-spec": 6, "requires": { @@ -938,84 +938,91 @@ }, "pymongo": { "hashes": [ - "sha256:022c91e2a41eefbcddc844c534520a13c6f613666c37b9fb9ed039eff47bd2e4", - 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8e69b30391e921ecfed76831cf06bc1348b883a7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 11 Dec 2023 10:18:54 +0000 Subject: [PATCH 06/38] Bump flask-apscheduler from 1.12.4 to 1.13.1 Bumps [flask-apscheduler](https://github.com/viniciuschiele/flask-apscheduler) from 1.12.4 to 1.13.1. - [Release notes](https://github.com/viniciuschiele/flask-apscheduler/releases) - [Changelog](https://github.com/viniciuschiele/flask-apscheduler/blob/master/CHANGELOG.md) - [Commits](https://github.com/viniciuschiele/flask-apscheduler/compare/1.12.4...1.13.1) --- updated-dependencies: - dependency-name: flask-apscheduler dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Pipfile | 2 +- Pipfile.lock | 28 ++++++++++++++-------------- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/Pipfile b/Pipfile index 9bb04cbf..b80bfa70 100644 --- a/Pipfile +++ b/Pipfile @@ -19,7 +19,7 @@ responses = "*" [packages] colorlog = "~=6.7" flask = "~=2.3" -flask-apscheduler = "~=1.12" +flask-apscheduler = "~=1.13" gunicorn = "~=21.2" more-itertools = "~=10.0" mysql-connector-python = "~=8.1" diff --git a/Pipfile.lock b/Pipfile.lock index bbcabdec..b7e20668 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "325332baeb13c762030635aef109abb92442519e470e17b7452f3027ed836973" + "sha256": "e8a87d180806d86ec26fc4d0e29654945b5a8ad9a25dda3d3f5910534fbac897" }, "pipfile-spec": 6, "requires": { @@ -182,11 +182,11 @@ }, "blinker": { "hashes": [ - "sha256:152090d27c1c5c722ee7e48504b02d76502811ce02e1523553b4cf8c8b3d3a8d", - "sha256:296320d6c28b006eb5e32d4712202dbcdcbf5dc482da298c2f44881c43884aaa" + "sha256:c3f865d4d54db7abc53758a01601cf343fe55b84c1de4e3fa910e420b438d5b9", + "sha256:e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182" ], - "markers": "python_version >= '3.7'", - "version": "==1.6.3" + "markers": "python_version >= '3.8'", + "version": "==1.7.0" }, "certifi": { "hashes": [ @@ -444,19 +444,20 @@ }, "flask": { "hashes": [ - "sha256:77fd4e1249d8c9923de34907236b747ced06e5467ecac1a7bb7115ae0e9670b0", - "sha256:8c2f9abd47a9e8df7f0c3f091ce9497d011dc3b31effcf4c85a6e2b50f4114ef" + "sha256:09c347a92aa7ff4a8e7f3206795f30d826654baf38b873d0744cd571ca609efc", + "sha256:f69fcd559dc907ed196ab9df0e48471709175e696d6e698dd4dbe940f96ce66b" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==2.3.2" + "version": "==2.3.3" }, "flask-apscheduler": { "hashes": [ - "sha256:681dae34dc6cc9403ce674795e53abd0bff540472129cfd3d3c93e0e1d502da8" + "sha256:b929846f026fb339b76360b0e4fc75da78b75c6d08625715bd0d37949bd607da" ], "index": "pypi", - "version": "==1.12.4" + "markers": "python_version >= '3.8'", + "version": "==1.13.1" }, "frozenlist": { "hashes": [ @@ -607,11 +608,11 @@ }, "importlib-metadata": { "hashes": [ - "sha256:3ebb78df84a805d7698245025b975d9d67053cd94c79245ba4b3eb694abe68bb", - "sha256:dbace7892d8c0c4ac1ad096662232f831d4e64f4c4545bd53016a3e9d4654743" + "sha256:7fc841f8b8332803464e5dc1c63a2e59121f46ca186c0e2e182e80bf8c1319f7", + "sha256:d97503976bb81f40a193d41ee6570868479c69d5068651eb039c40d850c59d67" ], "markers": "python_version < '3.10'", - "version": "==6.8.0" + "version": "==7.0.0" }, "itsdangerous": { "hashes": [ @@ -1233,7 +1234,6 @@ "sha256:507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc", "sha256:90a285dc0e42ad56b34e696398b8122ee4c681833fb35b8334a095d82c56da10" ], - "index": "pypi", "markers": "python_version >= '3.8'", "version": "==3.0.1" }, From 843edb1df321d91d0c2a81d623d8e557b0d038d6 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 2 Jan 2024 16:45:20 +0000 Subject: [PATCH 07/38] Bump tj-actions/changed-files from 23 to 41 in /.github/workflows Bumps [tj-actions/changed-files](https://github.com/tj-actions/changed-files) from 23 to 41. - [Release notes](https://github.com/tj-actions/changed-files/releases) - [Changelog](https://github.com/tj-actions/changed-files/blob/main/HISTORY.md) - [Commits](https://github.com/tj-actions/changed-files/compare/v23...v41) --- updated-dependencies: - dependency-name: tj-actions/changed-files dependency-type: direct:production ... Signed-off-by: dependabot[bot] --- .github/workflows/check_release_version.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/check_release_version.yml b/.github/workflows/check_release_version.yml index e5db52d7..3f441c5f 100644 --- a/.github/workflows/check_release_version.yml +++ b/.github/workflows/check_release_version.yml @@ -14,7 +14,7 @@ jobs: - name: Get specific changed files id: changed-files-specific - uses: tj-actions/changed-files@v23 + uses: tj-actions/changed-files@v41 with: files: | .release-version From 757fddc25dcb83602e8936cf7f08df6bf8fe66cb Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 9 Jan 2024 08:08:29 +0000 Subject: [PATCH 08/38] Bump more-itertools from 10.0.0 to 10.2.0 Bumps [more-itertools](https://github.com/more-itertools/more-itertools) from 10.0.0 to 10.2.0. - [Release notes](https://github.com/more-itertools/more-itertools/releases) - [Commits](https://github.com/more-itertools/more-itertools/compare/v10.0.0...v10.2.0) --- updated-dependencies: - dependency-name: more-itertools dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Pipfile | 2 +- Pipfile.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Pipfile b/Pipfile index 9bb04cbf..624751d1 100644 --- a/Pipfile +++ b/Pipfile @@ -21,7 +21,7 @@ colorlog = "~=6.7" flask = "~=2.3" flask-apscheduler = "~=1.12" gunicorn = "~=21.2" -more-itertools = "~=10.0" +more-itertools = "~=10.2" mysql-connector-python = "~=8.1" pandas = "~=2.0" pika = "~=1.3" diff --git a/Pipfile.lock b/Pipfile.lock index bbcabdec..400271b2 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "325332baeb13c762030635aef109abb92442519e470e17b7452f3027ed836973" + "sha256": "31e70220b76a2f407e3bc69f9b936eb0cef8a056ac62f5516ab15af5444bf336" }, "pipfile-spec": 6, "requires": { @@ -702,12 +702,12 @@ }, "more-itertools": { "hashes": [ - "sha256:928d514ffd22b5b0a8fce326d57f423a55d2ff783b093bab217eda71e732330f", - "sha256:cd65437d7c4b615ab81c0640c0480bc29a550ea032891977681efd28344d51e1" + "sha256:686b06abe565edfab151cb8fd385a05651e1fdf8f0a14191e4439283421f8684", + "sha256:8fccb480c43d3e99a00087634c06dd02b0d50fbf088b380de5a41a015ec239e1" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==10.0.0" + "version": "==10.2.0" }, "multidict": { "hashes": [ From e524d29ef96ed9f3db6a0cff30e60185fa3a2893 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 10 Jan 2024 10:21:12 +0000 Subject: [PATCH 09/38] Bump sqlalchemy from 2.0.19 to 2.0.25 Bumps [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) from 2.0.19 to 2.0.25. - [Release notes](https://github.com/sqlalchemy/sqlalchemy/releases) - [Changelog](https://github.com/sqlalchemy/sqlalchemy/blob/main/CHANGES.rst) - [Commits](https://github.com/sqlalchemy/sqlalchemy/commits) --- updated-dependencies: - dependency-name: sqlalchemy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 215 +++++++++++++++++++++++++++------------------------ 1 file changed, 112 insertions(+), 103 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 400271b2..6475bf14 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -527,66 +527,67 @@ }, "greenlet": { "hashes": [ - "sha256:0a02d259510b3630f330c86557331a3b0e0c79dac3d166e449a39363beaae174", - "sha256:0b6f9f8ca7093fd4433472fd99b5650f8a26dcd8ba410e14094c1e44cd3ceddd", - "sha256:100f78a29707ca1525ea47388cec8a049405147719f47ebf3895e7509c6446aa", - "sha256:1757936efea16e3f03db20efd0cd50a1c86b06734f9f7338a90c4ba85ec2ad5a", - "sha256:19075157a10055759066854a973b3d1325d964d498a805bb68a1f9af4aaef8ec", - "sha256:19bbdf1cce0346ef7341705d71e2ecf6f41a35c311137f29b8a2dc2341374565", - "sha256:20107edf7c2c3644c67c12205dc60b1bb11d26b2610b276f97d666110d1b511d", - "sha256:22f79120a24aeeae2b4471c711dcf4f8c736a2bb2fabad2a67ac9a55ea72523c", - 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"markers": "python_version >= '3.7'", - "version": "==7.2.7" + "index": "pypi", + "markers": "python_version >= '3.8'", + "version": "==7.4.0" }, "exceptiongroup": { "hashes": [ From a607124e6bc9aee5a3796baaf8d6f7393dbb353b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 10 Jan 2024 16:18:21 +0000 Subject: [PATCH 11/38] Bump black from 23.7.0 to 23.12.1 Bumps [black](https://github.com/psf/black) from 23.7.0 to 23.12.1. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/23.7.0...23.12.1) --- updated-dependencies: - dependency-name: black dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 70 ++++++++++++++++++++++++++-------------------------- 1 file changed, 35 insertions(+), 35 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index cba67d4b..825eb88f 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1362,32 +1362,32 @@ }, "black": { "hashes": [ - "sha256:01ede61aac8c154b55f35301fac3e730baf0c9cf8120f65a9cd61a81cfb4a0c3", - "sha256:022a582720b0d9480ed82576c920a8c1dde97cc38ff11d8d8859b3bd6ca9eedb", - "sha256:25cc308838fe71f7065df53aedd20327969d05671bac95b38fdf37ebe70ac087", - "sha256:27eb7a0c71604d5de083757fbdb245b1a4fae60e9596514c6ec497eb63f95320", - "sha256:327a8c2550ddc573b51e2c352adb88143464bb9d92c10416feb86b0f5aee5ff6", - "sha256:47e56d83aad53ca140da0af87678fb38e44fd6bc0af71eebab2d1f59b1acf1d3", - "sha256:501387a9edcb75d7ae8a4412bb8749900386eaef258f1aefab18adddea1936bc", - "sha256:552513d5cd5694590d7ef6f46e1767a4df9af168d449ff767b13b084c020e63f", - "sha256:5c4bc552ab52f6c1c506ccae05681fab58c3f72d59ae6e6639e8885e94fe2587", - 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[Commits](https://github.com/python/mypy/compare/v1.4.1...v1.8.0) --- updated-dependencies: - dependency-name: mypy dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 59 ++++++++++++++++++++++++++-------------------------- 1 file changed, 30 insertions(+), 29 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 825eb88f..8d6b2e6e 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1623,36 +1623,37 @@ }, "mypy": { "hashes": [ - "sha256:01fd2e9f85622d981fd9063bfaef1aed6e336eaacca00892cd2d82801ab7c042", - "sha256:0dde1d180cd84f0624c5dcaaa89c89775550a675aff96b5848de78fb11adabcd", - "sha256:141dedfdbfe8a04142881ff30ce6e6653c9685b354876b12e4fe6c78598b45e2", - "sha256:16f0db5b641ba159eff72cff08edc3875f2b62b2fa2bc24f68c1e7a4e8232d01", - "sha256:190b6bab0302cec4e9e6767d3eb66085aef2a1cc98fe04936d8a42ed2ba77bb7", - "sha256:2460a58faeea905aeb1b9b36f5065f2dc9a9c6e4c992a6499a2360c6c74ceca3", - "sha256:34a9239d5b3502c17f07fd7c0b2ae6b7dd7d7f6af35fbb5072c6208e76295816", - "sha256:43b592511672017f5b1a483527fd2684347fdffc041c9ef53428c8dc530f79a3", - "sha256:43d24f6437925ce50139a310a64b2ab048cb2d3694c84c71c3f2a1626d8101dc", - 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"index": "pypi", "markers": "python_version >= '3.7'", - "version": "==41.0.6" + "version": "==41.0.7" }, "dnspython": { "hashes": [ @@ -894,11 +899,12 @@ }, "paramiko": { "hashes": [ - "sha256:6a3777a961ac86dbef375c5f5b8d50014a1a96d0fd7f054a43bc880134b0ff77", - "sha256:b7bc5340a43de4287bbe22fe6de728aa2c22468b2a849615498dd944c2f275eb" + "sha256:43f0b51115a896f9c00f59618023484cb3a14b98bbceab43394a39c6739b7ee7", + "sha256:aac08f26a31dc4dffd92821527d1682d99d52f9ef6851968114a8728f3c274d3" ], + "index": "pypi", "markers": "python_version >= '3.6'", - "version": "==3.3.1" + "version": "==3.4.0" }, "pika": { "hashes": [ From 15fb93ee2d558dc6b630c5a6c3997aadff866cfa Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Wed, 10 Jan 2024 16:49:26 +0000 Subject: [PATCH 14/38] Bump pyodbc from 4.0.39 to 5.0.1 Bumps [pyodbc](https://github.com/mkleehammer/pyodbc) from 4.0.39 to 5.0.1. - [Release notes](https://github.com/mkleehammer/pyodbc/releases) - [Commits](https://github.com/mkleehammer/pyodbc/compare/4.0.39...5.0.1) --- updated-dependencies: - dependency-name: pyodbc dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- Pipfile | 2 +- Pipfile.lock | 72 +++++++++++++++++++++++++--------------------------- 2 files changed, 35 insertions(+), 39 deletions(-) diff --git a/Pipfile b/Pipfile index 624751d1..0add3604 100644 --- a/Pipfile +++ b/Pipfile @@ -27,7 +27,7 @@ pandas = "~=2.0" pika = "~=1.3" pymongo = "~=4.6" pymysql = "~=1.1" -pyodbc = "~=4.0" +pyodbc = "~=5.0" pysftp = "~=0.2" python-dotenv = "~=1.0" requests = "~=2.31" diff --git a/Pipfile.lock b/Pipfile.lock index 87e22a4d..13a9d8e6 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "31e70220b76a2f407e3bc69f9b936eb0cef8a056ac62f5516ab15af5444bf336" + "sha256": "f6ce15c95db70271b1cbd9dd4d1f771204e414b75942aec3f120a147590de5c3" }, "pipfile-spec": 6, "requires": { @@ -1058,45 +1058,41 @@ }, "pyodbc": { "hashes": [ - "sha256:05a0912e852ebddaffa8f235b0f3974475021dd8eb604eb46ea67af06efe1239", - "sha256:0f5901b57eaef0761f4cf02bca8e7c63f589fd0fd723a79f6ccf1ea1275372e5", - "sha256:1b3467157661615d5c30893efa1069b55c9ffa434097fc3ae3739e740d83d2ec", - 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"markers": "python_version >= '2.7' and python_version not in '3.0, 3.1, 3.2, 3.3, 3.4, 3.5'", - "version": "==4.0.39" + "markers": "python_version >= '3.8'", + "version": "==5.0.1" }, "pysftp": { "hashes": [ From 4d3d16c31105c8265ea4b79e3c533383160f668e Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 11 Jan 2024 07:56:04 +0000 Subject: [PATCH 15/38] Bump types-python-dateutil from 2.8.19.14 to 2.8.19.20240106 Bumps [types-python-dateutil](https://github.com/python/typeshed) from 2.8.19.14 to 2.8.19.20240106. - [Commits](https://github.com/python/typeshed/commits) --- updated-dependencies: - dependency-name: types-python-dateutil dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 13a9d8e6..305e9678 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1847,11 +1847,12 @@ }, "types-python-dateutil": { "hashes": [ - "sha256:1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b", - "sha256:f977b8de27787639986b4e28963263fd0e5158942b3ecef91b9335c130cb1ce9" + "sha256:1f8db221c3b98e6ca02ea83a58371b22c374f42ae5bbdf186db9c9a76581459f", + "sha256:efbbdc54590d0f16152fa103c9879c7d4a00e82078f6e2cf01769042165acaa2" ], "index": "pypi", - "version": "==2.8.19.14" + "markers": "python_version >= '3.8'", + "version": "==2.8.19.20240106" }, "types-pyyaml": { "hashes": [ From 74ed897326e9c7dcd16f3df66bc6b70002ae7e2d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 11 Jan 2024 13:04:30 +0000 Subject: [PATCH 16/38] Bump colorlog from 6.7.0 to 6.8.0 Bumps [colorlog](https://github.com/borntyping/python-colorlog) from 6.7.0 to 6.8.0. - [Release notes](https://github.com/borntyping/python-colorlog/releases) - [Commits](https://github.com/borntyping/python-colorlog/compare/v6.7.0...v6.8.0) --- updated-dependencies: - dependency-name: colorlog dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Pipfile | 2 +- Pipfile.lock | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Pipfile b/Pipfile index 0add3604..d97e1d65 100644 --- a/Pipfile +++ b/Pipfile @@ -17,7 +17,7 @@ types-python-dateutil = "*" responses = "*" [packages] -colorlog = "~=6.7" +colorlog = "~=6.8" flask = "~=2.3" flask-apscheduler = "~=1.12" gunicorn = "~=21.2" diff --git a/Pipfile.lock b/Pipfile.lock index 305e9678..71ea22d7 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "f6ce15c95db70271b1cbd9dd4d1f771204e414b75942aec3f120a147590de5c3" + "sha256": "1777b7c417bdf12c97566730805fe38b4447b06e75cbd366676a03ad1c7741ac" }, "pipfile-spec": 6, "requires": { @@ -366,12 +366,12 @@ }, "colorlog": { "hashes": [ - "sha256:0d33ca236784a1ba3ff9c532d4964126d8a2c44f1f0cb1d2b0728196f512f662", - "sha256:bd94bd21c1e13fac7bd3153f4bc3a7dc0eb0974b8bc2fdf1a989e474f6e582e5" + "sha256:4ed23b05a1154294ac99f511fabe8c1d6d4364ec1f7fc989c7fb515ccc29d375", + "sha256:fbb6fdf9d5685f2517f388fb29bb27d54e8654dd31f58bc2a3b217e967a95ca6" ], "index": "pypi", "markers": "python_version >= '3.6'", - "version": "==6.7.0" + "version": "==6.8.0" }, "cryptography": { "hashes": [ From a191ec8513a4da81f4f33ac9f9fa90405691c20c Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Jan 2024 07:23:23 +0000 Subject: [PATCH 17/38] Bump flake8-bugbear from 23.7.10 to 24.1.17 Bumps [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) from 23.7.10 to 24.1.17. - [Release notes](https://github.com/PyCQA/flake8-bugbear/releases) - [Commits](https://github.com/PyCQA/flake8-bugbear/compare/23.7.10...24.1.17) --- updated-dependencies: - dependency-name: flake8-bugbear dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 71ea22d7..08fdfd0c 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1356,11 +1356,11 @@ "develop": { "attrs": { "hashes": [ - "sha256:1f28b4522cdc2fb4256ac1a020c78acf9cba2c6b461ccd2c126f3aa8e8335d04", - "sha256:6279836d581513a26f1bf235f9acd333bc9115683f14f7e8fae46c98fc50e015" + "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30", + "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1" ], "markers": "python_version >= '3.7'", - "version": "==23.1.0" + "version": "==23.2.0" }, "black": { "hashes": [ @@ -1575,21 +1575,21 @@ }, "flake8": { "hashes": [ - "sha256:d5b3857f07c030bdb5bf41c7f53799571d75c4491748a3adcd47de929e34cd23", - "sha256:ffdfce58ea94c6580c77888a86506937f9a1a227dfcd15f245d694ae20a6b6e5" + "sha256:33f96621059e65eec474169085dc92bf26e7b2d47366b70be2f67ab80dc25132", + "sha256:a6dfbb75e03252917f2473ea9653f7cd799c3064e54d4c8140044c5c065f53c3" ], "index": "pypi", "markers": "python_full_version >= '3.8.1'", - "version": "==6.1.0" + "version": "==7.0.0" }, "flake8-bugbear": { "hashes": [ - "sha256:0ebdc7d8ec1ca8bd49347694562381f099f4de2f8ec6bda7a7dca65555d9e0d4", - "sha256:d99d005114020fbef47ed5e4aebafd22f167f9a0fbd0d8bf3c9e90612cb25c34" + "sha256:46cc840ddaed26507cd0ada530d1526418b717ee76c9b5dfdbd238b5eab34139", + "sha256:bcb388a4f3b516258749b1e690ee394c082eff742f44595e3754cf5c7781c2c7" ], "index": "pypi", "markers": "python_full_version >= '3.8.1'", - "version": "==23.7.10" + "version": "==24.1.17" }, "freezegun": { "hashes": [ @@ -1715,11 +1715,11 @@ }, "pyflakes": { "hashes": [ - "sha256:4132f6d49cb4dae6819e5379898f2b8cce3c5f23994194c24b77d5da2e36f774", - "sha256:a0aae034c444db0071aa077972ba4768d40c830d9539fd45bf4cd3f8f6992efc" + "sha256:1c61603ff154621fb2a9172037d84dca3500def8c8b630657d1701f026f8af3f", + "sha256:84b5be138a2dfbb40689ca07e2152deb896a65c3a3e24c251c5c62489568074a" ], "markers": "python_version >= '3.8'", - "version": "==3.1.0" + "version": "==3.2.0" }, "pytest": { "hashes": [ From 12727f7881ab5e2db7280e459b4d909f0206788d Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 18 Jan 2024 10:04:17 +0000 Subject: [PATCH 18/38] Bump jinja2 from 3.1.2 to 3.1.3 Bumps [jinja2](https://github.com/pallets/jinja) from 3.1.2 to 3.1.3. - [Release notes](https://github.com/pallets/jinja/releases) - [Changelog](https://github.com/pallets/jinja/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/jinja/compare/3.1.2...3.1.3) --- updated-dependencies: - dependency-name: jinja2 dependency-type: indirect ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 08fdfd0c..17ed62e7 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -629,11 +629,12 @@ }, "jinja2": { "hashes": [ - "sha256:31351a702a408a9e7595a8fc6150fc3f43bb6bf7e319770cbc0db9df9437e852", - "sha256:6088930bfe239f0e6710546ab9c19c9ef35e29792895fed6e6e31a023a182a61" + "sha256:7d6d50dd97d52cbc355597bd845fabfbac3f551e1f99619e39a35ce8c370b5fa", + "sha256:ac8bd6544d4bb2c9792bf3a159e80bba8fda7f07e81bc3aed565432d5925ba90" ], + "index": "pypi", "markers": "python_version >= '3.7'", - "version": "==3.1.2" + "version": "==3.1.3" }, "lab-share-lib": { "editable": false, From 874b9b19dbe053463b37a12f5b053408f8e37e35 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Tue, 30 Jan 2024 00:19:51 +0000 Subject: [PATCH 19/38] Bump aiohttp from 3.9.0 to 3.9.2 Bumps [aiohttp](https://github.com/aio-libs/aiohttp) from 3.9.0 to 3.9.2. - [Release notes](https://github.com/aio-libs/aiohttp/releases) - [Changelog](https://github.com/aio-libs/aiohttp/blob/master/CHANGES.rst) - [Commits](https://github.com/aio-libs/aiohttp/compare/v3.9.0...v3.9.2) --- updated-dependencies: - dependency-name: aiohttp dependency-type: indirect ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 300 +++++++++++++++++++++++++++------------------------ 1 file changed, 158 insertions(+), 142 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 17ed62e7..cb4deb95 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -18,86 +18,86 @@ "default": { "aiohttp": { "hashes": [ - "sha256:05857848da443c8c12110d99285d499b4e84d59918a21132e45c3f0804876994", - "sha256:05a183f1978802588711aed0dea31e697d760ce9055292db9dc1604daa9a8ded", - "sha256:09f23292d29135025e19e8ff4f0a68df078fe4ee013bca0105b2e803989de92d", - "sha256:11ca808f9a6b63485059f5f6e164ef7ec826483c1212a44f268b3653c91237d8", - "sha256:1736d87dad8ef46a8ec9cddd349fa9f7bd3a064c47dd6469c0d6763d3d49a4fc", - "sha256:1df43596b826022b14998f0460926ce261544fedefe0d2f653e1b20f49e96454", - "sha256:23170247ef89ffa842a02bbfdc425028574d9e010611659abeb24d890bc53bb8", - "sha256:2779f5e7c70f7b421915fd47db332c81de365678180a9f3ab404088f87ba5ff9", - 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[Commits](https://github.com/getsentry/responses/compare/0.23.3...0.24.1) --- updated-dependencies: - dependency-name: responses dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 214 +++++++++++++++++++++++++-------------------------- 1 file changed, 107 insertions(+), 107 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 34d4aedc..64711e54 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "e8a87d180806d86ec26fc4d0e29654945b5a8ad9a25dda3d3f5910534fbac897" + "sha256": "82fd5a98d2db0bb58a9c41563c755e2021812da72d90ff38911647844df0ff55" }, "pipfile-spec": 6, "requires": { @@ -1410,107 +1410,107 @@ }, "certifi": { "hashes": [ - "sha256:539cc1d13202e33ca466e88b2807e29f4c13049d6d87031a3c110744495cb082", - "sha256:92d6037539857d8206b8f6ae472e8b77db8058fec5937a1ef3f54304089edbb9" + "sha256:0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f", + "sha256:dc383c07b76109f368f6106eee2b593b04a011ea4d55f652c6ca24a754d1cdd1" ], "markers": "python_version >= '3.6'", - "version": "==2023.7.22" + "version": "==2024.2.2" }, "charset-normalizer": { "hashes": [ - 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"hashes": [ - "sha256:814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4", - "sha256:90b77e79eaa3eba6de819a0c442c0b4ceefc341a7a2ab77d7562bf49f425c5c2" + "sha256:9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca", + "sha256:c05567e9c24a6b9faaa835c4821bad0590fbb9d5779e7caa6e1cc4978e7eb24f" ], "markers": "python_version >= '3.5'", - "version": "==3.4" + "version": "==3.6" }, "iniconfig": { "hashes": [ @@ -1803,6 +1803,7 @@ "sha256:8d4e9c88387b0f5c7d5f281e55304de64cf7f9c0021a3525bd3b1c542da3b0e4", "sha256:9046c58c4395dff28dd494285c82ba00b546adfc7ef001486fbf0324bc174fba", "sha256:9eb6caa9a297fc2c2fb8862bc5370d0303ddba53ba97e71f08023b6cd73d16a8", + "sha256:a08c6f0fe150303c1c6b71ebcd7213c2858041a7e01975da3a99aed1e7a378ef", "sha256:a0cd17c15d3bb3fa06978b4e8958dcdc6e0174ccea823003a106c7d4d7899ac5", "sha256:afd7e57eddb1a54f0f1a974bc4391af8bcce0b444685d936840f125cf046d5bd", "sha256:b1275ad35a5d18c62a7220633c913e1b42d44b46ee12554e5fd39c70a243d6a3", @@ -1833,18 +1834,17 @@ "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f", "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1" ], - "index": "pypi", "markers": "python_version >= '3.7'", "version": "==2.31.0" }, "responses": { "hashes": [ - "sha256:205029e1cb334c21cb4ec64fc7599be48b859a0fd381a42443cdd600bfe8b16a", - "sha256:e6fbcf5d82172fecc0aa1860fd91e58cbfd96cee5e96da5b63fa6eb3caa10dd3" + "sha256:a2b43f4c08bfb9c9bd242568328c65a34b318741d3fab884ac843c5ceeb543f9", + "sha256:b127c6ca3f8df0eb9cc82fd93109a3007a86acb24871834c47b77765152ecf8c" ], "index": "pypi", - "markers": "python_version >= '3.7'", - "version": "==0.23.3" + "markers": "python_version >= '3.8'", + "version": "==0.24.1" }, "six": { "hashes": [ @@ -1888,11 +1888,11 @@ }, "urllib3": { "hashes": [ - "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84", - "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e" + "sha256:051d961ad0c62a94e50ecf1af379c3aba230c66c710493493560c0c223c49f20", + "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224" ], - "markers": "python_version >= '3.7'", - "version": "==2.0.7" + "markers": "python_version >= '3.8'", + "version": "==2.2.0" } } } From 419ad11a03880e8755b3fe497ac959400ac54106 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 8 Feb 2024 07:57:26 +0000 Subject: [PATCH 21/38] Bump flake8-bugbear from 24.1.17 to 24.2.6 Bumps [flake8-bugbear](https://github.com/PyCQA/flake8-bugbear) from 24.1.17 to 24.2.6. - [Release notes](https://github.com/PyCQA/flake8-bugbear/releases) - [Commits](https://github.com/PyCQA/flake8-bugbear/compare/24.1.17...24.2.6) --- updated-dependencies: - dependency-name: flake8-bugbear dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 64711e54..bd6625ff 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1601,12 +1601,12 @@ }, "flake8-bugbear": { "hashes": [ - "sha256:46cc840ddaed26507cd0ada530d1526418b717ee76c9b5dfdbd238b5eab34139", - "sha256:bcb388a4f3b516258749b1e690ee394c082eff742f44595e3754cf5c7781c2c7" + "sha256:663ef5de80cd32aacd39d362212983bc4636435a6f83700b4ed35acbd0b7d1b8", + "sha256:f9cb5f2a9e792dd80ff68e89a14c12eed8620af8b41a49d823b7a33064ac9658" ], "index": "pypi", "markers": "python_full_version >= '3.8.1'", - "version": "==24.1.17" + "version": "==24.2.6" }, "freezegun": { "hashes": [ From e3fc1048f511e207ddb733e64051bb55dd56ae11 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:01:29 +0000 Subject: [PATCH 22/38] Bump python-dotenv from 1.0.0 to 1.0.1 Bumps [python-dotenv](https://github.com/theskumar/python-dotenv) from 1.0.0 to 1.0.1. - [Release notes](https://github.com/theskumar/python-dotenv/releases) - [Changelog](https://github.com/theskumar/python-dotenv/blob/main/CHANGELOG.md) - [Commits](https://github.com/theskumar/python-dotenv/compare/v1.0.0...v1.0.1) --- updated-dependencies: - dependency-name: python-dotenv dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index bd6625ff..a8966f0e 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1129,12 +1129,12 @@ }, "python-dotenv": { "hashes": [ - "sha256:a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba", - "sha256:f5971a9226b701070a4bf2c38c89e5a3f0d64de8debda981d1db98583009122a" + "sha256:e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca", + "sha256:f7b63ef50f1b690dddf550d03497b66d609393b40b564ed0d674909a68ebf16a" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==1.0.0" + "version": "==1.0.1" }, "pytz": { "hashes": [ From 585205ae8e1641349834bb259861c739f307a4af Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:42:18 +0000 Subject: [PATCH 23/38] Bump coverage from 7.4.0 to 7.4.1 Bumps [coverage](https://github.com/nedbat/coveragepy) from 7.4.0 to 7.4.1. - [Release notes](https://github.com/nedbat/coveragepy/releases) - [Changelog](https://github.com/nedbat/coveragepy/blob/master/CHANGES.rst) - [Commits](https://github.com/nedbat/coveragepy/compare/7.4.0...7.4.1) --- updated-dependencies: - dependency-name: coverage dependency-type: direct:development update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 106 +++++++++++++++++++++++++-------------------------- 1 file changed, 53 insertions(+), 53 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index a8966f0e..694e6ba6 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1525,62 +1525,62 @@ "toml" ], "hashes": [ - "sha256:04387a4a6ecb330c1878907ce0dc04078ea72a869263e53c72a1ba5bbdf380ca", - "sha256:0676cd0ba581e514b7f726495ea75aba3eb20899d824636c6f59b0ed2f88c471", - "sha256:0e8d06778e8fbffccfe96331a3946237f87b1e1d359d7fbe8b06b96c95a5407a", - "sha256:0eb3c2f32dabe3a4aaf6441dde94f35687224dfd7eb2a7f47f3fd9428e421058", - "sha256:109f5985182b6b81fe33323ab4707011875198c41964f014579cf82cebf2bb85", - "sha256:13eaf476ec3e883fe3e5fe3707caeb88268a06284484a3daf8250259ef1ba143", - "sha256:164fdcc3246c69a6526a59b744b62e303039a81e42cfbbdc171c91a8cc2f9446", - "sha256:26776ff6c711d9d835557ee453082025d871e30b3fd6c27fcef14733f67f0590", - "sha256:26f66da8695719ccf90e794ed567a1549bb2644a706b41e9f6eae6816b398c4a", - 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Signed-off-by: dependabot[bot] --- Pipfile | 2 +- Pipfile.lock | 66 ++++++++++++++++++++++++++-------------------------- 2 files changed, 34 insertions(+), 34 deletions(-) diff --git a/Pipfile b/Pipfile index 2a4dbab9..a9d5e012 100644 --- a/Pipfile +++ b/Pipfile @@ -27,7 +27,7 @@ pandas = "~=2.0" pika = "~=1.3" pymongo = "~=4.6" pymysql = "~=1.1" -pyodbc = "~=5.0" +pyodbc = "~=5.1" pysftp = "~=0.2" python-dotenv = "~=1.0" requests = "~=2.31" diff --git a/Pipfile.lock b/Pipfile.lock index 694e6ba6..be0c9aa1 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "82fd5a98d2db0bb58a9c41563c755e2021812da72d90ff38911647844df0ff55" + "sha256": "07f47e0dbc332e8ff1e30127495573905bb74099255bd477047932897a686822" }, "pipfile-spec": 6, "requires": { @@ -1076,41 +1076,41 @@ }, "pyodbc": { "hashes": [ - "sha256:03d7d0b04d5a9156099ce8d03e92f3956783746fa9234eb6f5b5cfc12b645011", - "sha256:067015537a20cf893ae675384f99291eade66a7d59bc54f9dedee55ad4290b4c", - "sha256:17d25a51823a5c8631fd117c1d352425404cd2116fd75b55aac4cb79da2e8c85", - 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"version": "==5.0.1" + "version": "==5.1.0" }, "pysftp": { "hashes": [ From c41ac53f0cb8363c36abe4bbbc0c2202045e1f72 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 12 Feb 2024 19:24:04 +0000 Subject: [PATCH 25/38] Bump colorlog from 6.8.0 to 6.8.2 Bumps [colorlog](https://github.com/borntyping/python-colorlog) from 6.8.0 to 6.8.2. - [Release notes](https://github.com/borntyping/python-colorlog/releases) - [Commits](https://github.com/borntyping/python-colorlog/compare/v6.8.0...v6.8.2) --- updated-dependencies: - dependency-name: colorlog dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index be0c9aa1..80c7c0db 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -366,12 +366,12 @@ }, "colorlog": { "hashes": [ - "sha256:4ed23b05a1154294ac99f511fabe8c1d6d4364ec1f7fc989c7fb515ccc29d375", - "sha256:fbb6fdf9d5685f2517f388fb29bb27d54e8654dd31f58bc2a3b217e967a95ca6" + "sha256:3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44", + "sha256:4dcbb62368e2800cb3c5abd348da7e53f6c362dda502ec27c560b2e58a66bd33" ], "index": "pypi", "markers": "python_version >= '3.6'", - "version": "==6.8.0" + "version": "==6.8.2" }, "cryptography": { "hashes": [ From a28b12018321d71853633dac70597e93f575c6ad Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 19 Feb 2024 15:37:25 +0000 Subject: [PATCH 26/38] Bump pytest from 7.4.3 to 8.0.1 Bumps [pytest](https://github.com/pytest-dev/pytest) from 7.4.3 to 8.0.1. - [Release notes](https://github.com/pytest-dev/pytest/releases) - [Changelog](https://github.com/pytest-dev/pytest/blob/main/CHANGELOG.rst) - [Commits](https://github.com/pytest-dev/pytest/compare/7.4.3...8.0.1) --- updated-dependencies: - dependency-name: pytest dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 80c7c0db..c62e5557 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1716,11 +1716,11 @@ }, "pluggy": { "hashes": [ - "sha256:cf61ae8f126ac6f7c451172cf30e3e43d3ca77615509771b3a984a0730651e12", - "sha256:d89c696a773f8bd377d18e5ecda92b7a3793cbe66c87060a6fb58c7b6e1061f7" + "sha256:7db9f7b503d67d1c5b95f59773ebb58a8c1c288129a88665838012cfb07b8981", + "sha256:8c85c2876142a764e5b7548e7d9a0e0ddb46f5185161049a79b7e974454223be" ], "markers": "python_version >= '3.8'", - "version": "==1.3.0" + "version": "==1.4.0" }, "pycodestyle": { "hashes": [ @@ -1740,12 +1740,12 @@ }, "pytest": { "hashes": [ - "sha256:0d009c083ea859a71b76adf7c1d502e4bc170b80a8ef002da5806527b9591fac", - "sha256:d989d136982de4e3b29dabcc838ad581c64e8ed52c11fbe86ddebd9da0818cd5" + "sha256:267f6563751877d772019b13aacbe4e860d73fe8f651f28112e9ac37de7513ae", + "sha256:3e4f16fe1c0a9dc9d9389161c127c3edc5d810c38d6793042fb81d9f48a59fca" ], "index": "pypi", - "markers": "python_version >= '3.7'", - "version": "==7.4.3" + "markers": "python_version >= '3.8'", + "version": "==8.0.1" }, "pytest-cov": { "hashes": [ From 4d3f34b2219e6e16ecd285ee7dfab7d80d4dae60 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 19 Feb 2024 15:45:11 +0000 Subject: [PATCH 27/38] Bump flask from 2.3.2 to 3.0.2 Bumps [flask](https://github.com/pallets/flask) from 2.3.2 to 3.0.2. - [Release notes](https://github.com/pallets/flask/releases) - [Changelog](https://github.com/pallets/flask/blob/main/CHANGES.rst) - [Commits](https://github.com/pallets/flask/compare/2.3.2...3.0.2) --- updated-dependencies: - dependency-name: flask dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- Pipfile | 2 +- Pipfile.lock | 137 +++++++++++++++++++++++++-------------------------- 2 files changed, 69 insertions(+), 70 deletions(-) diff --git a/Pipfile b/Pipfile index a9d5e012..680b6116 100644 --- a/Pipfile +++ b/Pipfile @@ -18,7 +18,7 @@ responses = "*" [packages] colorlog = "~=6.8" -flask = "~=2.3" +flask = "~=3.0" flask-apscheduler = "~=1.13" gunicorn = "~=21.2" more-itertools = "~=10.2" diff --git a/Pipfile.lock b/Pipfile.lock index c62e5557..d5fba38c 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "07f47e0dbc332e8ff1e30127495573905bb74099255bd477047932897a686822" + "sha256": "f130ca89c2175aa102884ff4a28186f21a3de6b94f64fde85ee5e647fec0b99a" }, "pipfile-spec": 6, "requires": { @@ -449,12 +449,12 @@ }, "flask": { "hashes": [ - "sha256:09c347a92aa7ff4a8e7f3206795f30d826654baf38b873d0744cd571ca609efc", - "sha256:f69fcd559dc907ed196ab9df0e48471709175e696d6e698dd4dbe940f96ce66b" + 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updated-dependencies: - dependency-name: cryptography dependency-type: indirect ... 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"version": "==41.0.7" + "version": "==42.0.2" }, "dnspython": { "hashes": [ From 5895b28e3456ed37654d15645d12ede710656fff Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 19 Feb 2024 15:56:55 +0000 Subject: [PATCH 29/38] Bump black from 23.12.1 to 24.2.0 Bumps [black](https://github.com/psf/black) from 23.12.1 to 24.2.0. - [Release notes](https://github.com/psf/black/releases) - [Changelog](https://github.com/psf/black/blob/main/CHANGES.md) - [Commits](https://github.com/psf/black/compare/23.12.1...24.2.0) --- updated-dependencies: - dependency-name: black dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 60 ++++++++++++++++++++++++++-------------------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 9a587e2c..71a59d80 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1390,32 +1390,32 @@ }, "black": { "hashes": [ - "sha256:0808494f2b2df923ffc5723ed3c7b096bd76341f6213989759287611e9837d50", - "sha256:1fa88a0f74e50e4487477bc0bb900c6781dbddfdfa32691e780bf854c3b4a47f", - "sha256:25e57fd232a6d6ff3f4478a6fd0580838e47c93c83eaf1ccc92d4faf27112c4e", - "sha256:2d9e13db441c509a3763a7a3d9a49ccc1b4e974a47be4e08ade2a228876500ec", - "sha256:3e1b38b3135fd4c025c28c55ddfc236b05af657828a8a6abe5deec419a0b7055", - "sha256:3fa4be75ef2a6b96ea8d92b1587dd8cb3a35c7e3d51f0738ced0781c3aa3a5a3", - "sha256:4ce3ef14ebe8d9509188014d96af1c456a910d5b5cbf434a09fef7e024b3d0d5", - "sha256:4f0031eaa7b921db76decd73636ef3a12c942ed367d8c3841a0739412b260a54", - "sha256:602cfb1196dc692424c70b6507593a2b29aac0547c1be9a1d1365f0d964c353b", - 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"version": "==23.12.1" + "version": "==24.2.0" }, "certifi": { "hashes": [ @@ -1717,11 +1717,11 @@ }, "platformdirs": { "hashes": [ - "sha256:11c8f37bcca40db96d8144522d925583bdb7a31f7b0e37e3ed4318400a8e2380", - "sha256:906d548203468492d432bcb294d4bc2fff751bf84971fbb2c10918cc206ee420" + "sha256:0614df2a2f37e1a662acbd8e2b25b92ccf8632929bc6d43467e17fe89c75e068", + "sha256:ef0cc731df711022c174543cb70a9b5bd22e5a9337c8624ef2c2ceb8ddad8768" ], "markers": "python_version >= '3.8'", - "version": "==4.1.0" + "version": "==4.2.0" }, "pluggy": { "hashes": [ @@ -1889,11 +1889,11 @@ }, "typing-extensions": { "hashes": [ - "sha256:23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783", - "sha256:af72aea155e91adfc61c3ae9e0e342dbc0cba726d6cba4b6c72c1f34e47291cd" + "sha256:ada05f19b82a2ea6eeac4e7412a2328e70b5237f05f3ffef49cae6db558a914e", + "sha256:aee036f82b858bd4b43160c5dc2deb1780129223957eab47c3cac26b93b50e65" ], - "markers": "python_version >= '3.8'", - "version": "==4.9.0" + "markers": "python_version < '3.11'", + "version": "==4.10.0rc1" }, "urllib3": { "hashes": [ From 01b89ccdc5edb573c76969ed17011e31480de0f7 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Mon, 19 Feb 2024 16:00:58 +0000 Subject: [PATCH 30/38] Updated black refactoring files --- crawler/constants.py | 12 ++++++------ tests/file_processing/test_file_processing_1.py | 1 + 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/crawler/constants.py b/crawler/constants.py index a879b5f5..ad5e6cfa 100644 --- a/crawler/constants.py +++ b/crawler/constants.py @@ -130,12 +130,12 @@ TEST_DATA_ERROR_WRONG_STATE: Final[str] = "Run doesn't have status" TEST_DATA_ERROR_INVALID_PLATE_SPECS: Final[str] = "There is a problem with the plate specs for the run." TEST_DATA_ERROR_NUMBER_OF_PLATES: Final[str] = "Number of plates to generate must be between 1 and {0}." -TEST_DATA_ERROR_NUMBER_OF_POS_SAMPLES: Final[ - str -] = "One or more plates expected fewer than 0 or more than 96 positive samples." -TEST_DATA_ERROR_PLATE_CREATION_FAILED: Final[ - str -] = "One or more plates failed to generate data correctly. Please try again." +TEST_DATA_ERROR_NUMBER_OF_POS_SAMPLES: Final[str] = ( + "One or more plates expected fewer than 0 or more than 96 positive samples." +) +TEST_DATA_ERROR_PLATE_CREATION_FAILED: Final[str] = ( + "One or more plates failed to generate data correctly. Please try again." +) ### diff --git a/tests/file_processing/test_file_processing_1.py b/tests/file_processing/test_file_processing_1.py index 7be929cf..71b787c3 100644 --- a/tests/file_processing/test_file_processing_1.py +++ b/tests/file_processing/test_file_processing_1.py @@ -1,6 +1,7 @@ """ Split test_file_processing.py into numerous files until a larger refactor can test classes more succinctly. """ + from datetime import datetime, timezone from crawler.constants import FIELD_DATE_TESTED From 70084986e9002f3b62d84ee9f20e312a5e83d540 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 19 Feb 2024 16:05:14 +0000 Subject: [PATCH 31/38] Bump responses from 0.24.1 to 0.25.0 Bumps [responses](https://github.com/getsentry/responses) from 0.24.1 to 0.25.0. - [Release notes](https://github.com/getsentry/responses/releases) - [Changelog](https://github.com/getsentry/responses/blob/master/CHANGES) - [Commits](https://github.com/getsentry/responses/compare/0.24.1...0.25.0) --- updated-dependencies: - dependency-name: responses dependency-type: direct:development update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 71a59d80..2a38217c 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1848,12 +1848,12 @@ }, "responses": { "hashes": [ - "sha256:a2b43f4c08bfb9c9bd242568328c65a34b318741d3fab884ac843c5ceeb543f9", - "sha256:b127c6ca3f8df0eb9cc82fd93109a3007a86acb24871834c47b77765152ecf8c" + "sha256:01ae6a02b4f34e39bffceb0fc6786b67a25eae919c6368d05eabc8d9576c2a66", + "sha256:2f0b9c2b6437db4b528619a77e5d565e4ec2a9532162ac1a131a83529db7be1a" ], "index": "pypi", "markers": "python_version >= '3.8'", - "version": "==0.24.1" + "version": "==0.25.0" }, "six": { "hashes": [ @@ -1897,11 +1897,11 @@ }, "urllib3": { "hashes": [ - "sha256:051d961ad0c62a94e50ecf1af379c3aba230c66c710493493560c0c223c49f20", - "sha256:ce3711610ddce217e6d113a2732fafad960a03fd0318c91faa79481e35c11224" + "sha256:450b20ec296a467077128bff42b73080516e71b56ff59a60a02bef2232c4fa9d", + "sha256:d0570876c61ab9e520d776c38acbbb5b05a776d3f9ff98a5c8fd5162a444cf19" ], "markers": "python_version >= '3.8'", - "version": "==2.2.0" + "version": "==2.2.1" } } } From c71109a9f5e03947eafd55ec4b9477f7d0d77f40 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 19 Feb 2024 16:13:20 +0000 Subject: [PATCH 32/38] Bump sqlalchemy from 2.0.25 to 2.0.27 Bumps [sqlalchemy](https://github.com/sqlalchemy/sqlalchemy) from 2.0.25 to 2.0.27. - [Release notes](https://github.com/sqlalchemy/sqlalchemy/releases) - [Changelog](https://github.com/sqlalchemy/sqlalchemy/blob/main/CHANGES.rst) - [Commits](https://github.com/sqlalchemy/sqlalchemy/commits) --- updated-dependencies: - dependency-name: sqlalchemy dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] --- Pipfile.lock | 106 +++++++++++++++++++++++++-------------------------- 1 file changed, 53 insertions(+), 53 deletions(-) diff --git a/Pipfile.lock b/Pipfile.lock index 2a38217c..aeb12e24 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1180,67 +1180,67 @@ }, "sqlalchemy": { "hashes": [ - "sha256:0d3cab3076af2e4aa5693f89622bef7fa770c6fec967143e4da7508b3dceb9b9", - "sha256:0dacf67aee53b16f365c589ce72e766efaabd2b145f9de7c917777b575e3659d", - "sha256:10331f129982a19df4284ceac6fe87353ca3ca6b4ca77ff7d697209ae0a5915e", - "sha256:14a6f68e8fc96e5e8f5647ef6cda6250c780612a573d99e4d881581432ef1669", - "sha256:1b1180cda6df7af84fe72e4530f192231b1f29a7496951db4ff38dac1687202d", - "sha256:29049e2c299b5ace92cbed0c1610a7a236f3baf4c6b66eb9547c01179f638ec5", - "sha256:342d365988ba88ada8af320d43df4e0b13a694dbd75951f537b2d5e4cb5cd002", - "sha256:420362338681eec03f53467804541a854617faed7272fe71a1bfdb07336a381e", - "sha256:4344d059265cc8b1b1be351bfb88749294b87a8b2bbe21dfbe066c4199541ebd", - 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Signed-off-by: dependabot[bot] --- Pipfile | 2 +- Pipfile.lock | 51 ++++++++++++++++++++++++++++----------------------- 2 files changed, 29 insertions(+), 24 deletions(-) diff --git a/Pipfile b/Pipfile index 680b6116..66b0686b 100644 --- a/Pipfile +++ b/Pipfile @@ -22,7 +22,7 @@ flask = "~=3.0" flask-apscheduler = "~=1.13" gunicorn = "~=21.2" more-itertools = "~=10.2" -mysql-connector-python = "~=8.1" +mysql-connector-python = "~=8.3" pandas = "~=2.0" pika = "~=1.3" pymongo = "~=4.6" diff --git a/Pipfile.lock b/Pipfile.lock index aeb12e24..aa9b33b3 100644 --- a/Pipfile.lock +++ b/Pipfile.lock @@ -1,7 +1,7 @@ { "_meta": { "hash": { - "sha256": "f130ca89c2175aa102884ff4a28186f21a3de6b94f64fde85ee5e647fec0b99a" + "sha256": "9a413f0b17fb546083fac8ae38461e20640761502cc2609db1597d43a8ca2198" }, "pipfile-spec": 6, "requires": { @@ -824,31 +824,36 @@ }, "mysql-connector-python": { "hashes": [ - "sha256:1d292d8ee08a3e0103f3e9aba81f292c12c244c1d5345168375bf6842b2b3e9b", - 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b/tests/db/test_mysql.py index ee625740..8f30fc72 100644 --- a/tests/db/test_mysql.py +++ b/tests/db/test_mysql.py @@ -38,6 +38,25 @@ class MockMySQLConnection(MySQLConnectionAbstract): is_connected = MagicMock() ping = MagicMock() rollback = MagicMock() + cmd_change_user = MagicMock() + cmd_debug = MagicMock() + cmd_init_db = MagicMock() + cmd_ping = MagicMock() + cmd_process_kill = MagicMock() + cmd_query = MagicMock() + cmd_query_iter = MagicMock() + cmd_quit = MagicMock() + cmd_refresh = MagicMock() + cmd_reset_connection = MagicMock() + cmd_shutdown = MagicMock() + cmd_statistics = MagicMock() + cmd_stmt_close = MagicMock() + cmd_stmt_execute = MagicMock() + cmd_stmt_prepare = MagicMock() + cmd_stmt_reset = MagicMock() + cmd_stmt_send_long_data = MagicMock() + connection_id = MagicMock() + get_row = MagicMock() def test_create_mysql_connection_none(config): From 4a7d9414e417732d8d7e7b792bf30aac9781a649 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Tue, 20 Feb 2024 18:14:03 +0000 Subject: [PATCH 35/38] Fixing issues with black and mypy --- crawler/db/mysql.py | 7 +- crawler/helpers/general_helpers.py | 5 +- ..._populate_source_plate_and_sample_uuids.py | 3 +- tests/file_processing/test_file_processing.py | 123 +++++++++--------- 4 files changed, 71 insertions(+), 67 deletions(-) diff --git a/crawler/db/mysql.py b/crawler/db/mysql.py index 8432719e..81c73980 100644 --- a/crawler/db/mysql.py +++ b/crawler/db/mysql.py @@ -1,10 +1,11 @@ import logging from datetime import datetime from itertools import islice -from typing import Any, Dict, Generator, Iterable, List, cast +from typing import Any, Dict, Generator, Iterable, List, cast, Sequence import mysql.connector as mysql import sqlalchemy +from mysql.connector.types import MySQLConvertibleType from mysql.connector.connection_cext import MySQLConnectionAbstract from mysql.connector.cursor_cext import MySQLCursorAbstract from sqlalchemy.engine.base import Engine @@ -65,7 +66,7 @@ def create_mysql_connection(config: Config, readonly: bool = True) -> MySQLConne def run_mysql_executemany_query( - mysql_conn: MySQLConnectionAbstract, sql_query: str, values: List[Dict[str, str]] + mysql_conn: MySQLConnectionAbstract, sql_query: str, values: Sequence[Dict[str, MySQLConvertibleType]] ) -> None: """Writes the sample testing information into the MLWH. @@ -223,7 +224,7 @@ def partition(iterable: Iterable, partition_size: int) -> Generator[List[Any], N yield part -def reset_is_current_flags(cursor: MySQLCursorAbstract, rna_ids: List[str], chunk_size: int = 1000) -> None: +def reset_is_current_flags(cursor: MySQLCursorAbstract, rna_ids: List[MySQLConvertibleType], chunk_size: int = 1000) -> None: """Receives a cursor with an active connection and a list of rna_ids and runs an update resetting any is_current flags to false for all the specified rna ids in groups of chunk_size. diff --git a/crawler/helpers/general_helpers.py b/crawler/helpers/general_helpers.py index 3491b523..ddd953d9 100644 --- a/crawler/helpers/general_helpers.py +++ b/crawler/helpers/general_helpers.py @@ -5,7 +5,8 @@ from datetime import datetime from decimal import Decimal from http import HTTPStatus -from typing import Any, Dict, Iterable, List, Optional +from typing import Any, Dict, Iterable, List, Optional, Sequence +from mysql.connector.types import MySQLConvertibleType import pysftp import requests @@ -268,7 +269,7 @@ def map_mongo_sample_to_mysql(doc: SampleDoc, copy_date: bool = False) -> Dict[s return value -def set_is_current_on_mysql_samples(samples: Iterable[Dict[str, str]]) -> List[Dict[str, str]]: +def set_is_current_on_mysql_samples(samples: Iterable[Dict[str, str]]) -> Sequence[Dict[str, MySQLConvertibleType]]: """Creates a copy of the samples passed in, adding is_current values to each sample. is_current will be True for all samples unless there is a repeated RNA ID, in which case only the last one is set to True. diff --git a/migrations/back_populate_source_plate_and_sample_uuids.py b/migrations/back_populate_source_plate_and_sample_uuids.py index f463ce72..bbd9185e 100644 --- a/migrations/back_populate_source_plate_and_sample_uuids.py +++ b/migrations/back_populate_source_plate_and_sample_uuids.py @@ -7,6 +7,7 @@ from typing import Dict, List, Optional, cast from uuid import uuid4 +from mysql.connector.types import MySQLConvertibleType, RowType from mysql.connector.connection_cext import MySQLConnectionAbstract from pymongo.collection import Collection from pymongo.database import Database @@ -366,7 +367,7 @@ def prepare_mlwh_row(sample_doc): existing_samples = mysql_generator_from_connection(mysql_conn, query) log_mlwh_sample_fields("Before update", existing_samples) - row_data = [cast(Dict[str, str], row) for row in update_rows] + row_data = [cast(Dict[str, MySQLConvertibleType], row) for row in update_rows] run_mysql_executemany_query(mysql_conn, SQL_MLWH_UPDATE_SAMPLE_UUID_PLATE_UUID, row_data) # Log the new fields on the MLWH samples diff --git a/tests/file_processing/test_file_processing.py b/tests/file_processing/test_file_processing.py index 1e1d6cfe..78b87bf3 100644 --- a/tests/file_processing/test_file_processing.py +++ b/tests/file_processing/test_file_processing.py @@ -4,13 +4,14 @@ from datetime import datetime from decimal import Decimal from io import StringIO -from typing import List +from typing import List, cast, Dict from unittest.mock import MagicMock, patch import pytest from bson.decimal128 import Decimal128 from bson.objectid import ObjectId from mysql.connector.connection_cext import MySQLConnectionAbstract +from mysql.connector.types import RowItemType from crawler.constants import ( CENTRE_KEY_BACKUPS_FOLDER, @@ -1548,65 +1549,65 @@ def test_insert_samples_from_docs_into_mlwh( rows = cursor.fetchall() cursor.close() - assert rows[0][MLWH_MONGODB_ID] == "5f562d9931d9959b92544728" - assert rows[0][MLWH_ROOT_SAMPLE_ID] == "ABC00000004" - assert rows[0][MLWH_COG_UK_ID] == "TEST-123ABC" - assert rows[0][MLWH_RNA_ID] == "TC-rna-00000029_H11" - assert rows[0][MLWH_PLATE_BARCODE] == "TC-rna-00000029" - assert rows[0][MLWH_COORDINATE] == "H11" - assert rows[0][MLWH_RESULT] == "Negative" - assert rows[0][MLWH_DATE_TESTED] == date_tested_1 - assert rows[0][MLWH_SOURCE] == "Test Centre" - assert rows[0][MLWH_LAB_ID] == "TC" - assert rows[0][MLWH_CH1_TARGET] is None - assert rows[0][MLWH_CH1_RESULT] is None - assert rows[0][MLWH_CH1_CQ] is None - assert rows[0][MLWH_CH2_TARGET] is None - assert rows[0][MLWH_CH2_RESULT] is None - assert rows[0][MLWH_CH2_CQ] is None - assert rows[0][MLWH_CH3_TARGET] is None - assert rows[0][MLWH_CH3_RESULT] is None - assert rows[0][MLWH_CH3_CQ] is None - assert rows[0][MLWH_CH4_TARGET] is None - assert rows[0][MLWH_CH4_RESULT] is None - assert rows[0][MLWH_CH4_CQ] is None - assert rows[0][MLWH_FILTERED_POSITIVE] is None - assert rows[0][MLWH_FILTERED_POSITIVE_VERSION] is None - assert rows[0][MLWH_FILTERED_POSITIVE_TIMESTAMP] is None - assert rows[0][MLWH_CREATED_AT] is not None - assert rows[0][MLWH_UPDATED_AT] is not None - assert rows[0][MLWH_MUST_SEQUENCE] == 0 - assert rows[0][MLWH_PREFERENTIALLY_SEQUENCE] == 1 - - assert rows[1][MLWH_MONGODB_ID] == "5f562d9931d9959b92544729" - assert rows[1][MLWH_ROOT_SAMPLE_ID] == "ABC00000005" - assert rows[1][MLWH_COG_UK_ID] == "TEST-123ABD" - assert rows[1][MLWH_RNA_ID] == "TC-rna-00000029_H12" - assert rows[1][MLWH_PLATE_BARCODE] == "TC-rna-00000029" - assert rows[1][MLWH_COORDINATE] == "H12" - assert rows[1][MLWH_RESULT] == RESULT_VALUE_POSITIVE - assert rows[1][MLWH_DATE_TESTED] == date_tested_2 - assert rows[1][MLWH_SOURCE] == "Test Centre" - assert rows[1][MLWH_LAB_ID] == "TC" - assert rows[1][MLWH_CH1_TARGET] == "ORF1ab" - assert rows[1][MLWH_CH1_RESULT] == RESULT_VALUE_POSITIVE - assert rows[1][MLWH_CH1_CQ] == Decimal("21.28726211") - assert rows[1][MLWH_CH2_TARGET] == "N gene" - assert rows[1][MLWH_CH2_RESULT] == RESULT_VALUE_POSITIVE - assert rows[1][MLWH_CH2_CQ] == Decimal("18.12736661") - assert rows[1][MLWH_CH3_TARGET] == "S gene" - assert rows[1][MLWH_CH3_RESULT] == RESULT_VALUE_POSITIVE - assert rows[1][MLWH_CH3_CQ] == Decimal("22.63616273") - assert rows[1][MLWH_CH4_TARGET] == "MS2" - assert rows[1][MLWH_CH4_RESULT] == RESULT_VALUE_POSITIVE - assert rows[1][MLWH_CH4_CQ] == Decimal("26.25125612") - assert rows[1][MLWH_FILTERED_POSITIVE] == 1 - assert rows[1][MLWH_FILTERED_POSITIVE_VERSION] == "v2.3" - assert rows[1][MLWH_FILTERED_POSITIVE_TIMESTAMP] == filtered_positive_timestamp - assert rows[1][MLWH_CREATED_AT] is not None - assert rows[1][MLWH_UPDATED_AT] is not None - assert rows[1][MLWH_MUST_SEQUENCE] == 1 - assert rows[1][MLWH_PREFERENTIALLY_SEQUENCE] == 0 + assert cast(Dict[str, RowItemType], rows[0])[MLWH_MONGODB_ID] == "5f562d9931d9959b92544728" + assert cast(Dict[str, RowItemType], rows[0])[MLWH_ROOT_SAMPLE_ID] == "ABC00000004" + assert cast(Dict[str, RowItemType], rows[0])[MLWH_COG_UK_ID] == "TEST-123ABC" + assert cast(Dict[str, RowItemType], rows[0])[MLWH_RNA_ID] == "TC-rna-00000029_H11" + assert cast(Dict[str, RowItemType], rows[0])[MLWH_PLATE_BARCODE] == "TC-rna-00000029" + assert cast(Dict[str, RowItemType], rows[0])[MLWH_COORDINATE] == "H11" + assert cast(Dict[str, RowItemType], rows[0])[MLWH_RESULT] == "Negative" + assert cast(Dict[str, RowItemType], rows[0])[MLWH_DATE_TESTED] == date_tested_1 + assert cast(Dict[str, RowItemType], rows[0])[MLWH_SOURCE] == "Test Centre" + assert cast(Dict[str, RowItemType], rows[0])[MLWH_LAB_ID] == "TC" + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH1_TARGET] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH1_RESULT] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH1_CQ] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH2_TARGET] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH2_RESULT] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH2_CQ] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH3_TARGET] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH3_RESULT] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH3_CQ] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH4_TARGET] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH4_RESULT] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH4_CQ] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_FILTERED_POSITIVE] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_FILTERED_POSITIVE_VERSION] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_FILTERED_POSITIVE_TIMESTAMP] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_CREATED_AT] is not None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_UPDATED_AT] is not None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_MUST_SEQUENCE] == 0 + assert cast(Dict[str, RowItemType], rows[0])[MLWH_PREFERENTIALLY_SEQUENCE] == 1 + + assert cast(Dict[str, RowItemType], rows[1])[MLWH_MONGODB_ID] == "5f562d9931d9959b92544729" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_ROOT_SAMPLE_ID] == "ABC00000005" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_COG_UK_ID] == "TEST-123ABD" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_RNA_ID] == "TC-rna-00000029_H12" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_PLATE_BARCODE] == "TC-rna-00000029" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_COORDINATE] == "H12" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_RESULT] == RESULT_VALUE_POSITIVE + assert cast(Dict[str, RowItemType], rows[1])[MLWH_DATE_TESTED] == date_tested_2 + assert cast(Dict[str, RowItemType], rows[1])[MLWH_SOURCE] == "Test Centre" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_LAB_ID] == "TC" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH1_TARGET] == "ORF1ab" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH1_RESULT] == RESULT_VALUE_POSITIVE + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH1_CQ] == Decimal("21.28726211") + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH2_TARGET] == "N gene" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH2_RESULT] == RESULT_VALUE_POSITIVE + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH2_CQ] == Decimal("18.12736661") + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH3_TARGET] == "S gene" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH3_RESULT] == RESULT_VALUE_POSITIVE + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH3_CQ] == Decimal("22.63616273") + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH4_TARGET] == "MS2" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH4_RESULT] == RESULT_VALUE_POSITIVE + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH4_CQ] == Decimal("26.25125612") + assert cast(Dict[str, RowItemType], rows[1])[MLWH_FILTERED_POSITIVE] == 1 + assert cast(Dict[str, RowItemType], rows[1])[MLWH_FILTERED_POSITIVE_VERSION] == "v2.3" + assert cast(Dict[str, RowItemType], rows[1])[MLWH_FILTERED_POSITIVE_TIMESTAMP] == filtered_positive_timestamp + assert cast(Dict[str, RowItemType], rows[1])[MLWH_CREATED_AT] is not None + assert cast(Dict[str, RowItemType], rows[1])[MLWH_UPDATED_AT] is not None + assert cast(Dict[str, RowItemType], rows[1])[MLWH_MUST_SEQUENCE] == 1 + assert cast(Dict[str, RowItemType], rows[1])[MLWH_PREFERENTIALLY_SEQUENCE] == 0 def test_insert_samples_from_docs_into_mlwh_date_tested_missing(config, mlwh_connection): @@ -1676,7 +1677,7 @@ def test_insert_samples_from_docs_into_mlwh_date_tested_none( rows = cursor.fetchall() cursor.close() - assert rows[0][MLWH_DATE_TESTED] is None + assert cast(Dict[str, RowItemType], rows[0])[MLWH_DATE_TESTED] is None def test_insert_samples_from_docs_into_mlwh_returns_false_none_connection(config, mlwh_connection): From acc8a661045270298e196f517479fd3dd56d3bf5 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Wed, 21 Feb 2024 08:42:54 +0000 Subject: [PATCH 36/38] Fixing issues with black and mypy --- crawler/db/mysql.py | 4 +++- .../back_populate_source_plate_and_sample_uuids.py | 2 +- migrations/helpers/shared_helper.py | 9 ++++++--- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/crawler/db/mysql.py b/crawler/db/mysql.py index 81c73980..6323576b 100644 --- a/crawler/db/mysql.py +++ b/crawler/db/mysql.py @@ -224,7 +224,9 @@ def partition(iterable: Iterable, partition_size: int) -> Generator[List[Any], N yield part -def reset_is_current_flags(cursor: MySQLCursorAbstract, rna_ids: List[MySQLConvertibleType], chunk_size: int = 1000) -> None: +def reset_is_current_flags( + cursor: MySQLCursorAbstract, rna_ids: List[MySQLConvertibleType], chunk_size: int = 1000 +) -> None: """Receives a cursor with an active connection and a list of rna_ids and runs an update resetting any is_current flags to false for all the specified rna ids in groups of chunk_size. diff --git a/migrations/back_populate_source_plate_and_sample_uuids.py b/migrations/back_populate_source_plate_and_sample_uuids.py index bbd9185e..e7f76bfb 100644 --- a/migrations/back_populate_source_plate_and_sample_uuids.py +++ b/migrations/back_populate_source_plate_and_sample_uuids.py @@ -395,7 +395,7 @@ def mlwh_count_samples_from_mongo_ids(mysql_conn: MySQLConnectionAbstract, mongo if result is None: raise Exception("Query result was not valid") - return cast(int, result[0]) + return cast(int, cast(RowType, result)[0]) else: raise Exception("Cannot connect mysql") diff --git a/migrations/helpers/shared_helper.py b/migrations/helpers/shared_helper.py index 18023a3f..7f0db3fa 100644 --- a/migrations/helpers/shared_helper.py +++ b/migrations/helpers/shared_helper.py @@ -6,9 +6,10 @@ from contextlib import closing from csv import DictReader from datetime import datetime -from typing import Any, Dict, Iterator, List, Optional +from typing import Any, Dict, Iterator, List, Optional, cast from mysql.connector.connection_cext import MySQLConnectionAbstract +from mysql.connector.types import RowItemType from pymongo.collection import Collection from crawler.constants import ( @@ -117,11 +118,13 @@ def valid_filepath(s_filepath: str) -> bool: return False -def mysql_generator_from_connection(connection: MySQLConnectionAbstract, query: str) -> Iterator[Dict[str, Any]]: +def mysql_generator_from_connection( + connection: MySQLConnectionAbstract, query: str +) -> Iterator[Dict[str, RowItemType]]: with closing(connection.cursor(dictionary=True, buffered=False)) as cursor: cursor.execute(query) for row in cursor.fetchall(): - yield row + yield cast(Dict[str, RowItemType], row) def mysql_generator_from_config(config: Config, query: str) -> Iterator[Dict[str, Any]]: From eae5839deff4a604ffa1d40d5c10372b63d5fdc6 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Wed, 21 Feb 2024 11:43:25 +0000 Subject: [PATCH 37/38] Refactoring minor updates --- tests/db/test_mysql.py | 20 +-- tests/file_processing/test_file_processing.py | 121 +++++++++--------- 2 files changed, 72 insertions(+), 69 deletions(-) diff --git a/tests/db/test_mysql.py b/tests/db/test_mysql.py index 8f30fc72..ebc8cd35 100644 --- a/tests/db/test_mysql.py +++ b/tests/db/test_mysql.py @@ -28,16 +28,6 @@ class MockMySQLConnection(MySQLConnectionAbstract): _execute_query = MagicMock() _open_connection = MagicMock() close = MagicMock() - commit = MagicMock() - cursor = MagicMock() - database = MagicMock() - disconnect = MagicMock() - get_rows = MagicMock() - in_transaction = MagicMock() - info_query = MagicMock() - is_connected = MagicMock() - ping = MagicMock() - rollback = MagicMock() cmd_change_user = MagicMock() cmd_debug = MagicMock() cmd_init_db = MagicMock() @@ -55,8 +45,18 @@ class MockMySQLConnection(MySQLConnectionAbstract): cmd_stmt_prepare = MagicMock() cmd_stmt_reset = MagicMock() cmd_stmt_send_long_data = MagicMock() + commit = MagicMock() connection_id = MagicMock() + cursor = MagicMock() + database = MagicMock() + disconnect = MagicMock() get_row = MagicMock() + get_rows = MagicMock() + in_transaction = MagicMock() + info_query = MagicMock() + is_connected = MagicMock() + ping = MagicMock() + rollback = MagicMock() def test_create_mysql_connection_none(config): diff --git a/tests/file_processing/test_file_processing.py b/tests/file_processing/test_file_processing.py index 78b87bf3..56f97853 100644 --- a/tests/file_processing/test_file_processing.py +++ b/tests/file_processing/test_file_processing.py @@ -1549,65 +1549,68 @@ def test_insert_samples_from_docs_into_mlwh( rows = cursor.fetchall() cursor.close() - assert cast(Dict[str, RowItemType], rows[0])[MLWH_MONGODB_ID] == "5f562d9931d9959b92544728" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_ROOT_SAMPLE_ID] == "ABC00000004" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_COG_UK_ID] == "TEST-123ABC" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_RNA_ID] == "TC-rna-00000029_H11" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_PLATE_BARCODE] == "TC-rna-00000029" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_COORDINATE] == "H11" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_RESULT] == "Negative" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_DATE_TESTED] == date_tested_1 - assert cast(Dict[str, RowItemType], rows[0])[MLWH_SOURCE] == "Test Centre" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_LAB_ID] == "TC" - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH1_TARGET] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH1_RESULT] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH1_CQ] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH2_TARGET] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH2_RESULT] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH2_CQ] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH3_TARGET] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH3_RESULT] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH3_CQ] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH4_TARGET] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH4_RESULT] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CH4_CQ] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_FILTERED_POSITIVE] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_FILTERED_POSITIVE_VERSION] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_FILTERED_POSITIVE_TIMESTAMP] is None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_CREATED_AT] is not None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_UPDATED_AT] is not None - assert cast(Dict[str, RowItemType], rows[0])[MLWH_MUST_SEQUENCE] == 0 - assert cast(Dict[str, RowItemType], rows[0])[MLWH_PREFERENTIALLY_SEQUENCE] == 1 - - assert cast(Dict[str, RowItemType], rows[1])[MLWH_MONGODB_ID] == "5f562d9931d9959b92544729" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_ROOT_SAMPLE_ID] == "ABC00000005" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_COG_UK_ID] == "TEST-123ABD" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_RNA_ID] == "TC-rna-00000029_H12" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_PLATE_BARCODE] == "TC-rna-00000029" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_COORDINATE] == "H12" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_DATE_TESTED] == date_tested_2 - assert cast(Dict[str, RowItemType], rows[1])[MLWH_SOURCE] == "Test Centre" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_LAB_ID] == "TC" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH1_TARGET] == "ORF1ab" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH1_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH1_CQ] == Decimal("21.28726211") - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH2_TARGET] == "N gene" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH2_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH2_CQ] == Decimal("18.12736661") - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH3_TARGET] == "S gene" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH3_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH3_CQ] == Decimal("22.63616273") - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH4_TARGET] == "MS2" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH4_RESULT] == RESULT_VALUE_POSITIVE - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CH4_CQ] == Decimal("26.25125612") - assert cast(Dict[str, RowItemType], rows[1])[MLWH_FILTERED_POSITIVE] == 1 - assert cast(Dict[str, RowItemType], rows[1])[MLWH_FILTERED_POSITIVE_VERSION] == "v2.3" - assert cast(Dict[str, RowItemType], rows[1])[MLWH_FILTERED_POSITIVE_TIMESTAMP] == filtered_positive_timestamp - assert cast(Dict[str, RowItemType], rows[1])[MLWH_CREATED_AT] is not None - assert cast(Dict[str, RowItemType], rows[1])[MLWH_UPDATED_AT] is not None - assert cast(Dict[str, RowItemType], rows[1])[MLWH_MUST_SEQUENCE] == 1 - assert cast(Dict[str, RowItemType], rows[1])[MLWH_PREFERENTIALLY_SEQUENCE] == 0 + first_row = cast(Dict[str, RowItemType], rows[0]) + second_row = cast(Dict[str, RowItemType], rows[1]) + + assert first_row[MLWH_MONGODB_ID] == "5f562d9931d9959b92544728" + assert first_row[MLWH_ROOT_SAMPLE_ID] == "ABC00000004" + assert first_row[MLWH_COG_UK_ID] == "TEST-123ABC" + assert first_row[MLWH_RNA_ID] == "TC-rna-00000029_H11" + assert first_row[MLWH_PLATE_BARCODE] == "TC-rna-00000029" + assert first_row[MLWH_COORDINATE] == "H11" + assert first_row[MLWH_RESULT] == "Negative" + assert first_row[MLWH_DATE_TESTED] == date_tested_1 + assert first_row[MLWH_SOURCE] == "Test Centre" + assert first_row[MLWH_LAB_ID] == "TC" + assert first_row[MLWH_CH1_TARGET] is None + assert first_row[MLWH_CH1_RESULT] is None + assert first_row[MLWH_CH1_CQ] is None + assert first_row[MLWH_CH2_TARGET] is None + assert first_row[MLWH_CH2_RESULT] is None + assert first_row[MLWH_CH2_CQ] is None + assert first_row[MLWH_CH3_TARGET] is None + assert first_row[MLWH_CH3_RESULT] is None + assert first_row[MLWH_CH3_CQ] is None + assert first_row[MLWH_CH4_TARGET] is None + assert first_row[MLWH_CH4_RESULT] is None + assert first_row[MLWH_CH4_CQ] is None + assert first_row[MLWH_FILTERED_POSITIVE] is None + assert first_row[MLWH_FILTERED_POSITIVE_VERSION] is None + assert first_row[MLWH_FILTERED_POSITIVE_TIMESTAMP] is None + assert first_row[MLWH_CREATED_AT] is not None + assert first_row[MLWH_UPDATED_AT] is not None + assert first_row[MLWH_MUST_SEQUENCE] == 0 + assert first_row[MLWH_PREFERENTIALLY_SEQUENCE] == 1 + + assert second_row[MLWH_MONGODB_ID] == "5f562d9931d9959b92544729" + assert second_row[MLWH_ROOT_SAMPLE_ID] == "ABC00000005" + assert second_row[MLWH_COG_UK_ID] == "TEST-123ABD" + assert second_row[MLWH_RNA_ID] == "TC-rna-00000029_H12" + assert second_row[MLWH_PLATE_BARCODE] == "TC-rna-00000029" + assert second_row[MLWH_COORDINATE] == "H12" + assert second_row[MLWH_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_DATE_TESTED] == date_tested_2 + assert second_row[MLWH_SOURCE] == "Test Centre" + assert second_row[MLWH_LAB_ID] == "TC" + assert second_row[MLWH_CH1_TARGET] == "ORF1ab" + assert second_row[MLWH_CH1_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_CH1_CQ] == Decimal("21.28726211") + assert second_row[MLWH_CH2_TARGET] == "N gene" + assert second_row[MLWH_CH2_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_CH2_CQ] == Decimal("18.12736661") + assert second_row[MLWH_CH3_TARGET] == "S gene" + assert second_row[MLWH_CH3_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_CH3_CQ] == Decimal("22.63616273") + assert second_row[MLWH_CH4_TARGET] == "MS2" + assert second_row[MLWH_CH4_RESULT] == RESULT_VALUE_POSITIVE + assert second_row[MLWH_CH4_CQ] == Decimal("26.25125612") + assert second_row[MLWH_FILTERED_POSITIVE] == 1 + assert second_row[MLWH_FILTERED_POSITIVE_VERSION] == "v2.3" + assert second_row[MLWH_FILTERED_POSITIVE_TIMESTAMP] == filtered_positive_timestamp + assert second_row[MLWH_CREATED_AT] is not None + assert second_row[MLWH_UPDATED_AT] is not None + assert second_row[MLWH_MUST_SEQUENCE] == 1 + assert second_row[MLWH_PREFERENTIALLY_SEQUENCE] == 0 def test_insert_samples_from_docs_into_mlwh_date_tested_missing(config, mlwh_connection): From 0af4a2a128efb617b3a156c9646366a3dd9e7b97 Mon Sep 17 00:00:00 2001 From: Dasun Pubudumal Date: Thu, 22 Feb 2024 16:34:50 +0000 Subject: [PATCH 38/38] Update .release-version --- .release-version | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.release-version b/.release-version index d8b69897..fb2c0766 100644 --- a/.release-version +++ b/.release-version @@ -1 +1 @@ -2.12.0 +2.13.0