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Develop to master #146

Merged
merged 52 commits into from
Aug 22, 2024
Merged

Develop to master #146

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822ac1c
Adding retention instructions key
dasunpubudumal Jul 23, 2024
ee93d1c
Adding retention instructions key for tests
dasunpubudumal Jul 23, 2024
28ddc98
Updating consumed message properties
dasunpubudumal Jul 23, 2024
a882960
Updating consumed message properties
dasunpubudumal Jul 23, 2024
be0dc51
Updating consumed message properties
dasunpubudumal Jul 23, 2024
418df6d
Updating consumed message properties
dasunpubudumal Jul 23, 2024
e4bb754
Updating consumed message properties
dasunpubudumal Jul 23, 2024
0750412
Rollback the iterator count
dasunpubudumal Jul 23, 2024
58578e0
Rollback the iterator count
dasunpubudumal Jul 23, 2024
c07d17e
Rollback comments
dasunpubudumal Jul 23, 2024
e520cff
Fixing tests
dasunpubudumal Jul 23, 2024
3e0dd61
Fixing demo tools to use retention instructions at the correct location
dasunpubudumal Jul 26, 2024
613e884
Updating the demo publisher for testing locally
dasunpubudumal Jul 26, 2024
522c001
Updating enum name
dasunpubudumal Jul 26, 2024
3988f9b
Updating demo publisher.py
dasunpubudumal Jul 26, 2024
c0e49db
Updating demo publisher.py
dasunpubudumal Jul 26, 2024
4f6c316
chore: Update lab-share-lib dependency to commit 8ee103e8d3f539c23035…
dasunpubudumal Jul 30, 2024
83af9b6
Revert "chore: Update lab-share-lib dependency to commit 8ee103e8d3f5…
dasunpubudumal Jul 30, 2024
d878cfe
Merge branch 'updating-for-lab-share-lib' into 121-update-labware-pro…
dasunpubudumal Jul 30, 2024
28bdbe1
Adding latest lab-share-lib changes for version files
dasunpubudumal Jul 31, 2024
73d6ce9
Merge remote-tracking branch 'origin/develop' into 121-update-labware…
dasunpubudumal Jul 31, 2024
9105f88
Reverting v1.0.1
dasunpubudumal Jul 31, 2024
949989d
Revert the lockfile
dasunpubudumal Jul 31, 2024
92c4b56
Add the new version of lib share
dasunpubudumal Jul 31, 2024
5d887ba
Changes from lib
dasunpubudumal Aug 1, 2024
b9760db
chore: Update lab-share-lib dependency to commit 49ff65a8f15b9dbfe259…
dasunpubudumal Aug 1, 2024
03eb089
chore: Update lab-share-lib dependency to latest commit
dasunpubudumal Aug 1, 2024
f92666a
Update lab-share-lib dependency to commit 10408d2dce0c0a6f54a8b31fabd…
dasunpubudumal Aug 1, 2024
f5a5c4f
feat: Add retention instruction to TractionReceptionMessageRequest
dasunpubudumal Aug 1, 2024
4bc74b6
feat: Update retention instruction in TractionReceptionMessageRequest
dasunpubudumal Aug 1, 2024
a1f9075
chore: Update automated_release.yml to include tags for '*-uat'
dasunpubudumal Aug 1, 2024
4f20d65
chore: Revert the changes for automated release
dasunpubudumal Aug 1, 2024
b641824
feat: Add logic to create labware message in publisher.py
dasunpubudumal Aug 1, 2024
49e35c4
feat: Add support for creating labware message in publisher.py
dasunpubudumal Aug 1, 2024
a0106af
Adding missing retention instruction value
dasunpubudumal Aug 2, 2024
aabf55f
Update lab-share-lib dependency to commit 932737eb89664339106b66ec766…
dasunpubudumal Aug 2, 2024
cd54e62
Moving reader_schema_version to the encode func argument
dasunpubudumal Aug 2, 2024
0a4ed73
Moving reader_schema_version to the encode func argument
dasunpubudumal Aug 2, 2024
950c3a7
Update lab-share-lib dependency to commit 0fbfc68bb90b3b2b721c08a2a7b…
dasunpubudumal Aug 2, 2024
bffac79
Update lab-share-lib dependency to commit cb8c235403436fb268064120b9b…
dasunpubudumal Aug 3, 2024
e464ced
Update lab-share-lib dependency to version v1.1.0
dasunpubudumal Aug 5, 2024
aa07492
Modifying the demo script for sending messages without retention inst…
dasunpubudumal Aug 5, 2024
54f64dd
Update lab-share-lib dependency to commit 932737eb89664339106b66ec766…
dasunpubudumal Aug 5, 2024
f8f7d2b
Update lab-share-lib dependency to version v1.1.1
dasunpubudumal Aug 5, 2024
367f3f2
Update .release-version to version 2.2.0
dasunpubudumal Aug 5, 2024
6fb3746
Merge pull request #132 from sanger/121-update-labware-processor-to-f…
dasunpubudumal Aug 5, 2024
74217f0
chore: Update RabbitMQ configuration and dependencies
dasunpubudumal Aug 6, 2024
cb87f83
chore: Update RabbitMQ configuration and dependencies
dasunpubudumal Aug 6, 2024
fe1c50f
Merge pull request #140 from sanger/refactoring-configuration
dasunpubudumal Aug 7, 2024
7a213b2
Change test setup of mlwh vhost
dasunpubudumal Aug 18, 2024
3b97bb3
chore(deps-dev): Bump flake8-bugbear from 24.4.26 to 24.8.19
dependabot[bot] Aug 20, 2024
5268d4c
Merge pull request #142 from sanger/dependabot/pip/flake8-bugbear-24.…
dasunpubudumal Aug 22, 2024
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2 changes: 1 addition & 1 deletion .release-version
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Original file line number Diff line number Diff line change
@@ -1 +1 @@
2.1.0
2.2.0
2 changes: 1 addition & 1 deletion Pipfile
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Expand Up @@ -22,7 +22,7 @@ more-itertools = "~=10.3"
python-dotenv = "~=1.0"
requests = "~=2.31"
slackclient = "~=2.9"
lab-share-lib = {editable = false,git = 'https://github.com/sanger/lab-share-lib.git',ref = 'v1.0.1'}
lab-share-lib = {editable = false,git = 'https://github.com/sanger/lab-share-lib.git',ref = 'v1.1.1'}
requests-mock = "*"
types-requests = "*"
python-snappy = "*"
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511 changes: 269 additions & 242 deletions Pipfile.lock
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345 changes: 193 additions & 152 deletions schemas/create-labware/1-create-labware.avsc
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Original file line number Diff line number Diff line change
@@ -1,158 +1,199 @@
{
"namespace": "uk.ac.sanger.psd",
"type": "record",
"name": "CreateLabwareMessage",
"doc": "A create message to process new labware.",
"fields": [
{
"name": "messageUuid",
"doc": "Unique message ID.",
"type": {"name": "version4MessageUuid", "type": "fixed", "size": 36}
},
{
"name": "messageCreateDateUtc",
"doc": "Date (UTC) that the message was created.",
"type": { "type": "long", "logicalType": "timestamp-millis" }
},
{
"name": "labware",
"doc": "Labware to process.",
"type": {
"name": "Labware", "type": "record",
"doc": "Labware data.",
"fields": [
{
"name": "labwareType",
"type": "string"
},
{
"name": "barcode", "type": "string",
"doc": "The barcode for this labware."
},
{
"name": "samples",
"doc": "An array of data for samples on the labware.",
"type": "record",
"name": "CreateLabwareMessage",
"namespace": "uk.ac.sanger.psd",
"doc": "A create message to process new labware.",
"fields": [
{
"name": "messageUuid",
"type": {
"type": "fixed",
"name": "version4MessageUuid",
"size": 36
},
"doc": "Unique message ID."
},
{
"name": "messageCreateDateUtc",
"type": {
"type": "long",
"logicalType": "timestamp-millis"
},
"doc": "Date (UTC) that the message was created."
},
{
"name": "labware",
"type": {
"type": "array",
"items": {
"name": "Sample",
"type": "record",
"doc": "A labware sample",
"name": "Labware",
"doc": "Labware data.",
"fields": [
{
"name": "sampleUuid",
"doc": "Unique sample ID in UUID format.",
"type": "version4MessageUuid"
},
{
"name": "studyUuid",
"doc": "Unique study UUID where the sample belongs to",
"type": "version4MessageUuid"
},
{
"name": "sangerSampleId", "type": "string",
"doc": "Unique id to identify the sample inside Sanger lims"
},
{
"name": "location", "type": ["null", "string"], "default": null,
"doc": "The location for the sample inside the labware, or null if location is not relevant in labware (Eg: tube)."
},
{
"name": "supplierSampleName", "type": "string",
"doc": "Name given by the supplier of the sample"
},
{
"name": "volume", "type": "string",
"doc": "Volume of the sample."
},
{
"name": "concentration", "type": "string",
"doc": "Concentration of the sample."
},
{
"name": "publicName", "type": "string",
"doc": "Public name of the sample."
},
{
"name": "taxonId", "type": "string",
"doc": "Taxonomy Identifier."
},
{
"name": "commonName", "type": "string",
"doc": "Common name for the sample"
},
{
"name": "donorId", "type": "string",
"doc": "Identifier for the donor of the sample"
},
{
"name": "libraryType", "type": "string",
"doc": "Type of library created for sequencing"
},
{
"name": "countryOfOrigin", "type": "string",
"doc": "Country of origin for the sample"
},
{
"name": "sampleCollectionDateUtc",
"doc": "Sample Collection of the sample in UTC format.",
"type": { "type": "long", "logicalType": "timestamp-millis" }
},
{
"name": "costCode", "type": "string",
"doc": "Code for the project for billing purposes"
},
{
"name": "genomeSize", "type": "string",
"doc": "Size of genome"
},
{
"name": "accessionNumber", "type": "string",
"doc": "Accession number for publication in ENA/EBI"
},
{
"name": "shearedFemtoFragmentSize", "type": "string",
"doc": "Sheared Femto Fragment Size (bp)"
},
{
"name": "postSPRIConcentration", "type": "string",
"doc": "Post SPRI Concentration (ng/ul)"
},
{
"name": "postSPRIVolume", "type": "string",
"doc": "Post SPRI Volume (ul)"
},
{
"name": "finalNanoDrop280", "type": "string",
"doc": "Final NanoDrop 260/280"
},
{
"name": "finalNanoDrop230", "type": "string",
"doc": "Final NanoDrop 260/230"
},
{
"name": "finalNanoDrop", "type": "string",
"doc": "Final NanoDrop ng/ul"
},
{
"name": "shearingAndQCComments", "type": "string",
"doc": "Shearing & QC comments"
},
{
"name": "dateSubmittedUTC",
"doc": "Date submitted in UTC format.",
"type": { "type": "long", "logicalType": "timestamp-millis" }
},
{
"name": "priorityLevel", "type": "string",
"doc": "Priority level (if High or Medium)"
}
{
"name": "labwareType",
"type": "string"
},
{
"name": "barcode",
"type": "string",
"doc": "The barcode for this labware."
},
{
"name": "samples",
"type": {
"type": "array",
"items": {
"name": "Sample",
"type": "record",
"doc": "A labware sample",
"fields": [
{
"name": "sampleUuid",
"doc": "Unique sample ID in UUID format.",
"type": "version4MessageUuid"
},
{
"name": "studyUuid",
"doc": "Unique study UUID where the sample belongs to",
"type": "version4MessageUuid"
},
{
"name": "sangerSampleId",
"type": "string",
"doc": "Unique id to identify the sample inside Sanger lims"
},
{
"name": "location",
"type": [
"null",
"string"
],
"default": null,
"doc": "The location for the sample inside the labware, or null if location is not relevant in labware (Eg: tube)."
},
{
"name": "supplierSampleName",
"type": "string",
"doc": "Name given by the supplier of the sample"
},
{
"name": "volume",
"type": "string",
"doc": "Volume of the sample."
},
{
"name": "concentration",
"type": "string",
"doc": "Concentration of the sample."
},
{
"name": "publicName",
"type": "string",
"doc": "Public name of the sample."
},
{
"name": "taxonId",
"type": "string",
"doc": "Taxonomy Identifier."
},
{
"name": "commonName",
"type": "string",
"doc": "Common name for the sample"
},
{
"name": "donorId",
"type": "string",
"doc": "Identifier for the donor of the sample"
},
{
"name": "libraryType",
"type": "string",
"doc": "Type of library created for sequencing"
},
{
"name": "countryOfOrigin",
"type": "string",
"doc": "Country of origin for the sample"
},
{
"name": "sampleCollectionDateUtc",
"doc": "Sample Collection of the sample in UTC format.",
"type": {
"type": "long",
"logicalType": "timestamp-millis"
}
},
{
"name": "costCode",
"type": "string",
"doc": "Code for the project for billing purposes"
},
{
"name": "genomeSize",
"type": "string",
"doc": "Size of genome"
},
{
"name": "accessionNumber",
"type": "string",
"doc": "Accession number for publication in ENA/EBI"
},
{
"name": "shearedFemtoFragmentSize",
"type": "string",
"doc": "Sheared Femto Fragment Size (bp)"
},
{
"name": "postSPRIConcentration",
"type": "string",
"doc": "Post SPRI Concentration (ng/ul)"
},
{
"name": "postSPRIVolume",
"type": "string",
"doc": "Post SPRI Volume (ul)"
},
{
"name": "finalNanoDrop280",
"type": "string",
"doc": "Final NanoDrop 260/280"
},
{
"name": "finalNanoDrop230",
"type": "string",
"doc": "Final NanoDrop 260/230"
},
{
"name": "finalNanoDrop",
"type": "string",
"doc": "Final NanoDrop ng/ul"
},
{
"name": "shearingAndQCComments",
"type": "string",
"doc": "Shearing & QC comments"
},
{
"name": "dateSubmittedUTC",
"doc": "Date submitted in UTC format.",
"type": {
"type": "long",
"logicalType": "timestamp-millis"
}
},
{
"name": "priorityLevel",
"type": "string",
"doc": "Priority level (if High or Medium)"
}
]
}
},
"doc": "An array of data for samples on the labware."
}
]
}
}
}
]
}
}
]
},
"doc": "Labware to process."
}
]
}
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