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Merge pull request #132 from sanger/121-update-labware-processor-to-f…
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…acilitate-retention-instructions-updated

Adding retention instructions to the labware message
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@dasunpubudumal
dasunpubudumal authored Aug 5, 2024
2 parents 83af9b6 + 367f3f2 commit 6fb3746
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2 changes: 1 addition & 1 deletion .release-version
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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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505 changes: 266 additions & 239 deletions Pipfile.lock
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345 changes: 193 additions & 152 deletions schemas/create-labware/1-create-labware.avsc
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@@ -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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