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Troubleshooting","\u002Fconnector-development\u002Fguides\u002Fserial-troubleshooting\u002F","20.connector-development\u002F40.guides\u002F70.serial-troubleshooting",{"title":900,"path":901,"stem":902,"type":24,"device":6},"Testing","\u002Fconnector-development\u002Fguides\u002Ftesting\u002F","20.connector-development\u002F40.guides\u002F80.testing",{"title":904,"path":905,"stem":906,"children":907,"type":6,"device":6},"References","\u002Fconnector-development\u002Freference\u002F","20.connector-development\u002F50.reference\u002Findex",[908],{"title":904,"path":905,"stem":906,"type":200,"device":6},{"id":910,"title":194,"body":911,"description":1088,"device":6,"extension":1089,"links":6,"meta":1090,"navigation":1091,"path":1092,"seo":1093,"stem":428,"type":14,"__hash__":1094},"docs\u002F04.concepts\u002F08.observe\u002F10.overview.md",{"type":912,"value":913,"toc":1080},"minimark",[914,922,925,930,933,944,947,951,962,971,979,987,996,1000,1003,1019,1025,1029,1032,1069],[915,916,917],"p",{},[918,919],"img",{"alt":920,"src":921},"UniteLabs Data Lake Navigation","\u002Fimages\u002Fplatform\u002Fplatform_datalake_navigation.webp",[915,923,924],{},"UniteLabs provides a layered data infrastructure so workflows can ingest raw instrument files, persist structured records, and expose both to downstream analysis — without managing storage backends manually. Three components work together: Object Storage, the Data Warehouse, and File System Connectors.",[926,927,929],"h2",{"id":928},"how-the-data-layer-fits-together","How the data layer fits together",[915,931,932],{},"Data flows in one direction through the stack. Instruments write result files to local directories. File System Connectors detect new files via change subscriptions and forward them upstream. Object Storage (S3-compatible MinIO) holds every raw file as an immutable archive. ETL workflows — orchestrated by Prefect — pull files from Object Storage, parse them, and write structured records into the Data Warehouse (PostgreSQL).",[934,935,940],"pre",{"className":936,"code":938,"language":939},[937],"language-text","Instrument output\n      │\n      ▼\nFile System Connector  ──────────────────►  Object Storage (S3\u002FMinIO)\n(subscribe_changes)                               │\n                                                  ▼\n                                         ETL Workflow (Prefect)\n                                                  │\n                                                  ▼\n                                       Data Warehouse (PostgreSQL)\n","text",[941,942,938],"code",{"__ignoreMap":943},"",[915,945,946],{},"Each layer is independently accessible — analysts can query the Warehouse directly with DBeaver, and raw files in Object Storage are always available for reprocessing.",[926,948,950],{"id":949},"components","Components",[952,953,955],"card",{"icon":954,"title":430},"i-heroicons-circle-stack",[915,956,957,958],{},"S3-compatible file storage for raw instrument output and processing artifacts. Backed by MinIO with boto3-compatible APIs. ",[959,960,961],"a",{"href":431},"Learn more →",[952,963,966],{"icon":964,"title":965},"i-heroicons-table-cells","Data Sources",[915,967,968,969],{},"Managed PostgreSQL warehouse for structured experiment data. Define models with SQLModel and query from any Postgres client. ",[959,970,961],{"href":439},[952,972,974],{"icon":973,"title":169},"i-heroicons-folder-open",[915,975,976,977],{},"Monitor instrument directories in real time and trigger data pipelines on new files using the UniteLabs SDK. ",[959,978,961],{"href":170},[952,980,982],{"icon":981,"title":434},"i-heroicons-key",[915,983,984,985],{},"Securely store and retrieve credentials used by workflows and connectors. All data components load credentials at runtime from the secrets manager. ",[959,986,961],{"href":435},[952,988,991],{"icon":989,"title":990},"i-heroicons-share","Data Lineage",[915,992,993,994],{},"Follow material and labware through a workflow run. Review the history in the Platform, or read and stream events through the API. ",[959,995,961],{"href":443},[926,997,999],{"id":998},"credentials-and-secrets","Credentials and secrets",[915,1001,1002],{},"All data layer credentials are stored in the UniteLabs secrets manager — never hardcoded. Two key secrets the data layer depends on:",[1004,1005,1006,1013],"ul",{},[1007,1008,1009,1012],"li",{},[941,1010,1011],{},"datalake-admin"," — MinIO access key, secret key, endpoint URL, and bucket name",[1007,1014,1015,1018],{},[941,1016,1017],{},"warehouse-admin"," — PostgreSQL connection string for the managed warehouse",[915,1020,1021,1022,1024],{},"See ",[959,1023,434],{"href":435}," for setup steps.",[926,1026,1028],{"id":1027},"a-typical-data-pipeline","A typical data pipeline",[915,1030,1031],{},"Here is what happens end-to-end when a LabChip GXII Touch runs a protein analysis:",[1033,1034,1035,1049,1052,1059,1066],"ol",{},[1007,1036,1037,1038,1041,1042,1041,1045,1048],{},"The instrument writes three CSV files (",[941,1039,1040],{},"PeakTable",", ",[941,1043,1044],{},"SizeTable",[941,1046,1047],{},"WellTable",") to a local directory.",[1007,1050,1051],{},"A File System Connector monitors that directory and emits a change event for each new file.",[1007,1053,1054,1055,1058],{},"A Prefect ETL flow receives the event, uploads the raw file to Object Storage under ",[941,1056,1057],{},"data\u002Finstruments\u002Flabchip\u002F",", and records the file path in the Warehouse.",[1007,1060,1061,1062,1065],{},"Once all three files for a plate are present, the flow parses them, maps wells to Benchling sample IDs, and writes structured results to the ",[941,1063,1064],{},"labchip_results"," table.",[1007,1067,1068],{},"Downstream workflows and BI tools query the Warehouse directly.",[1070,1071,1074],"callout",{"color":1072,"icon":1073},"neutral","i-heroicons-magnifying-glass",[915,1075,1076,1077,1079],{},"See the ",[959,1078,173],{"href":174}," guide for a complete working implementation of this pattern.",{"title":943,"searchDepth":1081,"depth":1082,"links":1083},1,2,[1084,1085,1086,1087],{"id":928,"depth":1082,"text":929},{"id":949,"depth":1082,"text":950},{"id":998,"depth":1082,"text":999},{"id":1027,"depth":1082,"text":1028},"How UniteLabs handles data storage, secrets, and connectivity to external systems.","md",{},true,"\u002Fconcepts\u002Fobserve\u002Foverview",{"title":194,"description":1088},"JF4LJT3WpyqDZHKY60OF25CmWVOsDXdCmYYrHZ7ENVA",[1096,1098],{"title":380,"description":1097,"path":420},"How errors are classified, retried, and recovered at each level of the workflow hierarchy — from automatic step retries to operator-assisted recovery.",{"title":430,"description":1099,"path":431},"Store and retrieve files using UniteLabs S3-compatible object storage.",1791294180690]