@burdenoff/cli-sdk 2026.1102.1 → 2026.1102.3

package/dist/modules/labsofscience/index.cjs

@@ -97,7 +97,7 @@
       id experimentId runNumber status observations notes completedAt updatedAt
     }
   }
-`,V=`
+`,F=`
   query LabListNotebookEntries(
     $experimentId: ID
     $projectId: ID
@@ -117,7 +117,7 @@
       pageInfo { cursor hasMore }
     }
   }
-`,F=`
+`,V=`
   mutation LabCreateNotebookEntry($input: LabCreateNotebookEntryInput!) {
     labCreateNotebookEntry(input: $input) {
       id workspaceId projectId experimentId runId title body status
@@ -220,8 +220,11 @@
 `,nt=`
   query LabListPipelines {
     labListPipelines {
-      id workspaceId projectId name description engine version isActive
-      definition tags createdAt updatedAt
+      items {
+        id workspaceId projectId name description engine version isActive definition tags
+        createdAt updatedAt
+      }
+      pageInfo { cursor hasMore }
     }
   }
 `,rt=`
@@ -313,7 +316,8 @@
 `,lt=`
   query LabListInstruments($status: LabInstrumentStatus) {
     labListInstruments(status: $status) {
-      id name model location status requiresApproval custodianId tags createdAt
+      items { id name model location status requiresApproval custodianId tags createdAt }
+      pageInfo { cursor hasMore }
     }
   }
 `,gt=`
@@ -340,4 +344,4 @@
   query LabHealth {
     labHealth
   }
-`;function b(o,r){try{return JSON.parse(r)}catch{throw new u(`--${o} must be valid JSON`)}}function p(o){let r=Number.parseInt(o,10);if(Number.isNaN(r))throw new u(`Expected an integer but got "${o}"`);return r}function A(o){let r=Number.parseFloat(o);if(Number.isNaN(r))throw new u(`Expected a number but got "${o}"`);return r}function l(o){return o.split(",").map(r=>r.trim()).filter(r=>r.length>0)}function g(o,r){return {limit:o,offset:r}}function yt(o){let r=o.command("projects").description("Labsofscience research projects");r.command("list").description("List research projects").option("--status <s>","Filter by project status").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(P,{status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListProjects.items,{headers:["ID","Name","Code","Field","Status","Visibility"],rows:e.labListProjects.items.map(n=>[d(n.id,12),n.name,n.code??"-",n.field??"-",n.status,n.visibility])});}catch(e){i(e);}}),r.command("get").description("Get a research project by id").argument("<id>","Project ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(R,{id:t});if(!n.labProject)throw new u(`Project ${t} not found`);s(e,n.labProject);}catch(n){i(n);}}),r.command("create").description("Create a research project").requiredOption("--name <name>","Project name").option("--code <code>","Project code").option("--description <s>","Description").option("--field <s>","Research field").option("--pi <id>","Principal investigator user ID").option("--start-date <iso>","Start date (ISO)").option("--end-date <iso>","End date (ISO)").option("--status <s>","PLANNING|ACTIVE|ON_HOLD|COMPLETED|ARCHIVED","PLANNING").option("--visibility <v>","PRIVATE|WORKSPACE|PUBLIC","WORKSPACE").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,status:(t.status??"PLANNING").toUpperCase(),visibility:(t.visibility??"WORKSPACE").toUpperCase()};t.code&&(e.code=t.code),t.description&&(e.description=t.description),t.field&&(e.field=t.field),t.pi&&(e.principalInvestigatorId=t.pi),t.startDate&&(e.startDate=t.startDate),t.endDate&&(e.endDate=t.endDate),t.tags&&(e.tags=l(t.tags));let n=await a(O,{input:e});c(`Project created: ${n.labCreateProject.name}`),s(t,n.labCreateProject);}catch(e){i(e);}}),r.command("update").description("Update a research project").argument("<id>","Project ID").option("--name <name>","Project name").option("--code <code>","Project code").option("--description <s>","Description").option("--field <s>","Research field").option("--pi <id>","Principal investigator user ID").option("--start-date <iso>","Start date (ISO)").option("--end-date <iso>","End date (ISO)").option("--status <s>","Project status").option("--visibility <v>","Visibility").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.name&&(n.name=e.name),e.code&&(n.code=e.code),e.description!==void 0&&(n.description=e.description),e.field&&(n.field=e.field),e.pi&&(n.principalInvestigatorId=e.pi),e.startDate&&(n.startDate=e.startDate),e.endDate&&(n.endDate=e.endDate),e.status&&(n.status=e.status.toUpperCase()),e.visibility&&(n.visibility=e.visibility.toUpperCase()),e.tags&&(n.tags=l(e.tags)),!Object.keys(n).length)throw new u("No updates specified");let f=await a(D,{id:t,input:n});c("Project updated"),s(e,f.labUpdateProject);}catch(n){i(n);}}),r.command("archive").description("Archive a research project").argument("<id>","Project ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(S,{id:t});c(`Project archived: ${n.labArchiveProject}`),s(e,{archived:n.labArchiveProject});}catch(n){i(n);}});}function Ct(o){let r=o.command("experiments").description("Labsofscience experiments");r.command("list").description("List experiments").option("--project <id>","Filter by project ID").option("--status <s>","Filter by experiment status").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(_,{projectId:t.project,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListExperiments.items,{headers:["ID","Title","Status","Project","Lead"],rows:e.labListExperiments.items.map(n=>[d(n.id,12),n.title,n.status,d(n.projectId,12),n.leadResearcherId?d(n.leadResearcherId,12):"-"])});}catch(e){i(e);}}),r.command("get").description("Get an experiment by id").argument("<id>","Experiment ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(N,{id:t});if(!n.labExperiment)throw new u(`Experiment ${t} not found`);s(e,n.labExperiment);}catch(n){i(n);}}),r.command("create").description("Create an experiment").requiredOption("--project <id>","Project ID").requiredOption("--title <t>","Experiment title").option("--description <s>","Description").option("--hypothesis <s>","Hypothesis").option("--lead <id>","Lead researcher user ID").option("--protocol <id>","Protocol ID").option("--variables <json>","Variables JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={projectId:t.project,title:t.title};t.description&&(e.description=t.description),t.hypothesis&&(e.hypothesis=t.hypothesis),t.lead&&(e.leadResearcherId=t.lead),t.protocol&&(e.protocolId=t.protocol),t.variables&&(e.variables=b("variables",t.variables)),t.tags&&(e.tags=l(t.tags));let n=await a($,{input:e});c(`Experiment created: ${n.labCreateExperiment.title}`),s(t,n.labCreateExperiment);}catch(e){i(e);}}),r.command("update").description("Update an experiment").argument("<id>","Experiment ID").option("--title <t>","Experiment title").option("--description <s>","Description").option("--hypothesis <s>","Hypothesis").option("--lead <id>","Lead researcher user ID").option("--protocol <id>","Protocol ID").option("--variables <json>","Variables JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.title&&(n.title=e.title),e.description!==void 0&&(n.description=e.description),e.hypothesis!==void 0&&(n.hypothesis=e.hypothesis),e.lead&&(n.leadResearcherId=e.lead),e.protocol&&(n.protocolId=e.protocol),e.variables&&(n.variables=b("variables",e.variables)),e.tags&&(n.tags=l(e.tags)),!Object.keys(n).length)throw new u("No updates specified");let f=await a(j,{id:t,input:n});c("Experiment updated"),s(e,f.labUpdateExperiment);}catch(n){i(n);}}),r.command("transition").description("Advance an experiment through its lifecycle").argument("<id>","Experiment ID").requiredOption("--status <s>","DESIGN|RUNNING|ANALYSIS|COMPLETE|ABANDONED").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(B,{id:t,status:e.status.toUpperCase()});c(`Experiment moved to ${n.labTransitionExperiment.status}`),s(e,n.labTransitionExperiment);}catch(n){i(n);}});}function Et(o){let r=o.command("runs").description("Labsofscience reproducible experiment runs");r.command("list").description("List experiment runs").option("--experiment <id>","Filter by experiment ID").option("--status <s>","Filter by run status").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(q,{experimentId:t.experiment,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListRuns.items,{headers:["ID","Run #","Status","Experiment","Started","Completed"],rows:e.labListRuns.items.map(n=>[d(n.id,12),String(n.runNumber),n.status,d(n.experimentId,12),E(n.startedAt),E(n.completedAt)])});}catch(e){i(e);}}),r.command("start").description("Start a new reproducible run of an experiment").requiredOption("--experiment <id>","Experiment ID").option("--notes <s>","Run notes").option("--parameters <json>","Parameters JSON").option("-f, --format <format>","Output format").action(async t=>{try{let e={experimentId:t.experiment};t.notes&&(e.notes=t.notes),t.parameters&&(e.parameters=b("parameters",t.parameters));let n=await a(U,{input:e});c(`Run #${n.labStartRun.runNumber} started`),s(t,n.labStartRun);}catch(e){i(e);}}),r.command("complete").description("Record observations and complete a run with a terminal status").argument("<id>","Run ID").requiredOption("--status <s>","SUCCEEDED|FAILED|CANCELLED").option("--notes <s>","Result notes").option("--observations <json>","Observations JSON").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={id:t,status:e.status.toUpperCase()},f={};e.notes&&(f.notes=e.notes),e.observations&&(f.observations=b("observations",e.observations)),Object.keys(f).length&&(n.input=f);let w=await a(M,n);c(`Run #${w.labCompleteRun.runNumber} completed: ${w.labCompleteRun.status}`),s(e,w.labCompleteRun);}catch(n){i(n);}});}function ht(o){let r=o.command("notebook").description("Labsofscience electronic lab notebook (ELN)");r.command("list").description("List notebook entries").option("--experiment <id>","Filter by experiment ID").option("--project <id>","Filter by project ID").option("--status <s>","Filter by entry status").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(V,{experimentId:t.experiment,projectId:t.project,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListNotebookEntries.items,{headers:["ID","Title","Status","Project","Author"],rows:e.labListNotebookEntries.items.map(n=>[d(n.id,12),n.title,n.status,d(n.projectId,12),d(n.authorId,12)])});}catch(e){i(e);}}),r.command("create").description("Create a notebook entry").requiredOption("--project <id>","Project ID").requiredOption("--title <t>","Entry title").option("--body <s>","Entry body").option("--experiment <id>","Experiment ID").option("--run <id>","Run ID").option("--file-ids <csv>","Comma-separated wspace-files-svc File ids").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={projectId:t.project,title:t.title};t.body&&(e.body=t.body),t.experiment&&(e.experimentId=t.experiment),t.run&&(e.runId=t.run),t.fileIds&&(e.fileIds=l(t.fileIds)),t.tags&&(e.tags=l(t.tags));let n=await a(F,{input:e});c(`Notebook entry created: ${n.labCreateNotebookEntry.title}`),s(t,n.labCreateNotebookEntry);}catch(e){i(e);}}),r.command("sign").description("Sign a notebook entry (locks editable content)").argument("<id>","Entry ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(W,{id:t});c(`Notebook entry signed: ${n.labSignNotebookEntry.status}`),s(e,n.labSignNotebookEntry);}catch(n){i(n);}});}function At(o){let r=o.command("protocols").description("Labsofscience versioned protocols");r.command("list").description("List protocols").option("--status <s>","DRAFT|PUBLISHED|DEPRECATED").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(H,{status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListProtocols.items,{headers:["ID","Name","Status","Version","Est. min"],rows:e.labListProtocols.items.map(n=>[d(n.id,12),n.name,n.status,String(n.version),n.estimatedMinutes!=null?String(n.estimatedMinutes):"-"])});}catch(e){i(e);}}),r.command("get").description("Get a protocol by id").argument("<id>","Protocol ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(G,{id:t});if(!n.labProtocol)throw new u(`Protocol ${t} not found`);s(e,n.labProtocol);}catch(n){i(n);}}),r.command("create").description("Create a protocol").requiredOption("--name <name>","Protocol name").option("--summary <s>","Summary").option("--author <id>","Author user ID").option("--estimated-minutes <n>","Estimated minutes",p).option("--materials <csv>","Comma-separated materials").option("--safety-notes <s>","Safety notes").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.summary&&(e.summary=t.summary),t.author&&(e.authorId=t.author),t.estimatedMinutes!==void 0&&(e.estimatedMinutes=t.estimatedMinutes),t.materials&&(e.materials=l(t.materials)),t.safetyNotes&&(e.safetyNotes=t.safetyNotes),t.tags&&(e.tags=l(t.tags));let n=await a(z,{input:e});c(`Protocol created: ${n.labCreateProtocol.name}`),s(t,n.labCreateProtocol);}catch(e){i(e);}}),r.command("update").description("Update a protocol").argument("<id>","Protocol ID").option("--name <name>","Protocol name").option("--summary <s>","Summary").option("--estimated-minutes <n>","Estimated minutes",p).option("--materials <csv>","Comma-separated materials").option("--safety-notes <s>","Safety notes").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.name&&(n.name=e.name),e.summary!==void 0&&(n.summary=e.summary),e.estimatedMinutes!==void 0&&(n.estimatedMinutes=e.estimatedMinutes),e.materials&&(n.materials=l(e.materials)),e.safetyNotes!==void 0&&(n.safetyNotes=e.safetyNotes),e.tags&&(n.tags=l(e.tags)),!Object.keys(n).length)throw new u("No updates specified");let f=await a(J,{id:t,input:n});c("Protocol updated"),s(e,f.labUpdateProtocol);}catch(n){i(n);}}),r.command("publish").description("Publish a draft protocol, freezing its version").argument("<id>","Protocol ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(K,{id:t});c(`Protocol published: v${n.labPublishProtocol.version}`),s(e,n.labPublishProtocol);}catch(n){i(n);}}),r.command("add-step").description("Append a step to a protocol").requiredOption("--protocol <id>","Protocol ID").requiredOption("--instruction <s>","Step instruction").option("--kind <k>","PREPARATION|INCUBATION|MEASUREMENT|ANALYSIS|CLEANUP|SAFETY","PREPARATION").option("--ordinal <n>","Step ordinal",p).option("--duration-minutes <n>","Duration (minutes)",p).option("--critical","Mark step as critical").option("-f, --format <format>","Output format").action(async t=>{try{let e={protocolId:t.protocol,instruction:t.instruction,kind:(t.kind??"PREPARATION").toUpperCase()};t.ordinal!==void 0&&(e.ordinal=t.ordinal),t.durationMinutes!==void 0&&(e.durationMinutes=t.durationMinutes),t.critical&&(e.isCritical=!0);let n=await a(Y,{input:e});c(`Step added at ordinal ${n.labAddProtocolStep.ordinal}`),s(t,n.labAddProtocolStep);}catch(e){i(e);}});}function wt(o){let r=o.command("datasets").description("Labsofscience versioned datasets");r.command("list").description("List datasets").option("--kind <k>","RAW|PROCESSED|RESULT|REFERENCE").option("--status <s>","ACTIVE|LOCKED|ARCHIVED").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(X,{kind:t.kind?t.kind.toUpperCase():void 0,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListDatasets.items,{headers:["ID","Name","Kind","Status","Latest v"],rows:e.labListDatasets.items.map(n=>[d(n.id,12),n.name,n.kind,n.status,String(n.latestVersion)])});}catch(e){i(e);}}),r.command("get").description("Get a dataset by id").argument("<id>","Dataset ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(Q,{id:t});if(!n.labDataset)throw new u(`Dataset ${t} not found`);s(e,n.labDataset);}catch(n){i(n);}}),r.command("create").description("Create a dataset").requiredOption("--name <name>","Dataset name").option("--description <s>","Description").option("--kind <k>","RAW|PROCESSED|RESULT|REFERENCE","RAW").option("--experiment <id>","Experiment ID").option("--project <id>","Project ID").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,kind:(t.kind??"RAW").toUpperCase()};t.description&&(e.description=t.description),t.experiment&&(e.experimentId=t.experiment),t.project&&(e.projectId=t.project),t.tags&&(e.tags=l(t.tags));let n=await a(Z,{input:e});c(`Dataset created: ${n.labCreateDataset.name}`),s(t,n.labCreateDataset);}catch(e){i(e);}}),r.command("add-version").description("Append an immutable version to a dataset").requiredOption("--dataset <id>","Dataset ID").option("--file <id>","wspace-files-svc File id holding the snapshot bytes").option("--size-bytes <s>","Size in bytes").option("--row-count <n>","Row count",p).option("--checksum <s>","Checksum").option("--change-note <s>","Change note").option("-f, --format <format>","Output format").action(async t=>{try{let e={datasetId:t.dataset};t.file&&(e.fileId=t.file),t.sizeBytes&&(e.sizeBytes=t.sizeBytes),t.rowCount!==void 0&&(e.rowCount=t.rowCount),t.checksum&&(e.checksum=t.checksum),t.changeNote&&(e.changeNote=t.changeNote);let n=await a(tt,{input:e});c(`Dataset version added: v${n.labAddDatasetVersion.version}`),s(t,n.labAddDatasetVersion);}catch(e){i(e);}}),r.command("archive").description("Archive a dataset").argument("<id>","Dataset ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(et,{id:t});c(`Dataset archived: ${n.labArchiveDataset}`),s(e,{archived:n.labArchiveDataset});}catch(n){i(n);}});}function Lt(o){let r=o.command("pipelines").description("Labsofscience reproducible analysis pipelines");r.command("list").description("List analysis pipelines").option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(nt);s(t,e.labListPipelines,{headers:["ID","Name","Engine","Version","Active"],rows:e.labListPipelines.map(n=>[d(n.id,12),n.name,n.engine,String(n.version),n.isActive?"yes":"no"])});}catch(e){i(e);}}),r.command("create").description("Create an analysis pipeline").requiredOption("--name <name>","Pipeline name").option("--description <s>","Description").option("--engine <s>","Execution engine").option("--project <id>","Project ID").option("--definition <json>","Pipeline definition JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.description&&(e.description=t.description),t.engine&&(e.engine=t.engine),t.project&&(e.projectId=t.project),t.definition&&(e.definition=b("definition",t.definition)),t.tags&&(e.tags=l(t.tags));let n=await a(rt,{input:e});c(`Pipeline created: ${n.labCreatePipeline.name}`),s(t,n.labCreatePipeline);}catch(e){i(e);}}),r.command("run").description("Queue a reproducible pipeline run over a dataset version").requiredOption("--pipeline <id>","Pipeline ID").option("--dataset <id>","Dataset ID").option("--dataset-version <id>","Dataset version ID").option("--parameters <json>","Parameters JSON").option("-f, --format <format>","Output format").action(async t=>{try{let e={pipelineId:t.pipeline};t.dataset&&(e.datasetId=t.dataset),t.datasetVersion&&(e.datasetVersionId=t.datasetVersion),t.parameters&&(e.parameters=b("parameters",t.parameters));let n=await a(ot,{input:e});c(`Pipeline run queued: ${n.labRunPipeline.status}`),s(t,n.labRunPipeline);}catch(e){i(e);}}),r.command("list-runs").description("List pipeline runs").option("--pipeline <id>","Filter by pipeline ID").option("--status <s>","QUEUED|RUNNING|SUCCEEDED|FAILED|CANCELLED").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(it,{pipelineId:t.pipeline,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListPipelineRuns.items,{headers:["ID","Pipeline","Status","Started","Finished"],rows:e.labListPipelineRuns.items.map(n=>[d(n.id,12),d(n.pipelineId,12),n.status,E(n.startedAt),E(n.finishedAt)])});}catch(e){i(e);}}),r.command("transition-run").description("Advance a pipeline run through its execution lifecycle").argument("<id>","Pipeline run ID").requiredOption("--status <s>","QUEUED|RUNNING|SUCCEEDED|FAILED|CANCELLED").option("--log <s>","Execution log").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(st,{id:t,status:e.status.toUpperCase(),log:e.log});c(`Pipeline run moved to ${n.labTransitionPipelineRun.status}`),s(e,n.labTransitionPipelineRun);}catch(n){i(n);}});}function kt(o){let r=o.command("inventory").description("Labsofscience lab inventory (reagents, samples, consumables)");r.command("list").description("List inventory items").option("--category <c>","REAGENT|CHEMICAL|BIOLOGICAL|CONSUMABLE|EQUIPMENT_PART|SAMPLE").option("--status <s>","IN_STOCK|LOW|OUT_OF_STOCK|EXPIRED|QUARANTINED").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(ct,{category:t.category?t.category.toUpperCase():void 0,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListInventoryItems.items,{headers:["ID","Name","Category","Status","Qty","Unit"],rows:e.labListInventoryItems.items.map(n=>[d(n.id,12),n.name,n.category,n.status,String(n.quantity),n.unit])});}catch(e){i(e);}}),r.command("get").description("Get an inventory item by id").argument("<id>","Inventory item ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(at,{id:t});if(!n.labInventoryItem)throw new u(`Inventory item ${t} not found`);s(e,n.labInventoryItem);}catch(n){i(n);}}),r.command("create").description("Create an inventory item").requiredOption("--name <name>","Item name").option("--category <c>","REAGENT|CHEMICAL|BIOLOGICAL|CONSUMABLE|EQUIPMENT_PART|SAMPLE","REAGENT").option("--quantity <n>","Quantity",A).option("--unit <s>","Unit of measure").option("--reorder-level <n>","Reorder level",A).option("--location <s>","Storage location").option("--vendor <s>","Vendor").option("--catalog-number <s>","Catalog number").option("--lot-number <s>","Lot number").option("--expires-at <iso>","Expiry date (ISO)").option("--sds-file <id>","wspace-files-svc File id for the SDS").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,category:(t.category??"REAGENT").toUpperCase()};t.quantity!==void 0&&(e.quantity=t.quantity),t.unit&&(e.unit=t.unit),t.reorderLevel!==void 0&&(e.reorderLevel=t.reorderLevel),t.location&&(e.location=t.location),t.vendor&&(e.vendor=t.vendor),t.catalogNumber&&(e.catalogNumber=t.catalogNumber),t.lotNumber&&(e.lotNumber=t.lotNumber),t.expiresAt&&(e.expiresAt=t.expiresAt),t.sdsFile&&(e.sdsFileId=t.sdsFile),t.tags&&(e.tags=l(t.tags));let n=await a(pt,{input:e});c(`Inventory item created: ${n.labCreateInventoryItem.name}`),s(t,n.labCreateInventoryItem);}catch(e){i(e);}}),r.command("adjust").description("Apply a signed quantity delta and recompute stock status").argument("<id>","Inventory item ID").requiredOption("--delta <n>","Signed quantity delta (positive = restock)",A).option("--reason <s>","Reason for adjustment").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={delta:e.delta};e.reason&&(n.reason=e.reason);let f=await a(ut,{id:t,input:n});c(`Inventory adjusted: ${f.labAdjustInventory.quantity} ${f.labAdjustInventory.unit}`),s(e,f.labAdjustInventory);}catch(n){i(n);}}),r.command("archive").description("Archive an inventory item").argument("<id>","Inventory item ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(dt,{id:t});c(`Inventory item archived: ${n.labArchiveInventoryItem}`),s(e,{archived:n.labArchiveInventoryItem});}catch(n){i(n);}});}function xt(o){let r=o.command("instruments").description("Labsofscience instruments & bookings");r.command("list").description("List instruments").option("--status <s>","AVAILABLE|IN_USE|MAINTENANCE|OFFLINE").option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(lt,{status:t.status?t.status.toUpperCase():void 0});s(t,e.labListInstruments,{headers:["ID","Name","Model","Location","Status","Approval"],rows:e.labListInstruments.map(n=>[d(n.id,12),n.name,n.model??"-",n.location??"-",n.status,n.requiresApproval?"yes":"no"])});}catch(e){i(e);}}),r.command("get").description("Get an instrument by id").argument("<id>","Instrument ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(mt,{id:t});if(!n.labInstrument)throw new u(`Instrument ${t} not found`);s(e,n.labInstrument);}catch(n){i(n);}}),r.command("create").description("Create an instrument").requiredOption("--name <name>","Instrument name").option("--model <s>","Model").option("--location <s>","Location").option("--custodian <id>","Custodian user ID").option("--requires-approval","Bookings require approval").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.model&&(e.model=t.model),t.location&&(e.location=t.location),t.custodian&&(e.custodianId=t.custodian),t.requiresApproval&&(e.requiresApproval=!0),t.tags&&(e.tags=l(t.tags));let n=await a(gt,{input:e});c(`Instrument created: ${n.labCreateInstrument.name}`),s(t,n.labCreateInstrument);}catch(e){i(e);}}),r.command("book").description("Reserve an instrument for a time window").requiredOption("--instrument <id>","Instrument ID").requiredOption("--start <iso>","Start time (ISO)").requiredOption("--end <iso>","End time (ISO)").option("--experiment <id>","Experiment ID").option("--purpose <s>","Booking purpose").option("-f, --format <format>","Output format").action(async t=>{try{let e={instrumentId:t.instrument,startTime:t.start,endTime:t.end};t.experiment&&(e.experimentId=t.experiment),t.purpose&&(e.purpose=t.purpose);let n=await a(ft,{input:e});c(`Instrument booked: ${n.labBookInstrument.status}`),s(t,n.labBookInstrument);}catch(e){i(e);}}),r.command("cancel-booking").description("Cancel an instrument booking").argument("<id>","Booking ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(It,{id:t});c(`Booking cancelled: ${n.labCancelBooking.status}`),s(e,n.labCancelBooking);}catch(n){i(n);}});}function vt(o){o.command("health").description("Labsofscience service health check (public)").option("-f, --format <format>","Output format").action(async r=>{try{let t=await k(bt);c(t.labHealth),s(r,{health:t.labHealth});}catch(t){i(t);}});}var Ut={id:"labsofscience",version:"1.0.0",displayName:"Labsofscience",dependsOn:["auth","workspaces"],register(o,r){T(r);let t=o.command("labsofscience").description("Labsofscience science & discovery platform");yt(t),Ct(t),Et(t),ht(t),At(t),wt(t),Lt(t),kt(t),xt(t),vt(t);}},jn=Ut;module.exports=jn;
+`;function b(o,r){try{return JSON.parse(r)}catch{throw new u(`--${o} must be valid JSON`)}}function p(o){let r=Number.parseInt(o,10);if(Number.isNaN(r))throw new u(`Expected an integer but got "${o}"`);return r}function A(o){let r=Number.parseFloat(o);if(Number.isNaN(r))throw new u(`Expected a number but got "${o}"`);return r}function l(o){return o.split(",").map(r=>r.trim()).filter(r=>r.length>0)}function g(o,r){return {limit:o,offset:r}}function yt(o){let r=o.command("projects").description("Labsofscience research projects");r.command("list").description("List research projects").option("--status <s>","Filter by project status").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(P,{status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListProjects.items,{headers:["ID","Name","Code","Field","Status","Visibility"],rows:e.labListProjects.items.map(n=>[d(n.id,12),n.name,n.code??"-",n.field??"-",n.status,n.visibility])});}catch(e){i(e);}}),r.command("get").description("Get a research project by id").argument("<id>","Project ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(R,{id:t});if(!n.labProject)throw new u(`Project ${t} not found`);s(e,n.labProject);}catch(n){i(n);}}),r.command("create").description("Create a research project").requiredOption("--name <name>","Project name").option("--code <code>","Project code").option("--description <s>","Description").option("--field <s>","Research field").option("--pi <id>","Principal investigator user ID").option("--start-date <iso>","Start date (ISO)").option("--end-date <iso>","End date (ISO)").option("--status <s>","PLANNING|ACTIVE|ON_HOLD|COMPLETED|ARCHIVED","PLANNING").option("--visibility <v>","PRIVATE|WORKSPACE|PUBLIC","WORKSPACE").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,status:(t.status??"PLANNING").toUpperCase(),visibility:(t.visibility??"WORKSPACE").toUpperCase()};t.code&&(e.code=t.code),t.description&&(e.description=t.description),t.field&&(e.field=t.field),t.pi&&(e.principalInvestigatorId=t.pi),t.startDate&&(e.startDate=t.startDate),t.endDate&&(e.endDate=t.endDate),t.tags&&(e.tags=l(t.tags));let n=await a(O,{input:e});c(`Project created: ${n.labCreateProject.name}`),s(t,n.labCreateProject);}catch(e){i(e);}}),r.command("update").description("Update a research project").argument("<id>","Project ID").option("--name <name>","Project name").option("--code <code>","Project code").option("--description <s>","Description").option("--field <s>","Research field").option("--pi <id>","Principal investigator user ID").option("--start-date <iso>","Start date (ISO)").option("--end-date <iso>","End date (ISO)").option("--status <s>","Project status").option("--visibility <v>","Visibility").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.name&&(n.name=e.name),e.code&&(n.code=e.code),e.description!==void 0&&(n.description=e.description),e.field&&(n.field=e.field),e.pi&&(n.principalInvestigatorId=e.pi),e.startDate&&(n.startDate=e.startDate),e.endDate&&(n.endDate=e.endDate),e.status&&(n.status=e.status.toUpperCase()),e.visibility&&(n.visibility=e.visibility.toUpperCase()),e.tags&&(n.tags=l(e.tags)),!Object.keys(n).length)throw new u("No updates specified");let f=await a(D,{id:t,input:n});c("Project updated"),s(e,f.labUpdateProject);}catch(n){i(n);}}),r.command("archive").description("Archive a research project").argument("<id>","Project ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(S,{id:t});c(`Project archived: ${n.labArchiveProject}`),s(e,{archived:n.labArchiveProject});}catch(n){i(n);}});}function Ct(o){let r=o.command("experiments").description("Labsofscience experiments");r.command("list").description("List experiments").option("--project <id>","Filter by project ID").option("--status <s>","Filter by experiment status").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(_,{projectId:t.project,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListExperiments.items,{headers:["ID","Title","Status","Project","Lead"],rows:e.labListExperiments.items.map(n=>[d(n.id,12),n.title,n.status,d(n.projectId,12),n.leadResearcherId?d(n.leadResearcherId,12):"-"])});}catch(e){i(e);}}),r.command("get").description("Get an experiment by id").argument("<id>","Experiment ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(N,{id:t});if(!n.labExperiment)throw new u(`Experiment ${t} not found`);s(e,n.labExperiment);}catch(n){i(n);}}),r.command("create").description("Create an experiment").requiredOption("--project <id>","Project ID").requiredOption("--title <t>","Experiment title").option("--description <s>","Description").option("--hypothesis <s>","Hypothesis").option("--lead <id>","Lead researcher user ID").option("--protocol <id>","Protocol ID").option("--variables <json>","Variables JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={projectId:t.project,title:t.title};t.description&&(e.description=t.description),t.hypothesis&&(e.hypothesis=t.hypothesis),t.lead&&(e.leadResearcherId=t.lead),t.protocol&&(e.protocolId=t.protocol),t.variables&&(e.variables=b("variables",t.variables)),t.tags&&(e.tags=l(t.tags));let n=await a($,{input:e});c(`Experiment created: ${n.labCreateExperiment.title}`),s(t,n.labCreateExperiment);}catch(e){i(e);}}),r.command("update").description("Update an experiment").argument("<id>","Experiment ID").option("--title <t>","Experiment title").option("--description <s>","Description").option("--hypothesis <s>","Hypothesis").option("--lead <id>","Lead researcher user ID").option("--protocol <id>","Protocol ID").option("--variables <json>","Variables JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.title&&(n.title=e.title),e.description!==void 0&&(n.description=e.description),e.hypothesis!==void 0&&(n.hypothesis=e.hypothesis),e.lead&&(n.leadResearcherId=e.lead),e.protocol&&(n.protocolId=e.protocol),e.variables&&(n.variables=b("variables",e.variables)),e.tags&&(n.tags=l(e.tags)),!Object.keys(n).length)throw new u("No updates specified");let f=await a(j,{id:t,input:n});c("Experiment updated"),s(e,f.labUpdateExperiment);}catch(n){i(n);}}),r.command("transition").description("Advance an experiment through its lifecycle").argument("<id>","Experiment ID").requiredOption("--status <s>","DESIGN|RUNNING|ANALYSIS|COMPLETE|ABANDONED").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(B,{id:t,status:e.status.toUpperCase()});c(`Experiment moved to ${n.labTransitionExperiment.status}`),s(e,n.labTransitionExperiment);}catch(n){i(n);}});}function Et(o){let r=o.command("runs").description("Labsofscience reproducible experiment runs");r.command("list").description("List experiment runs").option("--experiment <id>","Filter by experiment ID").option("--status <s>","Filter by run status").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(q,{experimentId:t.experiment,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListRuns.items,{headers:["ID","Run #","Status","Experiment","Started","Completed"],rows:e.labListRuns.items.map(n=>[d(n.id,12),String(n.runNumber),n.status,d(n.experimentId,12),E(n.startedAt),E(n.completedAt)])});}catch(e){i(e);}}),r.command("start").description("Start a new reproducible run of an experiment").requiredOption("--experiment <id>","Experiment ID").option("--notes <s>","Run notes").option("--parameters <json>","Parameters JSON").option("-f, --format <format>","Output format").action(async t=>{try{let e={experimentId:t.experiment};t.notes&&(e.notes=t.notes),t.parameters&&(e.parameters=b("parameters",t.parameters));let n=await a(U,{input:e});c(`Run #${n.labStartRun.runNumber} started`),s(t,n.labStartRun);}catch(e){i(e);}}),r.command("complete").description("Record observations and complete a run with a terminal status").argument("<id>","Run ID").requiredOption("--status <s>","SUCCEEDED|FAILED|CANCELLED").option("--notes <s>","Result notes").option("--observations <json>","Observations JSON").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={id:t,status:e.status.toUpperCase()},f={};e.notes&&(f.notes=e.notes),e.observations&&(f.observations=b("observations",e.observations)),Object.keys(f).length&&(n.input=f);let w=await a(M,n);c(`Run #${w.labCompleteRun.runNumber} completed: ${w.labCompleteRun.status}`),s(e,w.labCompleteRun);}catch(n){i(n);}});}function ht(o){let r=o.command("notebook").description("Labsofscience electronic lab notebook (ELN)");r.command("list").description("List notebook entries").option("--experiment <id>","Filter by experiment ID").option("--project <id>","Filter by project ID").option("--status <s>","Filter by entry status").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(F,{experimentId:t.experiment,projectId:t.project,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListNotebookEntries.items,{headers:["ID","Title","Status","Project","Author"],rows:e.labListNotebookEntries.items.map(n=>[d(n.id,12),n.title,n.status,d(n.projectId,12),d(n.authorId,12)])});}catch(e){i(e);}}),r.command("create").description("Create a notebook entry").requiredOption("--project <id>","Project ID").requiredOption("--title <t>","Entry title").option("--body <s>","Entry body").option("--experiment <id>","Experiment ID").option("--run <id>","Run ID").option("--file-ids <csv>","Comma-separated wspace-files-svc File ids").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={projectId:t.project,title:t.title};t.body&&(e.body=t.body),t.experiment&&(e.experimentId=t.experiment),t.run&&(e.runId=t.run),t.fileIds&&(e.fileIds=l(t.fileIds)),t.tags&&(e.tags=l(t.tags));let n=await a(V,{input:e});c(`Notebook entry created: ${n.labCreateNotebookEntry.title}`),s(t,n.labCreateNotebookEntry);}catch(e){i(e);}}),r.command("sign").description("Sign a notebook entry (locks editable content)").argument("<id>","Entry ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(W,{id:t});c(`Notebook entry signed: ${n.labSignNotebookEntry.status}`),s(e,n.labSignNotebookEntry);}catch(n){i(n);}});}function At(o){let r=o.command("protocols").description("Labsofscience versioned protocols");r.command("list").description("List protocols").option("--status <s>","DRAFT|PUBLISHED|DEPRECATED").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(H,{status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListProtocols.items,{headers:["ID","Name","Status","Version","Est. min"],rows:e.labListProtocols.items.map(n=>[d(n.id,12),n.name,n.status,String(n.version),n.estimatedMinutes!=null?String(n.estimatedMinutes):"-"])});}catch(e){i(e);}}),r.command("get").description("Get a protocol by id").argument("<id>","Protocol ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(G,{id:t});if(!n.labProtocol)throw new u(`Protocol ${t} not found`);s(e,n.labProtocol);}catch(n){i(n);}}),r.command("create").description("Create a protocol").requiredOption("--name <name>","Protocol name").option("--summary <s>","Summary").option("--author <id>","Author user ID").option("--estimated-minutes <n>","Estimated minutes",p).option("--materials <csv>","Comma-separated materials").option("--safety-notes <s>","Safety notes").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.summary&&(e.summary=t.summary),t.author&&(e.authorId=t.author),t.estimatedMinutes!==void 0&&(e.estimatedMinutes=t.estimatedMinutes),t.materials&&(e.materials=l(t.materials)),t.safetyNotes&&(e.safetyNotes=t.safetyNotes),t.tags&&(e.tags=l(t.tags));let n=await a(z,{input:e});c(`Protocol created: ${n.labCreateProtocol.name}`),s(t,n.labCreateProtocol);}catch(e){i(e);}}),r.command("update").description("Update a protocol").argument("<id>","Protocol ID").option("--name <name>","Protocol name").option("--summary <s>","Summary").option("--estimated-minutes <n>","Estimated minutes",p).option("--materials <csv>","Comma-separated materials").option("--safety-notes <s>","Safety notes").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.name&&(n.name=e.name),e.summary!==void 0&&(n.summary=e.summary),e.estimatedMinutes!==void 0&&(n.estimatedMinutes=e.estimatedMinutes),e.materials&&(n.materials=l(e.materials)),e.safetyNotes!==void 0&&(n.safetyNotes=e.safetyNotes),e.tags&&(n.tags=l(e.tags)),!Object.keys(n).length)throw new u("No updates specified");let f=await a(J,{id:t,input:n});c("Protocol updated"),s(e,f.labUpdateProtocol);}catch(n){i(n);}}),r.command("publish").description("Publish a draft protocol, freezing its version").argument("<id>","Protocol ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(K,{id:t});c(`Protocol published: v${n.labPublishProtocol.version}`),s(e,n.labPublishProtocol);}catch(n){i(n);}}),r.command("add-step").description("Append a step to a protocol").requiredOption("--protocol <id>","Protocol ID").requiredOption("--instruction <s>","Step instruction").option("--kind <k>","PREPARATION|INCUBATION|MEASUREMENT|ANALYSIS|CLEANUP|SAFETY","PREPARATION").option("--ordinal <n>","Step ordinal",p).option("--duration-minutes <n>","Duration (minutes)",p).option("--critical","Mark step as critical").option("-f, --format <format>","Output format").action(async t=>{try{let e={protocolId:t.protocol,instruction:t.instruction,kind:(t.kind??"PREPARATION").toUpperCase()};t.ordinal!==void 0&&(e.ordinal=t.ordinal),t.durationMinutes!==void 0&&(e.durationMinutes=t.durationMinutes),t.critical&&(e.isCritical=!0);let n=await a(Y,{input:e});c(`Step added at ordinal ${n.labAddProtocolStep.ordinal}`),s(t,n.labAddProtocolStep);}catch(e){i(e);}});}function wt(o){let r=o.command("datasets").description("Labsofscience versioned datasets");r.command("list").description("List datasets").option("--kind <k>","RAW|PROCESSED|RESULT|REFERENCE").option("--status <s>","ACTIVE|LOCKED|ARCHIVED").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(X,{kind:t.kind?t.kind.toUpperCase():void 0,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListDatasets.items,{headers:["ID","Name","Kind","Status","Latest v"],rows:e.labListDatasets.items.map(n=>[d(n.id,12),n.name,n.kind,n.status,String(n.latestVersion)])});}catch(e){i(e);}}),r.command("get").description("Get a dataset by id").argument("<id>","Dataset ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(Q,{id:t});if(!n.labDataset)throw new u(`Dataset ${t} not found`);s(e,n.labDataset);}catch(n){i(n);}}),r.command("create").description("Create a dataset").requiredOption("--name <name>","Dataset name").option("--description <s>","Description").option("--kind <k>","RAW|PROCESSED|RESULT|REFERENCE","RAW").option("--experiment <id>","Experiment ID").option("--project <id>","Project ID").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,kind:(t.kind??"RAW").toUpperCase()};t.description&&(e.description=t.description),t.experiment&&(e.experimentId=t.experiment),t.project&&(e.projectId=t.project),t.tags&&(e.tags=l(t.tags));let n=await a(Z,{input:e});c(`Dataset created: ${n.labCreateDataset.name}`),s(t,n.labCreateDataset);}catch(e){i(e);}}),r.command("add-version").description("Append an immutable version to a dataset").requiredOption("--dataset <id>","Dataset ID").option("--file <id>","wspace-files-svc File id holding the snapshot bytes").option("--size-bytes <s>","Size in bytes").option("--row-count <n>","Row count",p).option("--checksum <s>","Checksum").option("--change-note <s>","Change note").option("-f, --format <format>","Output format").action(async t=>{try{let e={datasetId:t.dataset};t.file&&(e.fileId=t.file),t.sizeBytes&&(e.sizeBytes=t.sizeBytes),t.rowCount!==void 0&&(e.rowCount=t.rowCount),t.checksum&&(e.checksum=t.checksum),t.changeNote&&(e.changeNote=t.changeNote);let n=await a(tt,{input:e});c(`Dataset version added: v${n.labAddDatasetVersion.version}`),s(t,n.labAddDatasetVersion);}catch(e){i(e);}}),r.command("archive").description("Archive a dataset").argument("<id>","Dataset ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(et,{id:t});c(`Dataset archived: ${n.labArchiveDataset}`),s(e,{archived:n.labArchiveDataset});}catch(n){i(n);}});}function Lt(o){let r=o.command("pipelines").description("Labsofscience reproducible analysis pipelines");r.command("list").description("List analysis pipelines").option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(nt);s(t,e.labListPipelines.items,{headers:["ID","Name","Engine","Version","Active"],rows:e.labListPipelines.items.map(n=>[d(n.id,12),n.name,n.engine,String(n.version),n.isActive?"yes":"no"])});}catch(e){i(e);}}),r.command("create").description("Create an analysis pipeline").requiredOption("--name <name>","Pipeline name").option("--description <s>","Description").option("--engine <s>","Execution engine").option("--project <id>","Project ID").option("--definition <json>","Pipeline definition JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.description&&(e.description=t.description),t.engine&&(e.engine=t.engine),t.project&&(e.projectId=t.project),t.definition&&(e.definition=b("definition",t.definition)),t.tags&&(e.tags=l(t.tags));let n=await a(rt,{input:e});c(`Pipeline created: ${n.labCreatePipeline.name}`),s(t,n.labCreatePipeline);}catch(e){i(e);}}),r.command("run").description("Queue a reproducible pipeline run over a dataset version").requiredOption("--pipeline <id>","Pipeline ID").option("--dataset <id>","Dataset ID").option("--dataset-version <id>","Dataset version ID").option("--parameters <json>","Parameters JSON").option("-f, --format <format>","Output format").action(async t=>{try{let e={pipelineId:t.pipeline};t.dataset&&(e.datasetId=t.dataset),t.datasetVersion&&(e.datasetVersionId=t.datasetVersion),t.parameters&&(e.parameters=b("parameters",t.parameters));let n=await a(ot,{input:e});c(`Pipeline run queued: ${n.labRunPipeline.status}`),s(t,n.labRunPipeline);}catch(e){i(e);}}),r.command("list-runs").description("List pipeline runs").option("--pipeline <id>","Filter by pipeline ID").option("--status <s>","QUEUED|RUNNING|SUCCEEDED|FAILED|CANCELLED").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(it,{pipelineId:t.pipeline,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListPipelineRuns.items,{headers:["ID","Pipeline","Status","Started","Finished"],rows:e.labListPipelineRuns.items.map(n=>[d(n.id,12),d(n.pipelineId,12),n.status,E(n.startedAt),E(n.finishedAt)])});}catch(e){i(e);}}),r.command("transition-run").description("Advance a pipeline run through its execution lifecycle").argument("<id>","Pipeline run ID").requiredOption("--status <s>","QUEUED|RUNNING|SUCCEEDED|FAILED|CANCELLED").option("--log <s>","Execution log").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(st,{id:t,status:e.status.toUpperCase(),log:e.log});c(`Pipeline run moved to ${n.labTransitionPipelineRun.status}`),s(e,n.labTransitionPipelineRun);}catch(n){i(n);}});}function kt(o){let r=o.command("inventory").description("Labsofscience lab inventory (reagents, samples, consumables)");r.command("list").description("List inventory items").option("--category <c>","REAGENT|CHEMICAL|BIOLOGICAL|CONSUMABLE|EQUIPMENT_PART|SAMPLE").option("--status <s>","IN_STOCK|LOW|OUT_OF_STOCK|EXPIRED|QUARANTINED").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(ct,{category:t.category?t.category.toUpperCase():void 0,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListInventoryItems.items,{headers:["ID","Name","Category","Status","Qty","Unit"],rows:e.labListInventoryItems.items.map(n=>[d(n.id,12),n.name,n.category,n.status,String(n.quantity),n.unit])});}catch(e){i(e);}}),r.command("get").description("Get an inventory item by id").argument("<id>","Inventory item ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(at,{id:t});if(!n.labInventoryItem)throw new u(`Inventory item ${t} not found`);s(e,n.labInventoryItem);}catch(n){i(n);}}),r.command("create").description("Create an inventory item").requiredOption("--name <name>","Item name").option("--category <c>","REAGENT|CHEMICAL|BIOLOGICAL|CONSUMABLE|EQUIPMENT_PART|SAMPLE","REAGENT").option("--quantity <n>","Quantity",A).option("--unit <s>","Unit of measure").option("--reorder-level <n>","Reorder level",A).option("--location <s>","Storage location").option("--vendor <s>","Vendor").option("--catalog-number <s>","Catalog number").option("--lot-number <s>","Lot number").option("--expires-at <iso>","Expiry date (ISO)").option("--sds-file <id>","wspace-files-svc File id for the SDS").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,category:(t.category??"REAGENT").toUpperCase()};t.quantity!==void 0&&(e.quantity=t.quantity),t.unit&&(e.unit=t.unit),t.reorderLevel!==void 0&&(e.reorderLevel=t.reorderLevel),t.location&&(e.location=t.location),t.vendor&&(e.vendor=t.vendor),t.catalogNumber&&(e.catalogNumber=t.catalogNumber),t.lotNumber&&(e.lotNumber=t.lotNumber),t.expiresAt&&(e.expiresAt=t.expiresAt),t.sdsFile&&(e.sdsFileId=t.sdsFile),t.tags&&(e.tags=l(t.tags));let n=await a(pt,{input:e});c(`Inventory item created: ${n.labCreateInventoryItem.name}`),s(t,n.labCreateInventoryItem);}catch(e){i(e);}}),r.command("adjust").description("Apply a signed quantity delta and recompute stock status").argument("<id>","Inventory item ID").requiredOption("--delta <n>","Signed quantity delta (positive = restock)",A).option("--reason <s>","Reason for adjustment").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={delta:e.delta};e.reason&&(n.reason=e.reason);let f=await a(ut,{id:t,input:n});c(`Inventory adjusted: ${f.labAdjustInventory.quantity} ${f.labAdjustInventory.unit}`),s(e,f.labAdjustInventory);}catch(n){i(n);}}),r.command("archive").description("Archive an inventory item").argument("<id>","Inventory item ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(dt,{id:t});c(`Inventory item archived: ${n.labArchiveInventoryItem}`),s(e,{archived:n.labArchiveInventoryItem});}catch(n){i(n);}});}function xt(o){let r=o.command("instruments").description("Labsofscience instruments & bookings");r.command("list").description("List instruments").option("--status <s>","AVAILABLE|IN_USE|MAINTENANCE|OFFLINE").option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(lt,{status:t.status?t.status.toUpperCase():void 0});s(t,e.labListInstruments.items,{headers:["ID","Name","Model","Location","Status","Approval"],rows:e.labListInstruments.items.map(n=>[d(n.id,12),n.name,n.model??"-",n.location??"-",n.status,n.requiresApproval?"yes":"no"])});}catch(e){i(e);}}),r.command("get").description("Get an instrument by id").argument("<id>","Instrument ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(mt,{id:t});if(!n.labInstrument)throw new u(`Instrument ${t} not found`);s(e,n.labInstrument);}catch(n){i(n);}}),r.command("create").description("Create an instrument").requiredOption("--name <name>","Instrument name").option("--model <s>","Model").option("--location <s>","Location").option("--custodian <id>","Custodian user ID").option("--requires-approval","Bookings require approval").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.model&&(e.model=t.model),t.location&&(e.location=t.location),t.custodian&&(e.custodianId=t.custodian),t.requiresApproval&&(e.requiresApproval=!0),t.tags&&(e.tags=l(t.tags));let n=await a(gt,{input:e});c(`Instrument created: ${n.labCreateInstrument.name}`),s(t,n.labCreateInstrument);}catch(e){i(e);}}),r.command("book").description("Reserve an instrument for a time window").requiredOption("--instrument <id>","Instrument ID").requiredOption("--start <iso>","Start time (ISO)").requiredOption("--end <iso>","End time (ISO)").option("--experiment <id>","Experiment ID").option("--purpose <s>","Booking purpose").option("-f, --format <format>","Output format").action(async t=>{try{let e={instrumentId:t.instrument,startTime:t.start,endTime:t.end};t.experiment&&(e.experimentId=t.experiment),t.purpose&&(e.purpose=t.purpose);let n=await a(ft,{input:e});c(`Instrument booked: ${n.labBookInstrument.status}`),s(t,n.labBookInstrument);}catch(e){i(e);}}),r.command("cancel-booking").description("Cancel an instrument booking").argument("<id>","Booking ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(It,{id:t});c(`Booking cancelled: ${n.labCancelBooking.status}`),s(e,n.labCancelBooking);}catch(n){i(n);}});}function vt(o){o.command("health").description("Labsofscience service health check (public)").option("-f, --format <format>","Output format").action(async r=>{try{let t=await k(bt);c(t.labHealth),s(r,{health:t.labHealth});}catch(t){i(t);}});}var Ut={id:"labsofscience",version:"1.0.0",displayName:"Labsofscience",dependsOn:["auth","workspaces"],register(o,r){T(r);let t=o.command("labsofscience").description("Labsofscience science & discovery platform");yt(t),Ct(t),Et(t),ht(t),At(t),wt(t),Lt(t),kt(t),xt(t),vt(t);}},jn=Ut;module.exports=jn;

package/dist/modules/labsofscience/index.js

@@ -1,4 +1,4 @@
-import {a,b,h as h$1,p,g,i,o as o$1,d as d$1}from'../../chunk-W4JZR7RJ.js';import {o}from'../../chunk-YIY5IDXQ.js';var P=`
+import {a,b,i,r,h as h$1,k as k$1,q as q$1,d as d$1}from'../../chunk-O6UCQ5IT.js';import {o}from'../../chunk-YIY5IDXQ.js';var P=`
   query LabProject($id: ID!) {
     labProject(id: $id) {
       id workspaceId name code description field status visibility
@@ -220,8 +220,11 @@ import {a,b,h as h$1,p,g,i,o as o$1,d as d$1}from'../../chunk-W4JZR7RJ.js';impor
 `,X=`
   query LabListPipelines {
     labListPipelines {
-      id workspaceId projectId name description engine version isActive
-      definition tags createdAt updatedAt
+      items {
+        id workspaceId projectId name description engine version isActive definition tags
+        createdAt updatedAt
+      }
+      pageInfo { cursor hasMore }
     }
   }
 `,Q=`
@@ -313,7 +316,8 @@ import {a,b,h as h$1,p,g,i,o as o$1,d as d$1}from'../../chunk-W4JZR7RJ.js';impor
 `,pt=`
   query LabListInstruments($status: LabInstrumentStatus) {
     labListInstruments(status: $status) {
-      id name model location status requiresApproval custodianId tags createdAt
+      items { id name model location status requiresApproval custodianId tags createdAt }
+      pageInfo { cursor hasMore }
     }
   }
 `,dt=`
@@ -340,4 +344,4 @@ import {a,b,h as h$1,p,g,i,o as o$1,d as d$1}from'../../chunk-W4JZR7RJ.js';impor
   query LabHealth {
     labHealth
   }
-`;function y(p,i){try{return JSON.parse(i)}catch{throw new o(`--${p} must be valid JSON`)}}function d(p){let i=Number.parseInt(p,10);if(Number.isNaN(i))throw new o(`Expected an integer but got "${p}"`);return i}function A(p){let i=Number.parseFloat(p);if(Number.isNaN(i))throw new o(`Expected a number but got "${p}"`);return i}function c(p){return p.split(",").map(i=>i.trim()).filter(i=>i.length>0)}function l(p,i){return {limit:p,offset:i}}function lt(p$1){let i$1=p$1.command("projects").description("Labsofscience research projects");i$1.command("list").description("List research projects").option("--status <s>","Filter by project status").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(h,{status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});h$1(t,e.labListProjects.items,{headers:["ID","Name","Code","Field","Status","Visibility"],rows:e.labListProjects.items.map(n=>[p(n.id,12),n.name,n.code??"-",n.field??"-",n.status,n.visibility])});}catch(e){g(e);}}),i$1.command("get").description("Get a research project by id").argument("<id>","Project ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(P,{id:t});if(!n.labProject)throw new o(`Project ${t} not found`);h$1(e,n.labProject);}catch(n){g(n);}}),i$1.command("create").description("Create a research project").requiredOption("--name <name>","Project name").option("--code <code>","Project code").option("--description <s>","Description").option("--field <s>","Research field").option("--pi <id>","Principal investigator user ID").option("--start-date <iso>","Start date (ISO)").option("--end-date <iso>","End date (ISO)").option("--status <s>","PLANNING|ACTIVE|ON_HOLD|COMPLETED|ARCHIVED","PLANNING").option("--visibility <v>","PRIVATE|WORKSPACE|PUBLIC","WORKSPACE").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,status:(t.status??"PLANNING").toUpperCase(),visibility:(t.visibility??"WORKSPACE").toUpperCase()};t.code&&(e.code=t.code),t.description&&(e.description=t.description),t.field&&(e.field=t.field),t.pi&&(e.principalInvestigatorId=t.pi),t.startDate&&(e.startDate=t.startDate),t.endDate&&(e.endDate=t.endDate),t.tags&&(e.tags=c(t.tags));let n=await b(N,{input:e});i(`Project created: ${n.labCreateProject.name}`),h$1(t,n.labCreateProject);}catch(e){g(e);}}),i$1.command("update").description("Update a research project").argument("<id>","Project ID").option("--name <name>","Project name").option("--code <code>","Project code").option("--description <s>","Description").option("--field <s>","Research field").option("--pi <id>","Principal investigator user ID").option("--start-date <iso>","Start date (ISO)").option("--end-date <iso>","End date (ISO)").option("--status <s>","Project status").option("--visibility <v>","Visibility").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.name&&(n.name=e.name),e.code&&(n.code=e.code),e.description!==void 0&&(n.description=e.description),e.field&&(n.field=e.field),e.pi&&(n.principalInvestigatorId=e.pi),e.startDate&&(n.startDate=e.startDate),e.endDate&&(n.endDate=e.endDate),e.status&&(n.status=e.status.toUpperCase()),e.visibility&&(n.visibility=e.visibility.toUpperCase()),e.tags&&(n.tags=c(e.tags)),!Object.keys(n).length)throw new o("No updates specified");let g=await b(v,{id:t,input:n});i("Project updated"),h$1(e,g.labUpdateProject);}catch(n){g(n);}}),i$1.command("archive").description("Archive a research project").argument("<id>","Project ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(O,{id:t});i(`Project archived: ${n.labArchiveProject}`),h$1(e,{archived:n.labArchiveProject});}catch(n){g(n);}});}function gt(p$1){let i$1=p$1.command("experiments").description("Labsofscience experiments");i$1.command("list").description("List experiments").option("--project <id>","Filter by project ID").option("--status <s>","Filter by experiment status").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(T,{projectId:t.project,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});h$1(t,e.labListExperiments.items,{headers:["ID","Title","Status","Project","Lead"],rows:e.labListExperiments.items.map(n=>[p(n.id,12),n.title,n.status,p(n.projectId,12),n.leadResearcherId?p(n.leadResearcherId,12):"-"])});}catch(e){g(e);}}),i$1.command("get").description("Get an experiment by id").argument("<id>","Experiment ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(D,{id:t});if(!n.labExperiment)throw new o(`Experiment ${t} not found`);h$1(e,n.labExperiment);}catch(n){g(n);}}),i$1.command("create").description("Create an experiment").requiredOption("--project <id>","Project ID").requiredOption("--title <t>","Experiment title").option("--description <s>","Description").option("--hypothesis <s>","Hypothesis").option("--lead <id>","Lead researcher user ID").option("--protocol <id>","Protocol ID").option("--variables <json>","Variables JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={projectId:t.project,title:t.title};t.description&&(e.description=t.description),t.hypothesis&&(e.hypothesis=t.hypothesis),t.lead&&(e.leadResearcherId=t.lead),t.protocol&&(e.protocolId=t.protocol),t.variables&&(e.variables=y("variables",t.variables)),t.tags&&(e.tags=c(t.tags));let n=await b(w,{input:e});i(`Experiment created: ${n.labCreateExperiment.title}`),h$1(t,n.labCreateExperiment);}catch(e){g(e);}}),i$1.command("update").description("Update an experiment").argument("<id>","Experiment ID").option("--title <t>","Experiment title").option("--description <s>","Description").option("--hypothesis <s>","Hypothesis").option("--lead <id>","Lead researcher user ID").option("--protocol <id>","Protocol ID").option("--variables <json>","Variables JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.title&&(n.title=e.title),e.description!==void 0&&(n.description=e.description),e.hypothesis!==void 0&&(n.hypothesis=e.hypothesis),e.lead&&(n.leadResearcherId=e.lead),e.protocol&&(n.protocolId=e.protocol),e.variables&&(n.variables=y("variables",e.variables)),e.tags&&(n.tags=c(e.tags)),!Object.keys(n).length)throw new o("No updates specified");let g=await b(S,{id:t,input:n});i("Experiment updated"),h$1(e,g.labUpdateExperiment);}catch(n){g(n);}}),i$1.command("transition").description("Advance an experiment through its lifecycle").argument("<id>","Experiment ID").requiredOption("--status <s>","DESIGN|RUNNING|ANALYSIS|COMPLETE|ABANDONED").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(_,{id:t,status:e.status.toUpperCase()});i(`Experiment moved to ${n.labTransitionExperiment.status}`),h$1(e,n.labTransitionExperiment);}catch(n){g(n);}});}function ft(p$1){let i$1=p$1.command("runs").description("Labsofscience reproducible experiment runs");i$1.command("list").description("List experiment runs").option("--experiment <id>","Filter by experiment ID").option("--status <s>","Filter by run status").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(x,{experimentId:t.experiment,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});h$1(t,e.labListRuns.items,{headers:["ID","Run #","Status","Experiment","Started","Completed"],rows:e.labListRuns.items.map(n=>[p(n.id,12),String(n.runNumber),n.status,p(n.experimentId,12),o$1(n.startedAt),o$1(n.completedAt)])});}catch(e){g(e);}}),i$1.command("start").description("Start a new reproducible run of an experiment").requiredOption("--experiment <id>","Experiment ID").option("--notes <s>","Run notes").option("--parameters <json>","Parameters JSON").option("-f, --format <format>","Output format").action(async t=>{try{let e={experimentId:t.experiment};t.notes&&(e.notes=t.notes),t.parameters&&(e.parameters=y("parameters",t.parameters));let n=await b(k,{input:e});i(`Run #${n.labStartRun.runNumber} started`),h$1(t,n.labStartRun);}catch(e){g(e);}}),i$1.command("complete").description("Record observations and complete a run with a terminal status").argument("<id>","Run ID").requiredOption("--status <s>","SUCCEEDED|FAILED|CANCELLED").option("--notes <s>","Result notes").option("--observations <json>","Observations JSON").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={id:t,status:e.status.toUpperCase()},g={};e.notes&&(g.notes=e.notes),e.observations&&(g.observations=y("observations",e.observations)),Object.keys(g).length&&(n.input=g);let L=await b($,n);i(`Run #${L.labCompleteRun.runNumber} completed: ${L.labCompleteRun.status}`),h$1(e,L.labCompleteRun);}catch(n){g(n);}});}function It(p$1){let i$1=p$1.command("notebook").description("Labsofscience electronic lab notebook (ELN)");i$1.command("list").description("List notebook entries").option("--experiment <id>","Filter by experiment ID").option("--project <id>","Filter by project ID").option("--status <s>","Filter by entry status").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(B,{experimentId:t.experiment,projectId:t.project,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});h$1(t,e.labListNotebookEntries.items,{headers:["ID","Title","Status","Project","Author"],rows:e.labListNotebookEntries.items.map(n=>[p(n.id,12),n.title,n.status,p(n.projectId,12),p(n.authorId,12)])});}catch(e){g(e);}}),i$1.command("create").description("Create a notebook entry").requiredOption("--project <id>","Project ID").requiredOption("--title <t>","Entry title").option("--body <s>","Entry body").option("--experiment <id>","Experiment ID").option("--run <id>","Run ID").option("--file-ids <csv>","Comma-separated wspace-files-svc File ids").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={projectId:t.project,title:t.title};t.body&&(e.body=t.body),t.experiment&&(e.experimentId=t.experiment),t.run&&(e.runId=t.run),t.fileIds&&(e.fileIds=c(t.fileIds)),t.tags&&(e.tags=c(t.tags));let n=await b(j,{input:e});i(`Notebook entry created: ${n.labCreateNotebookEntry.title}`),h$1(t,n.labCreateNotebookEntry);}catch(e){g(e);}}),i$1.command("sign").description("Sign a notebook entry (locks editable content)").argument("<id>","Entry ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(U,{id:t});i(`Notebook entry signed: ${n.labSignNotebookEntry.status}`),h$1(e,n.labSignNotebookEntry);}catch(n){g(n);}});}function bt(p$1){let i$1=p$1.command("protocols").description("Labsofscience versioned protocols");i$1.command("list").description("List protocols").option("--status <s>","DRAFT|PUBLISHED|DEPRECATED").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(q,{status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});h$1(t,e.labListProtocols.items,{headers:["ID","Name","Status","Version","Est. min"],rows:e.labListProtocols.items.map(n=>[p(n.id,12),n.name,n.status,String(n.version),n.estimatedMinutes!=null?String(n.estimatedMinutes):"-"])});}catch(e){g(e);}}),i$1.command("get").description("Get a protocol by id").argument("<id>","Protocol ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(M,{id:t});if(!n.labProtocol)throw new o(`Protocol ${t} not found`);h$1(e,n.labProtocol);}catch(n){g(n);}}),i$1.command("create").description("Create a protocol").requiredOption("--name <name>","Protocol name").option("--summary <s>","Summary").option("--author <id>","Author user ID").option("--estimated-minutes <n>","Estimated minutes",d).option("--materials <csv>","Comma-separated materials").option("--safety-notes <s>","Safety notes").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.summary&&(e.summary=t.summary),t.author&&(e.authorId=t.author),t.estimatedMinutes!==void 0&&(e.estimatedMinutes=t.estimatedMinutes),t.materials&&(e.materials=c(t.materials)),t.safetyNotes&&(e.safetyNotes=t.safetyNotes),t.tags&&(e.tags=c(t.tags));let n=await b(V,{input:e});i(`Protocol created: ${n.labCreateProtocol.name}`),h$1(t,n.labCreateProtocol);}catch(e){g(e);}}),i$1.command("update").description("Update a protocol").argument("<id>","Protocol ID").option("--name <name>","Protocol name").option("--summary <s>","Summary").option("--estimated-minutes <n>","Estimated minutes",d).option("--materials <csv>","Comma-separated materials").option("--safety-notes <s>","Safety notes").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.name&&(n.name=e.name),e.summary!==void 0&&(n.summary=e.summary),e.estimatedMinutes!==void 0&&(n.estimatedMinutes=e.estimatedMinutes),e.materials&&(n.materials=c(e.materials)),e.safetyNotes!==void 0&&(n.safetyNotes=e.safetyNotes),e.tags&&(n.tags=c(e.tags)),!Object.keys(n).length)throw new o("No updates specified");let g=await b(F,{id:t,input:n});i("Protocol updated"),h$1(e,g.labUpdateProtocol);}catch(n){g(n);}}),i$1.command("publish").description("Publish a draft protocol, freezing its version").argument("<id>","Protocol ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(H,{id:t});i(`Protocol published: v${n.labPublishProtocol.version}`),h$1(e,n.labPublishProtocol);}catch(n){g(n);}}),i$1.command("add-step").description("Append a step to a protocol").requiredOption("--protocol <id>","Protocol ID").requiredOption("--instruction <s>","Step instruction").option("--kind <k>","PREPARATION|INCUBATION|MEASUREMENT|ANALYSIS|CLEANUP|SAFETY","PREPARATION").option("--ordinal <n>","Step ordinal",d).option("--duration-minutes <n>","Duration (minutes)",d).option("--critical","Mark step as critical").option("-f, --format <format>","Output format").action(async t=>{try{let e={protocolId:t.protocol,instruction:t.instruction,kind:(t.kind??"PREPARATION").toUpperCase()};t.ordinal!==void 0&&(e.ordinal=t.ordinal),t.durationMinutes!==void 0&&(e.durationMinutes=t.durationMinutes),t.critical&&(e.isCritical=!0);let n=await b(J,{input:e});i(`Step added at ordinal ${n.labAddProtocolStep.ordinal}`),h$1(t,n.labAddProtocolStep);}catch(e){g(e);}});}function yt(p$1){let i$1=p$1.command("datasets").description("Labsofscience versioned datasets");i$1.command("list").description("List datasets").option("--kind <k>","RAW|PROCESSED|RESULT|REFERENCE").option("--status <s>","ACTIVE|LOCKED|ARCHIVED").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(W,{kind:t.kind?t.kind.toUpperCase():void 0,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});h$1(t,e.labListDatasets.items,{headers:["ID","Name","Kind","Status","Latest v"],rows:e.labListDatasets.items.map(n=>[p(n.id,12),n.name,n.kind,n.status,String(n.latestVersion)])});}catch(e){g(e);}}),i$1.command("get").description("Get a dataset by id").argument("<id>","Dataset ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(G,{id:t});if(!n.labDataset)throw new o(`Dataset ${t} not found`);h$1(e,n.labDataset);}catch(n){g(n);}}),i$1.command("create").description("Create a dataset").requiredOption("--name <name>","Dataset name").option("--description <s>","Description").option("--kind <k>","RAW|PROCESSED|RESULT|REFERENCE","RAW").option("--experiment <id>","Experiment ID").option("--project <id>","Project ID").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,kind:(t.kind??"RAW").toUpperCase()};t.description&&(e.description=t.description),t.experiment&&(e.experimentId=t.experiment),t.project&&(e.projectId=t.project),t.tags&&(e.tags=c(t.tags));let n=await b(z,{input:e});i(`Dataset created: ${n.labCreateDataset.name}`),h$1(t,n.labCreateDataset);}catch(e){g(e);}}),i$1.command("add-version").description("Append an immutable version to a dataset").requiredOption("--dataset <id>","Dataset ID").option("--file <id>","wspace-files-svc File id holding the snapshot bytes").option("--size-bytes <s>","Size in bytes").option("--row-count <n>","Row count",d).option("--checksum <s>","Checksum").option("--change-note <s>","Change note").option("-f, --format <format>","Output format").action(async t=>{try{let e={datasetId:t.dataset};t.file&&(e.fileId=t.file),t.sizeBytes&&(e.sizeBytes=t.sizeBytes),t.rowCount!==void 0&&(e.rowCount=t.rowCount),t.checksum&&(e.checksum=t.checksum),t.changeNote&&(e.changeNote=t.changeNote);let n=await b(K,{input:e});i(`Dataset version added: v${n.labAddDatasetVersion.version}`),h$1(t,n.labAddDatasetVersion);}catch(e){g(e);}}),i$1.command("archive").description("Archive a dataset").argument("<id>","Dataset ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(Y,{id:t});i(`Dataset archived: ${n.labArchiveDataset}`),h$1(e,{archived:n.labArchiveDataset});}catch(n){g(n);}});}function Et(p$1){let i$1=p$1.command("pipelines").description("Labsofscience reproducible analysis pipelines");i$1.command("list").description("List analysis pipelines").option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(X);h$1(t,e.labListPipelines,{headers:["ID","Name","Engine","Version","Active"],rows:e.labListPipelines.map(n=>[p(n.id,12),n.name,n.engine,String(n.version),n.isActive?"yes":"no"])});}catch(e){g(e);}}),i$1.command("create").description("Create an analysis pipeline").requiredOption("--name <name>","Pipeline name").option("--description <s>","Description").option("--engine <s>","Execution engine").option("--project <id>","Project ID").option("--definition <json>","Pipeline definition JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.description&&(e.description=t.description),t.engine&&(e.engine=t.engine),t.project&&(e.projectId=t.project),t.definition&&(e.definition=y("definition",t.definition)),t.tags&&(e.tags=c(t.tags));let n=await b(Q,{input:e});i(`Pipeline created: ${n.labCreatePipeline.name}`),h$1(t,n.labCreatePipeline);}catch(e){g(e);}}),i$1.command("run").description("Queue a reproducible pipeline run over a dataset version").requiredOption("--pipeline <id>","Pipeline ID").option("--dataset <id>","Dataset ID").option("--dataset-version <id>","Dataset version ID").option("--parameters <json>","Parameters JSON").option("-f, --format <format>","Output format").action(async t=>{try{let e={pipelineId:t.pipeline};t.dataset&&(e.datasetId=t.dataset),t.datasetVersion&&(e.datasetVersionId=t.datasetVersion),t.parameters&&(e.parameters=y("parameters",t.parameters));let n=await b(Z,{input:e});i(`Pipeline run queued: ${n.labRunPipeline.status}`),h$1(t,n.labRunPipeline);}catch(e){g(e);}}),i$1.command("list-runs").description("List pipeline runs").option("--pipeline <id>","Filter by pipeline ID").option("--status <s>","QUEUED|RUNNING|SUCCEEDED|FAILED|CANCELLED").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(tt,{pipelineId:t.pipeline,status:t.status?t.status.toUpperCase():void 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<c>","REAGENT|CHEMICAL|BIOLOGICAL|CONSUMABLE|EQUIPMENT_PART|SAMPLE").option("--status <s>","IN_STOCK|LOW|OUT_OF_STOCK|EXPIRED|QUARANTINED").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(it,{category:t.category?t.category.toUpperCase():void 0,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});h$1(t,e.labListInventoryItems.items,{headers:["ID","Name","Category","Status","Qty","Unit"],rows:e.labListInventoryItems.items.map(n=>[p(n.id,12),n.name,n.category,n.status,String(n.quantity),n.unit])});}catch(e){g(e);}}),i$1.command("get").description("Get an inventory item by id").argument("<id>","Inventory item ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(nt,{id:t});if(!n.labInventoryItem)throw new o(`Inventory item ${t} not found`);h$1(e,n.labInventoryItem);}catch(n){g(n);}}),i$1.command("create").description("Create an inventory item").requiredOption("--name <name>","Item name").option("--category <c>","REAGENT|CHEMICAL|BIOLOGICAL|CONSUMABLE|EQUIPMENT_PART|SAMPLE","REAGENT").option("--quantity <n>","Quantity",A).option("--unit <s>","Unit of measure").option("--reorder-level <n>","Reorder level",A).option("--location <s>","Storage location").option("--vendor <s>","Vendor").option("--catalog-number <s>","Catalog number").option("--lot-number <s>","Lot number").option("--expires-at <iso>","Expiry date (ISO)").option("--sds-file <id>","wspace-files-svc File id for the SDS").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,category:(t.category??"REAGENT").toUpperCase()};t.quantity!==void 0&&(e.quantity=t.quantity),t.unit&&(e.unit=t.unit),t.reorderLevel!==void 0&&(e.reorderLevel=t.reorderLevel),t.location&&(e.location=t.location),t.vendor&&(e.vendor=t.vendor),t.catalogNumber&&(e.catalogNumber=t.catalogNumber),t.lotNumber&&(e.lotNumber=t.lotNumber),t.expiresAt&&(e.expiresAt=t.expiresAt),t.sdsFile&&(e.sdsFileId=t.sdsFile),t.tags&&(e.tags=c(t.tags));let n=await b(ot,{input:e});i(`Inventory item created: ${n.labCreateInventoryItem.name}`),h$1(t,n.labCreateInventoryItem);}catch(e){g(e);}}),i$1.command("adjust").description("Apply a signed quantity delta and recompute stock status").argument("<id>","Inventory item ID").requiredOption("--delta <n>","Signed quantity delta (positive = restock)",A).option("--reason <s>","Reason for adjustment").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={delta:e.delta};e.reason&&(n.reason=e.reason);let g=await b(at,{id:t,input:n});i(`Inventory adjusted: ${g.labAdjustInventory.quantity} ${g.labAdjustInventory.unit}`),h$1(e,g.labAdjustInventory);}catch(n){g(n);}}),i$1.command("archive").description("Archive an inventory item").argument("<id>","Inventory item ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(rt,{id:t});i(`Inventory item archived: ${n.labArchiveInventoryItem}`),h$1(e,{archived:n.labArchiveInventoryItem});}catch(n){g(n);}});}function Lt(p$1){let i$1=p$1.command("instruments").description("Labsofscience instruments & bookings");i$1.command("list").description("List instruments").option("--status <s>","AVAILABLE|IN_USE|MAINTENANCE|OFFLINE").option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(pt,{status:t.status?t.status.toUpperCase():void 0});h$1(t,e.labListInstruments,{headers:["ID","Name","Model","Location","Status","Approval"],rows:e.labListInstruments.map(n=>[p(n.id,12),n.name,n.model??"-",n.location??"-",n.status,n.requiresApproval?"yes":"no"])});}catch(e){g(e);}}),i$1.command("get").description("Get an instrument by id").argument("<id>","Instrument ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(st,{id:t});if(!n.labInstrument)throw new o(`Instrument ${t} not found`);h$1(e,n.labInstrument);}catch(n){g(n);}}),i$1.command("create").description("Create an instrument").requiredOption("--name <name>","Instrument name").option("--model <s>","Model").option("--location <s>","Location").option("--custodian <id>","Custodian user ID").option("--requires-approval","Bookings require approval").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.model&&(e.model=t.model),t.location&&(e.location=t.location),t.custodian&&(e.custodianId=t.custodian),t.requiresApproval&&(e.requiresApproval=!0),t.tags&&(e.tags=c(t.tags));let n=await b(dt,{input:e});i(`Instrument created: ${n.labCreateInstrument.name}`),h$1(t,n.labCreateInstrument);}catch(e){g(e);}}),i$1.command("book").description("Reserve an instrument for a time window").requiredOption("--instrument <id>","Instrument ID").requiredOption("--start <iso>","Start time (ISO)").requiredOption("--end <iso>","End time (ISO)").option("--experiment <id>","Experiment ID").option("--purpose <s>","Booking purpose").option("-f, --format <format>","Output format").action(async t=>{try{let e={instrumentId:t.instrument,startTime:t.start,endTime:t.end};t.experiment&&(e.experimentId=t.experiment),t.purpose&&(e.purpose=t.purpose);let n=await b(mt,{input:e});i(`Instrument booked: ${n.labBookInstrument.status}`),h$1(t,n.labBookInstrument);}catch(e){g(e);}}),i$1.command("cancel-booking").description("Cancel an instrument booking").argument("<id>","Booking ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(ct,{id:t});i(`Booking cancelled: ${n.labCancelBooking.status}`),h$1(e,n.labCancelBooking);}catch(n){g(n);}});}function Ct(p){p.command("health").description("Labsofscience service health check (public)").option("-f, --format <format>","Output format").action(async i$1=>{try{let t=await d$1(ut);i(t.labHealth),h$1(i$1,{health:t.labHealth});}catch(t){g(t);}});}var Rt={id:"labsofscience",version:"1.0.0",displayName:"Labsofscience",dependsOn:["auth","workspaces"],register(p,i){a(i);let t=p.command("labsofscience").description("Labsofscience science & discovery platform");lt(t),gt(t),ft(t),It(t),bt(t),yt(t),Et(t),At(t),Lt(t),Ct(t);}},Ie=Rt;export{Ie as default};
+`;function y(p,i){try{return JSON.parse(i)}catch{throw new o(`--${p} must be valid JSON`)}}function d(p){let i=Number.parseInt(p,10);if(Number.isNaN(i))throw new o(`Expected an integer but got "${p}"`);return i}function A(p){let i=Number.parseFloat(p);if(Number.isNaN(i))throw new o(`Expected a number but got "${p}"`);return i}function c(p){return p.split(",").map(i=>i.trim()).filter(i=>i.length>0)}function l(p,i){return {limit:p,offset:i}}function lt(p){let i$1=p.command("projects").description("Labsofscience research projects");i$1.command("list").description("List research projects").option("--status <s>","Filter by project status").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(h,{status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});i(t,e.labListProjects.items,{headers:["ID","Name","Code","Field","Status","Visibility"],rows:e.labListProjects.items.map(n=>[r(n.id,12),n.name,n.code??"-",n.field??"-",n.status,n.visibility])});}catch(e){h$1(e);}}),i$1.command("get").description("Get a research project by id").argument("<id>","Project ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(P,{id:t});if(!n.labProject)throw new o(`Project ${t} not found`);i(e,n.labProject);}catch(n){h$1(n);}}),i$1.command("create").description("Create a research project").requiredOption("--name <name>","Project name").option("--code <code>","Project code").option("--description <s>","Description").option("--field <s>","Research field").option("--pi <id>","Principal investigator user ID").option("--start-date <iso>","Start date (ISO)").option("--end-date <iso>","End date (ISO)").option("--status <s>","PLANNING|ACTIVE|ON_HOLD|COMPLETED|ARCHIVED","PLANNING").option("--visibility <v>","PRIVATE|WORKSPACE|PUBLIC","WORKSPACE").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,status:(t.status??"PLANNING").toUpperCase(),visibility:(t.visibility??"WORKSPACE").toUpperCase()};t.code&&(e.code=t.code),t.description&&(e.description=t.description),t.field&&(e.field=t.field),t.pi&&(e.principalInvestigatorId=t.pi),t.startDate&&(e.startDate=t.startDate),t.endDate&&(e.endDate=t.endDate),t.tags&&(e.tags=c(t.tags));let n=await b(N,{input:e});k$1(`Project created: ${n.labCreateProject.name}`),i(t,n.labCreateProject);}catch(e){h$1(e);}}),i$1.command("update").description("Update a research project").argument("<id>","Project ID").option("--name <name>","Project name").option("--code <code>","Project code").option("--description <s>","Description").option("--field <s>","Research field").option("--pi <id>","Principal investigator user ID").option("--start-date <iso>","Start date (ISO)").option("--end-date <iso>","End date (ISO)").option("--status <s>","Project status").option("--visibility <v>","Visibility").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.name&&(n.name=e.name),e.code&&(n.code=e.code),e.description!==void 0&&(n.description=e.description),e.field&&(n.field=e.field),e.pi&&(n.principalInvestigatorId=e.pi),e.startDate&&(n.startDate=e.startDate),e.endDate&&(n.endDate=e.endDate),e.status&&(n.status=e.status.toUpperCase()),e.visibility&&(n.visibility=e.visibility.toUpperCase()),e.tags&&(n.tags=c(e.tags)),!Object.keys(n).length)throw new o("No updates specified");let g=await b(v,{id:t,input:n});k$1("Project updated"),i(e,g.labUpdateProject);}catch(n){h$1(n);}}),i$1.command("archive").description("Archive a research project").argument("<id>","Project ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(O,{id:t});k$1(`Project archived: ${n.labArchiveProject}`),i(e,{archived:n.labArchiveProject});}catch(n){h$1(n);}});}function gt(p){let i$1=p.command("experiments").description("Labsofscience experiments");i$1.command("list").description("List experiments").option("--project <id>","Filter by project ID").option("--status <s>","Filter by experiment status").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(T,{projectId:t.project,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});i(t,e.labListExperiments.items,{headers:["ID","Title","Status","Project","Lead"],rows:e.labListExperiments.items.map(n=>[r(n.id,12),n.title,n.status,r(n.projectId,12),n.leadResearcherId?r(n.leadResearcherId,12):"-"])});}catch(e){h$1(e);}}),i$1.command("get").description("Get an experiment by id").argument("<id>","Experiment ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(D,{id:t});if(!n.labExperiment)throw new o(`Experiment ${t} not found`);i(e,n.labExperiment);}catch(n){h$1(n);}}),i$1.command("create").description("Create an experiment").requiredOption("--project <id>","Project ID").requiredOption("--title <t>","Experiment title").option("--description <s>","Description").option("--hypothesis <s>","Hypothesis").option("--lead <id>","Lead researcher user ID").option("--protocol <id>","Protocol ID").option("--variables <json>","Variables JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={projectId:t.project,title:t.title};t.description&&(e.description=t.description),t.hypothesis&&(e.hypothesis=t.hypothesis),t.lead&&(e.leadResearcherId=t.lead),t.protocol&&(e.protocolId=t.protocol),t.variables&&(e.variables=y("variables",t.variables)),t.tags&&(e.tags=c(t.tags));let n=await b(w,{input:e});k$1(`Experiment created: ${n.labCreateExperiment.title}`),i(t,n.labCreateExperiment);}catch(e){h$1(e);}}),i$1.command("update").description("Update an experiment").argument("<id>","Experiment ID").option("--title <t>","Experiment title").option("--description <s>","Description").option("--hypothesis <s>","Hypothesis").option("--lead <id>","Lead researcher user ID").option("--protocol <id>","Protocol ID").option("--variables <json>","Variables JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.title&&(n.title=e.title),e.description!==void 0&&(n.description=e.description),e.hypothesis!==void 0&&(n.hypothesis=e.hypothesis),e.lead&&(n.leadResearcherId=e.lead),e.protocol&&(n.protocolId=e.protocol),e.variables&&(n.variables=y("variables",e.variables)),e.tags&&(n.tags=c(e.tags)),!Object.keys(n).length)throw new o("No updates specified");let g=await b(S,{id:t,input:n});k$1("Experiment updated"),i(e,g.labUpdateExperiment);}catch(n){h$1(n);}}),i$1.command("transition").description("Advance an experiment through its lifecycle").argument("<id>","Experiment ID").requiredOption("--status <s>","DESIGN|RUNNING|ANALYSIS|COMPLETE|ABANDONED").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(_,{id:t,status:e.status.toUpperCase()});k$1(`Experiment moved to ${n.labTransitionExperiment.status}`),i(e,n.labTransitionExperiment);}catch(n){h$1(n);}});}function ft(p){let i$1=p.command("runs").description("Labsofscience reproducible experiment runs");i$1.command("list").description("List experiment runs").option("--experiment <id>","Filter by experiment ID").option("--status <s>","Filter by run status").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(x,{experimentId:t.experiment,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});i(t,e.labListRuns.items,{headers:["ID","Run #","Status","Experiment","Started","Completed"],rows:e.labListRuns.items.map(n=>[r(n.id,12),String(n.runNumber),n.status,r(n.experimentId,12),q$1(n.startedAt),q$1(n.completedAt)])});}catch(e){h$1(e);}}),i$1.command("start").description("Start a new reproducible run of an experiment").requiredOption("--experiment <id>","Experiment ID").option("--notes <s>","Run notes").option("--parameters <json>","Parameters JSON").option("-f, --format <format>","Output format").action(async t=>{try{let e={experimentId:t.experiment};t.notes&&(e.notes=t.notes),t.parameters&&(e.parameters=y("parameters",t.parameters));let n=await b(k,{input:e});k$1(`Run #${n.labStartRun.runNumber} started`),i(t,n.labStartRun);}catch(e){h$1(e);}}),i$1.command("complete").description("Record observations and complete a run with a terminal status").argument("<id>","Run ID").requiredOption("--status <s>","SUCCEEDED|FAILED|CANCELLED").option("--notes <s>","Result notes").option("--observations <json>","Observations JSON").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={id:t,status:e.status.toUpperCase()},g={};e.notes&&(g.notes=e.notes),e.observations&&(g.observations=y("observations",e.observations)),Object.keys(g).length&&(n.input=g);let L=await b($,n);k$1(`Run #${L.labCompleteRun.runNumber} completed: ${L.labCompleteRun.status}`),i(e,L.labCompleteRun);}catch(n){h$1(n);}});}function It(p){let i$1=p.command("notebook").description("Labsofscience electronic lab notebook (ELN)");i$1.command("list").description("List notebook entries").option("--experiment <id>","Filter by experiment ID").option("--project <id>","Filter by project ID").option("--status <s>","Filter by entry status").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(B,{experimentId:t.experiment,projectId:t.project,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});i(t,e.labListNotebookEntries.items,{headers:["ID","Title","Status","Project","Author"],rows:e.labListNotebookEntries.items.map(n=>[r(n.id,12),n.title,n.status,r(n.projectId,12),r(n.authorId,12)])});}catch(e){h$1(e);}}),i$1.command("create").description("Create a notebook entry").requiredOption("--project <id>","Project ID").requiredOption("--title <t>","Entry title").option("--body <s>","Entry body").option("--experiment <id>","Experiment ID").option("--run <id>","Run ID").option("--file-ids <csv>","Comma-separated wspace-files-svc File ids").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={projectId:t.project,title:t.title};t.body&&(e.body=t.body),t.experiment&&(e.experimentId=t.experiment),t.run&&(e.runId=t.run),t.fileIds&&(e.fileIds=c(t.fileIds)),t.tags&&(e.tags=c(t.tags));let n=await b(j,{input:e});k$1(`Notebook entry created: ${n.labCreateNotebookEntry.title}`),i(t,n.labCreateNotebookEntry);}catch(e){h$1(e);}}),i$1.command("sign").description("Sign a notebook entry (locks editable content)").argument("<id>","Entry ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(U,{id:t});k$1(`Notebook entry signed: ${n.labSignNotebookEntry.status}`),i(e,n.labSignNotebookEntry);}catch(n){h$1(n);}});}function bt(p){let i$1=p.command("protocols").description("Labsofscience versioned protocols");i$1.command("list").description("List protocols").option("--status <s>","DRAFT|PUBLISHED|DEPRECATED").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(q,{status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});i(t,e.labListProtocols.items,{headers:["ID","Name","Status","Version","Est. min"],rows:e.labListProtocols.items.map(n=>[r(n.id,12),n.name,n.status,String(n.version),n.estimatedMinutes!=null?String(n.estimatedMinutes):"-"])});}catch(e){h$1(e);}}),i$1.command("get").description("Get a protocol by id").argument("<id>","Protocol ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(M,{id:t});if(!n.labProtocol)throw new o(`Protocol ${t} not found`);i(e,n.labProtocol);}catch(n){h$1(n);}}),i$1.command("create").description("Create a protocol").requiredOption("--name <name>","Protocol name").option("--summary <s>","Summary").option("--author <id>","Author user ID").option("--estimated-minutes <n>","Estimated minutes",d).option("--materials <csv>","Comma-separated materials").option("--safety-notes <s>","Safety notes").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.summary&&(e.summary=t.summary),t.author&&(e.authorId=t.author),t.estimatedMinutes!==void 0&&(e.estimatedMinutes=t.estimatedMinutes),t.materials&&(e.materials=c(t.materials)),t.safetyNotes&&(e.safetyNotes=t.safetyNotes),t.tags&&(e.tags=c(t.tags));let n=await b(V,{input:e});k$1(`Protocol created: ${n.labCreateProtocol.name}`),i(t,n.labCreateProtocol);}catch(e){h$1(e);}}),i$1.command("update").description("Update a protocol").argument("<id>","Protocol ID").option("--name <name>","Protocol name").option("--summary <s>","Summary").option("--estimated-minutes <n>","Estimated minutes",d).option("--materials <csv>","Comma-separated materials").option("--safety-notes <s>","Safety notes").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.name&&(n.name=e.name),e.summary!==void 0&&(n.summary=e.summary),e.estimatedMinutes!==void 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(minutes)",d).option("--critical","Mark step as critical").option("-f, --format <format>","Output format").action(async t=>{try{let e={protocolId:t.protocol,instruction:t.instruction,kind:(t.kind??"PREPARATION").toUpperCase()};t.ordinal!==void 0&&(e.ordinal=t.ordinal),t.durationMinutes!==void 0&&(e.durationMinutes=t.durationMinutes),t.critical&&(e.isCritical=!0);let n=await b(J,{input:e});k$1(`Step added at ordinal ${n.labAddProtocolStep.ordinal}`),i(t,n.labAddProtocolStep);}catch(e){h$1(e);}});}function yt(p){let i$1=p.command("datasets").description("Labsofscience versioned datasets");i$1.command("list").description("List datasets").option("--kind <k>","RAW|PROCESSED|RESULT|REFERENCE").option("--status <s>","ACTIVE|LOCKED|ARCHIVED").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(W,{kind:t.kind?t.kind.toUpperCase():void 0,status:t.status?t.status.toUpperCase():void 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e={name:t.name,kind:(t.kind??"RAW").toUpperCase()};t.description&&(e.description=t.description),t.experiment&&(e.experimentId=t.experiment),t.project&&(e.projectId=t.project),t.tags&&(e.tags=c(t.tags));let n=await b(z,{input:e});k$1(`Dataset created: ${n.labCreateDataset.name}`),i(t,n.labCreateDataset);}catch(e){h$1(e);}}),i$1.command("add-version").description("Append an immutable version to a dataset").requiredOption("--dataset <id>","Dataset ID").option("--file <id>","wspace-files-svc File id holding the snapshot bytes").option("--size-bytes <s>","Size in bytes").option("--row-count <n>","Row count",d).option("--checksum <s>","Checksum").option("--change-note <s>","Change note").option("-f, --format <format>","Output format").action(async t=>{try{let e={datasetId:t.dataset};t.file&&(e.fileId=t.file),t.sizeBytes&&(e.sizeBytes=t.sizeBytes),t.rowCount!==void 0&&(e.rowCount=t.rowCount),t.checksum&&(e.checksum=t.checksum),t.changeNote&&(e.changeNote=t.changeNote);let n=await b(K,{input:e});k$1(`Dataset version added: v${n.labAddDatasetVersion.version}`),i(t,n.labAddDatasetVersion);}catch(e){h$1(e);}}),i$1.command("archive").description("Archive a dataset").argument("<id>","Dataset ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(Y,{id:t});k$1(`Dataset archived: ${n.labArchiveDataset}`),i(e,{archived:n.labArchiveDataset});}catch(n){h$1(n);}});}function Et(p){let i$1=p.command("pipelines").description("Labsofscience reproducible analysis pipelines");i$1.command("list").description("List analysis pipelines").option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(X);i(t,e.labListPipelines.items,{headers:["ID","Name","Engine","Version","Active"],rows:e.labListPipelines.items.map(n=>[r(n.id,12),n.name,n.engine,String(n.version),n.isActive?"yes":"no"])});}catch(e){h$1(e);}}),i$1.command("create").description("Create an analysis pipeline").requiredOption("--name <name>","Pipeline 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e={pipelineId:t.pipeline};t.dataset&&(e.datasetId=t.dataset),t.datasetVersion&&(e.datasetVersionId=t.datasetVersion),t.parameters&&(e.parameters=y("parameters",t.parameters));let n=await b(Z,{input:e});k$1(`Pipeline run queued: ${n.labRunPipeline.status}`),i(t,n.labRunPipeline);}catch(e){h$1(e);}}),i$1.command("list-runs").description("List pipeline runs").option("--pipeline <id>","Filter by pipeline ID").option("--status <s>","QUEUED|RUNNING|SUCCEEDED|FAILED|CANCELLED").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(tt,{pipelineId:t.pipeline,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});i(t,e.labListPipelineRuns.items,{headers:["ID","Pipeline","Status","Started","Finished"],rows:e.labListPipelineRuns.items.map(n=>[r(n.id,12),r(n.pipelineId,12),n.status,q$1(n.startedAt),q$1(n.finishedAt)])});}catch(e){h$1(e);}}),i$1.command("transition-run").description("Advance a pipeline run through its execution lifecycle").argument("<id>","Pipeline run ID").requiredOption("--status <s>","QUEUED|RUNNING|SUCCEEDED|FAILED|CANCELLED").option("--log <s>","Execution log").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(et,{id:t,status:e.status.toUpperCase(),log:e.log});k$1(`Pipeline run moved to ${n.labTransitionPipelineRun.status}`),i(e,n.labTransitionPipelineRun);}catch(n){h$1(n);}});}function At(p){let i$1=p.command("inventory").description("Labsofscience lab inventory (reagents, samples, consumables)");i$1.command("list").description("List inventory items").option("--category <c>","REAGENT|CHEMICAL|BIOLOGICAL|CONSUMABLE|EQUIPMENT_PART|SAMPLE").option("--status <s>","IN_STOCK|LOW|OUT_OF_STOCK|EXPIRED|QUARANTINED").option("--limit <n>","Page size",d,50).option("--offset <n>","Offset",d,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(it,{category:t.category?t.category.toUpperCase():void 0,status:t.status?t.status.toUpperCase():void 0,pagination:l(t.limit,t.offset)});i(t,e.labListInventoryItems.items,{headers:["ID","Name","Category","Status","Qty","Unit"],rows:e.labListInventoryItems.items.map(n=>[r(n.id,12),n.name,n.category,n.status,String(n.quantity),n.unit])});}catch(e){h$1(e);}}),i$1.command("get").description("Get an inventory item by id").argument("<id>","Inventory item ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(nt,{id:t});if(!n.labInventoryItem)throw new o(`Inventory item ${t} not found`);i(e,n.labInventoryItem);}catch(n){h$1(n);}}),i$1.command("create").description("Create an inventory item").requiredOption("--name <name>","Item name").option("--category <c>","REAGENT|CHEMICAL|BIOLOGICAL|CONSUMABLE|EQUIPMENT_PART|SAMPLE","REAGENT").option("--quantity <n>","Quantity",A).option("--unit <s>","Unit of measure").option("--reorder-level <n>","Reorder level",A).option("--location <s>","Storage location").option("--vendor <s>","Vendor").option("--catalog-number <s>","Catalog number").option("--lot-number <s>","Lot number").option("--expires-at <iso>","Expiry date (ISO)").option("--sds-file <id>","wspace-files-svc File id for the SDS").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name,category:(t.category??"REAGENT").toUpperCase()};t.quantity!==void 0&&(e.quantity=t.quantity),t.unit&&(e.unit=t.unit),t.reorderLevel!==void 0&&(e.reorderLevel=t.reorderLevel),t.location&&(e.location=t.location),t.vendor&&(e.vendor=t.vendor),t.catalogNumber&&(e.catalogNumber=t.catalogNumber),t.lotNumber&&(e.lotNumber=t.lotNumber),t.expiresAt&&(e.expiresAt=t.expiresAt),t.sdsFile&&(e.sdsFileId=t.sdsFile),t.tags&&(e.tags=c(t.tags));let n=await b(ot,{input:e});k$1(`Inventory item created: ${n.labCreateInventoryItem.name}`),i(t,n.labCreateInventoryItem);}catch(e){h$1(e);}}),i$1.command("adjust").description("Apply a signed quantity delta and recompute stock status").argument("<id>","Inventory item ID").requiredOption("--delta <n>","Signed quantity delta (positive = restock)",A).option("--reason <s>","Reason for adjustment").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={delta:e.delta};e.reason&&(n.reason=e.reason);let g=await b(at,{id:t,input:n});k$1(`Inventory adjusted: ${g.labAdjustInventory.quantity} ${g.labAdjustInventory.unit}`),i(e,g.labAdjustInventory);}catch(n){h$1(n);}}),i$1.command("archive").description("Archive an inventory item").argument("<id>","Inventory item ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(rt,{id:t});k$1(`Inventory item archived: ${n.labArchiveInventoryItem}`),i(e,{archived:n.labArchiveInventoryItem});}catch(n){h$1(n);}});}function Lt(p){let i$1=p.command("instruments").description("Labsofscience instruments & bookings");i$1.command("list").description("List instruments").option("--status <s>","AVAILABLE|IN_USE|MAINTENANCE|OFFLINE").option("-f, --format <format>","Output format").action(async t=>{try{let e=await b(pt,{status:t.status?t.status.toUpperCase():void 0});i(t,e.labListInstruments.items,{headers:["ID","Name","Model","Location","Status","Approval"],rows:e.labListInstruments.items.map(n=>[r(n.id,12),n.name,n.model??"-",n.location??"-",n.status,n.requiresApproval?"yes":"no"])});}catch(e){h$1(e);}}),i$1.command("get").description("Get an instrument by id").argument("<id>","Instrument ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(st,{id:t});if(!n.labInstrument)throw new o(`Instrument ${t} not found`);i(e,n.labInstrument);}catch(n){h$1(n);}}),i$1.command("create").description("Create an instrument").requiredOption("--name <name>","Instrument name").option("--model <s>","Model").option("--location <s>","Location").option("--custodian <id>","Custodian user ID").option("--requires-approval","Bookings require approval").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={name:t.name};t.model&&(e.model=t.model),t.location&&(e.location=t.location),t.custodian&&(e.custodianId=t.custodian),t.requiresApproval&&(e.requiresApproval=!0),t.tags&&(e.tags=c(t.tags));let n=await b(dt,{input:e});k$1(`Instrument created: ${n.labCreateInstrument.name}`),i(t,n.labCreateInstrument);}catch(e){h$1(e);}}),i$1.command("book").description("Reserve an instrument for a time window").requiredOption("--instrument <id>","Instrument ID").requiredOption("--start <iso>","Start time (ISO)").requiredOption("--end <iso>","End time (ISO)").option("--experiment <id>","Experiment ID").option("--purpose <s>","Booking purpose").option("-f, --format <format>","Output format").action(async t=>{try{let e={instrumentId:t.instrument,startTime:t.start,endTime:t.end};t.experiment&&(e.experimentId=t.experiment),t.purpose&&(e.purpose=t.purpose);let n=await b(mt,{input:e});k$1(`Instrument booked: ${n.labBookInstrument.status}`),i(t,n.labBookInstrument);}catch(e){h$1(e);}}),i$1.command("cancel-booking").description("Cancel an instrument booking").argument("<id>","Booking ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await b(ct,{id:t});k$1(`Booking cancelled: ${n.labCancelBooking.status}`),i(e,n.labCancelBooking);}catch(n){h$1(n);}});}function Ct(p){p.command("health").description("Labsofscience service health check (public)").option("-f, --format <format>","Output format").action(async i$1=>{try{let t=await d$1(ut);k$1(t.labHealth),i(i$1,{health:t.labHealth});}catch(t){h$1(t);}});}var Rt={id:"labsofscience",version:"1.0.0",displayName:"Labsofscience",dependsOn:["auth","workspaces"],register(p,i){a(i);let t=p.command("labsofscience").description("Labsofscience science & discovery platform");lt(t),gt(t),ft(t),It(t),bt(t),yt(t),Et(t),At(t),Lt(t),Ct(t);}},Ie=Rt;export{Ie as default};