@burdenoff/cli-sdk 2026.627.5 → 2026.629.1

package/dist/modules/labsofscience/index.cjs

@@ -0,0 +1,343 @@
+'use strict';require('graphql-request'),require('cross-fetch'),require('commander');var u=class extends Error{exitCode;hint;constructor(o,t){super(o),this.name="CliUserError",this.exitCode=t?.exitCode??1,this.hint=t?.hint;}},h=class extends u{constructor(o,t){super(o,{exitCode:2,hint:t?.hint??"Run `<product> auth login` to authenticate."}),this.name="CliAuthError";}},y=class extends Error{cause;constructor(o,t){super(o),this.name="CliInternalError",this.cause=t;}};var L=null;function T(r){L=r;}function C(){if(!L)throw new y("vibecontrols module helpers used before setHelpersContext was called");return L}function qt(){let r=C();if(!r.auth.isAuthenticated())throw new h(`Authentication required. Run \`${r.productName} auth login\`.`)}async function a(r,o){return qt(),C().gql.workspace.request(r,o)}async function k(r,o){return C().gql.workspaceAuthOnly.request(r,o)}function i(r){let o=r instanceof Error?r.message:String(r);throw new u(o)}function s(r,o,t){C().output.formatAndOutput(r,o,t);}function c(r){C().output.printSuccess(r);}function E(r){return C().output.formatDate(r)}function d(r,o){return C().output.truncate(r,o)}var R=`
+  query LabProject($id: ID!) {
+    labProject(id: $id) {
+      id workspaceId name code description field status visibility
+      principalInvestigatorId startDate endDate tags createdAt updatedAt
+    }
+  }
+`,P=`
+  query LabListProjects($status: LabProjectStatus, $pagination: PaginationInput) {
+    labListProjects(status: $status, pagination: $pagination) {
+      items {
+        id name code field status visibility principalInvestigatorId
+        startDate endDate createdAt
+      }
+      pageInfo { cursor hasMore }
+    }
+  }
+`,O=`
+  mutation LabCreateProject($input: LabCreateProjectInput!) {
+    labCreateProject(input: $input) {
+      id workspaceId name code description field status visibility
+      principalInvestigatorId startDate endDate tags createdAt
+    }
+  }
+`,D=`
+  mutation LabUpdateProject($id: ID!, $input: LabUpdateProjectInput!) {
+    labUpdateProject(id: $id, input: $input) {
+      id name code description field status visibility
+      principalInvestigatorId startDate endDate tags updatedAt
+    }
+  }
+`,S=`
+  mutation LabArchiveProject($id: ID!) {
+    labArchiveProject(id: $id)
+  }
+`,N=`
+  query LabExperiment($id: ID!) {
+    labExperiment(id: $id) {
+      id workspaceId projectId title description hypothesis status
+      leadResearcherId protocolId variables tags createdAt updatedAt
+    }
+  }
+`,_=`
+  query LabListExperiments(
+    $projectId: ID
+    $status: LabExperimentStatus
+    $pagination: PaginationInput
+  ) {
+    labListExperiments(projectId: $projectId, status: $status, pagination: $pagination) {
+      items {
+        id projectId title status hypothesis leadResearcherId protocolId
+        tags createdAt
+      }
+      pageInfo { cursor hasMore }
+    }
+  }
+`,$=`
+  mutation LabCreateExperiment($input: LabCreateExperimentInput!) {
+    labCreateExperiment(input: $input) {
+      id workspaceId projectId title description hypothesis status
+      leadResearcherId protocolId variables tags createdAt
+    }
+  }
+`,j=`
+  mutation LabUpdateExperiment($id: ID!, $input: LabUpdateExperimentInput!) {
+    labUpdateExperiment(id: $id, input: $input) {
+      id title description hypothesis status leadResearcherId protocolId
+      variables tags updatedAt
+    }
+  }
+`,B=`
+  mutation LabTransitionExperiment($id: ID!, $status: LabExperimentStatus!) {
+    labTransitionExperiment(id: $id, status: $status) {
+      id title status updatedAt
+    }
+  }
+`,q=`
+  query LabListRuns($experimentId: ID, $status: LabRunStatus, $pagination: PaginationInput) {
+    labListRuns(experimentId: $experimentId, status: $status, pagination: $pagination) {
+      items {
+        id experimentId runNumber status performedById startedAt
+        completedAt createdAt
+      }
+      pageInfo { cursor hasMore }
+    }
+  }
+`,U=`
+  mutation LabStartRun($input: LabCreateRunInput!) {
+    labStartRun(input: $input) {
+      id workspaceId experimentId runNumber status parameters notes
+      performedById startedAt createdAt
+    }
+  }
+`,M=`
+  mutation LabCompleteRun($id: ID!, $status: LabRunStatus!, $input: LabRecordRunResultsInput) {
+    labCompleteRun(id: $id, status: $status, input: $input) {
+      id experimentId runNumber status observations notes completedAt updatedAt
+    }
+  }
+`,F=`
+  query LabListNotebookEntries(
+    $experimentId: ID
+    $projectId: ID
+    $status: LabNotebookEntryStatus
+    $pagination: PaginationInput
+  ) {
+    labListNotebookEntries(
+      experimentId: $experimentId
+      projectId: $projectId
+      status: $status
+      pagination: $pagination
+    ) {
+      items {
+        id projectId experimentId runId title status authorId signedById
+        signedAt witnessedById tags createdAt
+      }
+      pageInfo { cursor hasMore }
+    }
+  }
+`,V=`
+  mutation LabCreateNotebookEntry($input: LabCreateNotebookEntryInput!) {
+    labCreateNotebookEntry(input: $input) {
+      id workspaceId projectId experimentId runId title body status
+      authorId tags createdAt
+    }
+  }
+`,W=`
+  mutation LabSignNotebookEntry($id: ID!) {
+    labSignNotebookEntry(id: $id) {
+      id title status authorId signedById signedAt updatedAt
+    }
+  }
+`,G=`
+  query LabProtocol($id: ID!) {
+    labProtocol(id: $id) {
+      id workspaceId name summary status version estimatedMinutes
+      materials safetyNotes authorId publishedAt tags createdAt updatedAt
+      steps {
+        id ordinal kind instruction durationMinutes isCritical
+      }
+    }
+  }
+`,H=`
+  query LabListProtocols($status: LabProtocolStatus, $pagination: PaginationInput) {
+    labListProtocols(status: $status, pagination: $pagination) {
+      items {
+        id name summary status version estimatedMinutes authorId
+        publishedAt tags createdAt
+      }
+      pageInfo { cursor hasMore }
+    }
+  }
+`,z=`
+  mutation LabCreateProtocol($input: LabCreateProtocolInput!) {
+    labCreateProtocol(input: $input) {
+      id workspaceId name summary status version estimatedMinutes
+      materials safetyNotes authorId tags createdAt
+    }
+  }
+`,J=`
+  mutation LabUpdateProtocol($id: ID!, $input: LabUpdateProtocolInput!) {
+    labUpdateProtocol(id: $id, input: $input) {
+      id name summary status version estimatedMinutes materials
+      safetyNotes tags updatedAt
+    }
+  }
+`,K=`
+  mutation LabPublishProtocol($id: ID!) {
+    labPublishProtocol(id: $id) {
+      id name status version publishedAt updatedAt
+    }
+  }
+`,Y=`
+  mutation LabAddProtocolStep($input: LabAddProtocolStepInput!) {
+    labAddProtocolStep(input: $input) {
+      id protocolId ordinal kind instruction durationMinutes isCritical createdAt
+    }
+  }
+`,Q=`
+  query LabDataset($id: ID!) {
+    labDataset(id: $id) {
+      id workspaceId name description kind status experimentId projectId
+      latestVersion tags createdAt updatedAt
+      versions {
+        id version sizeBytes rowCount checksum changeNote createdAt
+      }
+    }
+  }
+`,X=`
+  query LabListDatasets(
+    $kind: LabDatasetKind
+    $status: LabDatasetStatus
+    $pagination: PaginationInput
+  ) {
+    labListDatasets(kind: $kind, status: $status, pagination: $pagination) {
+      items {
+        id name description kind status experimentId projectId
+        latestVersion tags createdAt
+      }
+      pageInfo { cursor hasMore }
+    }
+  }
+`,Z=`
+  mutation LabCreateDataset($input: LabCreateDatasetInput!) {
+    labCreateDataset(input: $input) {
+      id workspaceId name description kind status experimentId projectId
+      latestVersion tags createdAt
+    }
+  }
+`,tt=`
+  mutation LabAddDatasetVersion($input: LabAddDatasetVersionInput!) {
+    labAddDatasetVersion(input: $input) {
+      id datasetId version sizeBytes rowCount checksum changeNote createdAt
+    }
+  }
+`,et=`
+  mutation LabArchiveDataset($id: ID!) {
+    labArchiveDataset(id: $id)
+  }
+`,nt=`
+  query LabListPipelines {
+    labListPipelines {
+      id workspaceId projectId name description engine version isActive
+      definition tags createdAt updatedAt
+    }
+  }
+`,ot=`
+  mutation LabCreatePipeline($input: LabCreatePipelineInput!) {
+    labCreatePipeline(input: $input) {
+      id workspaceId projectId name description engine version isActive
+      definition tags createdAt
+    }
+  }
+`,rt=`
+  mutation LabRunPipeline($input: LabRunPipelineInput!) {
+    labRunPipeline(input: $input) {
+      id workspaceId pipelineId datasetId datasetVersionId status
+      parameters triggeredById startedAt createdAt
+    }
+  }
+`,it=`
+  query LabListPipelineRuns(
+    $pipelineId: ID
+    $status: LabPipelineRunStatus
+    $pagination: PaginationInput
+  ) {
+    labListPipelineRuns(pipelineId: $pipelineId, status: $status, pagination: $pagination) {
+      items {
+        id pipelineId datasetId datasetVersionId outputDatasetId status
+        triggeredById startedAt finishedAt createdAt
+      }
+      pageInfo { cursor hasMore }
+    }
+  }
+`,st=`
+  mutation LabTransitionPipelineRun(
+    $id: ID!
+    $status: LabPipelineRunStatus!
+    $log: String
+  ) {
+    labTransitionPipelineRun(id: $id, status: $status, log: $log) {
+      id pipelineId status log startedAt finishedAt updatedAt
+    }
+  }
+`,at=`
+  query LabInventoryItem($id: ID!) {
+    labInventoryItem(id: $id) {
+      id workspaceId name category status quantity unit reorderLevel
+      location vendor catalogNumber lotNumber expiresAt tags createdAt updatedAt
+    }
+  }
+`,ct=`
+  query LabListInventoryItems(
+    $category: LabInventoryCategory
+    $status: LabInventoryStatus
+    $pagination: PaginationInput
+  ) {
+    labListInventoryItems(category: $category, status: $status, pagination: $pagination) {
+      items {
+        id name category status quantity unit reorderLevel location
+        vendor expiresAt tags createdAt
+      }
+      pageInfo { cursor hasMore }
+    }
+  }
+`,pt=`
+  mutation LabCreateInventoryItem($input: LabCreateInventoryItemInput!) {
+    labCreateInventoryItem(input: $input) {
+      id workspaceId name category status quantity unit reorderLevel
+      location vendor catalogNumber lotNumber expiresAt tags createdAt
+    }
+  }
+`,ut=`
+  mutation LabAdjustInventory($id: ID!, $input: LabAdjustInventoryInput!) {
+    labAdjustInventory(id: $id, input: $input) {
+      id name category status quantity unit reorderLevel updatedAt
+    }
+  }
+`,dt=`
+  mutation LabArchiveInventoryItem($id: ID!) {
+    labArchiveInventoryItem(id: $id)
+  }
+`,mt=`
+  query LabInstrument($id: ID!) {
+    labInstrument(id: $id) {
+      id workspaceId name model location status requiresApproval
+      custodianId tags createdAt updatedAt
+      bookings {
+        id startTime endTime status purpose bookedById experimentId
+      }
+    }
+  }
+`,lt=`
+  query LabListInstruments($status: LabInstrumentStatus) {
+    labListInstruments(status: $status) {
+      id name model location status requiresApproval custodianId tags createdAt
+    }
+  }
+`,gt=`
+  mutation LabCreateInstrument($input: LabCreateInstrumentInput!) {
+    labCreateInstrument(input: $input) {
+      id workspaceId name model location status requiresApproval
+      custodianId tags createdAt
+    }
+  }
+`,ft=`
+  mutation LabBookInstrument($input: LabBookInstrumentInput!) {
+    labBookInstrument(input: $input) {
+      id workspaceId instrumentId bookedById experimentId startTime
+      endTime status purpose createdAt
+    }
+  }
+`,It=`
+  mutation LabCancelBooking($id: ID!) {
+    labCancelBooking(id: $id) {
+      id instrumentId status startTime endTime updatedAt
+    }
+  }
+`,bt=`
+  query LabHealth {
+    labHealth
+  }
+`;function b(r,o){try{return JSON.parse(o)}catch{throw new u(`--${r} must be valid JSON`)}}function p(r){let o=Number.parseInt(r,10);if(Number.isNaN(o))throw new u(`Expected an integer but got "${r}"`);return o}function A(r){let o=Number.parseFloat(r);if(Number.isNaN(o))throw new u(`Expected a number but got "${r}"`);return o}function l(r){return r.split(",").map(o=>o.trim()).filter(o=>o.length>0)}function g(r,o){return {limit:r,offset:o}}function yt(r){let o=r.command("projects").description("Labsofscience research projects");o.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);}}),o.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);}}),o.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);}}),o.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);}}),o.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(r){let o=r.command("experiments").description("Labsofscience experiments");o.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);}}),o.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 ${t} not found`);s(e,n.labExperiment);}catch(n){i(n);}}),o.command("create").description("Create an experiment").requiredOption("--project <id>","Project ID").requiredOption("--title <t>","Experiment title").option("--description <s>","Description").option("--hypothesis <s>","Hypothesis").option("--lead <id>","Lead researcher user ID").option("--protocol <id>","Protocol ID").option("--variables <json>","Variables JSON").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async t=>{try{let e={projectId:t.project,title:t.title};t.description&&(e.description=t.description),t.hypothesis&&(e.hypothesis=t.hypothesis),t.lead&&(e.leadResearcherId=t.lead),t.protocol&&(e.protocolId=t.protocol),t.variables&&(e.variables=b("variables",t.variables)),t.tags&&(e.tags=l(t.tags));let n=await a($,{input:e});c(`Experiment created: ${n.labCreateExperiment.title}`),s(t,n.labCreateExperiment);}catch(e){i(e);}}),o.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);}}),o.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 ${n.labTransitionExperiment.status}`),s(e,n.labTransitionExperiment);}catch(n){i(n);}});}function Et(r){let o=r.command("runs").description("Labsofscience reproducible experiment runs");o.command("list").description("List experiment runs").option("--experiment <id>","Filter by experiment ID").option("--status <s>","Filter by run status").option("--limit <n>","Page size",p,50).option("--offset <n>","Offset",p,0).option("-f, --format <format>","Output format").action(async t=>{try{let e=await a(q,{experimentId:t.experiment,status:t.status?t.status.toUpperCase():void 0,pagination:g(t.limit,t.offset)});s(t,e.labListRuns.items,{headers:["ID","Run #","Status","Experiment","Started","Completed"],rows:e.labListRuns.items.map(n=>[d(n.id,12),String(n.runNumber),n.status,d(n.experimentId,12),E(n.startedAt),E(n.completedAt)])});}catch(e){i(e);}}),o.command("start").description("Start a new reproducible run of an experiment").requiredOption("--experiment <id>","Experiment ID").option("--notes <s>","Run notes").option("--parameters <json>","Parameters JSON").option("-f, --format <format>","Output format").action(async t=>{try{let e={experimentId:t.experiment};t.notes&&(e.notes=t.notes),t.parameters&&(e.parameters=b("parameters",t.parameters));let n=await a(U,{input:e});c(`Run #${n.labStartRun.runNumber} started`),s(t,n.labStartRun);}catch(e){i(e);}}),o.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(r){let o=r.command("notebook").description("Labsofscience electronic lab notebook (ELN)");o.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);}}),o.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);}}),o.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(r){let o=r.command("protocols").description("Labsofscience versioned protocols");o.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);}}),o.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);}}),o.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: ${n.labCreateProtocol.name}`),s(t,n.labCreateProtocol);}catch(e){i(e);}}),o.command("update").description("Update a protocol").argument("<id>","Protocol ID").option("--name <name>","Protocol name").option("--summary <s>","Summary").option("--estimated-minutes <n>","Estimated minutes",p).option("--materials <csv>","Comma-separated materials").option("--safety-notes <s>","Safety notes").option("--tags <csv>","Comma-separated tags").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n={};if(e.name&&(n.name=e.name),e.summary!==void 0&&(n.summary=e.summary),e.estimatedMinutes!==void 0&&(n.estimatedMinutes=e.estimatedMinutes),e.materials&&(n.materials=l(e.materials)),e.safetyNotes!==void 0&&(n.safetyNotes=e.safetyNotes),e.tags&&(n.tags=l(e.tags)),!Object.keys(n).length)throw new u("No updates specified");let f=await a(J,{id:t,input:n});c("Protocol updated"),s(e,f.labUpdateProtocol);}catch(n){i(n);}}),o.command("publish").description("Publish a draft protocol, freezing its version").argument("<id>","Protocol ID").option("-f, --format <format>","Output format").action(async(t,e)=>{try{let n=await a(K,{id:t});c(`Protocol published: v${n.labPublishProtocol.version}`),s(e,n.labPublishProtocol);}catch(n){i(n);}}),o.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(r){let o=r.command("datasets").description("Labsofscience versioned datasets");o.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);}}),o.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);}}),o.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: ${n.labCreateDataset.name}`),s(t,n.labCreateDataset);}catch(e){i(e);}}),o.command("add-version").description("Append an immutable version to a dataset").requiredOption("--dataset <id>","Dataset ID").option("--file <id>","wspace-files-svc File id holding the snapshot bytes").option("--size-bytes <s>","Size in bytes").option("--row-count <n>","Row count",p).option("--checksum <s>","Checksum").option("--change-note <s>","Change note").option("-f, --format <format>","Output format").action(async t=>{try{let e={datasetId:t.dataset};t.file&&(e.fileId=t.file),t.sizeBytes&&(e.sizeBytes=t.sizeBytes),t.rowCount!==void 0&&(e.rowCount=t.rowCount),t.checksum&&(e.checksum=t.checksum),t.changeNote&&(e.changeNote=t.changeNote);let n=await a(tt,{input:e});c(`Dataset version added: v${n.labAddDatasetVersion.version}`),s(t,n.labAddDatasetVersion);}catch(e){i(e);}}),o.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(r){let o=r.command("pipelines").description("Labsofscience reproducible analysis pipelines");o.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);}}),o.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(ot,{input:e});c(`Pipeline created: ${n.labCreatePipeline.name}`),s(t,n.labCreatePipeline);}catch(e){i(e);}}),o.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(rt,{input:e});c(`Pipeline run queued: ${n.labRunPipeline.status}`),s(t,n.labRunPipeline);}catch(e){i(e);}}),o.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);}}),o.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(r){let o=r.command("inventory").description("Labsofscience lab inventory (reagents, samples, consumables)");o.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);}}),o.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);}}),o.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);}}),o.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);}}),o.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(r){let o=r.command("instruments").description("Labsofscience instruments & bookings");o.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);}}),o.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);}}),o.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);}}),o.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);}}),o.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(r){r.command("health").description("Labsofscience service health check (public)").option("-f, --format <format>","Output format").action(async o=>{try{let t=await k(bt);c(t.labHealth),s(o,{health:t.labHealth});}catch(t){i(t);}});}var Ut={id:"labsofscience",version:"1.0.0",displayName:"Labsofscience",dependsOn:["auth","workspaces"],register(r,o){T(o);let t=r.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.d.cts

@@ -0,0 +1,7 @@
+import { C as CliModule } from '../../module-DxCuik6L.cjs';
+import 'commander';
+import 'graphql-request';
+
+declare const labsofscienceModule: CliModule;
+
+export { labsofscienceModule as default };

package/dist/modules/labsofscience/index.d.ts

@@ -0,0 +1,7 @@
+import { C as CliModule } from '../../module-DxCuik6L.js';
+import 'commander';
+import 'graphql-request';
+
+declare const labsofscienceModule: CliModule;
+
+export { labsofscienceModule as default };