@inflexa-ai/harness 0.41.1 → 0.41.2

package/dist/contracts/report-blocks.d.ts

@@ -190,8 +190,8 @@ export declare const ChartAnnotationSchema: z.ZodDiscriminatedUnion<[z.ZodObject
     kind: z.ZodLiteral<"point-labels">;
     column: z.ZodString;
     order: z.ZodEnum<{
-        desc: "desc";
         asc: "asc";
+        desc: "desc";
     }>;
     n: z.ZodNumber;
 }, z.core.$strict>], "kind">;
@@ -288,8 +288,8 @@ export declare const ChartCompositionSchema: z.ZodObject<{
         kind: z.ZodLiteral<"point-labels">;
         column: z.ZodString;
         order: z.ZodEnum<{
-            desc: "desc";
             asc: "asc";
+            desc: "desc";
         }>;
         n: z.ZodNumber;
     }, z.core.$strict>], "kind">>>;
@@ -367,8 +367,8 @@ export declare const ClaimBlockSchema: z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -519,8 +519,8 @@ export declare const TableBlockSchema: z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -561,8 +561,8 @@ export declare const ChartBlockSchema: z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -715,8 +715,8 @@ export declare const ChartBlockSchema: z.ZodObject<{
             kind: z.ZodLiteral<"point-labels">;
             column: z.ZodString;
             order: z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>;
             n: z.ZodNumber;
         }, z.core.$strict>], "kind">>>;
@@ -826,8 +826,8 @@ export declare const ATOM_BLOCK_SCHEMAS: readonly [z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -974,8 +974,8 @@ export declare const ATOM_BLOCK_SCHEMAS: readonly [z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -1005,8 +1005,8 @@ export declare const ATOM_BLOCK_SCHEMAS: readonly [z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -1159,8 +1159,8 @@ export declare const ATOM_BLOCK_SCHEMAS: readonly [z.ZodObject<{
             kind: z.ZodLiteral<"point-labels">;
             column: z.ZodString;
             order: z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>;
             n: z.ZodNumber;
         }, z.core.$strict>], "kind">>>;

package/dist/contracts/report-reference.d.ts

@@ -59,8 +59,8 @@ export declare const RowBoundSchema: z.ZodObject<{
     column: z.ZodString;
     count: z.ZodNumber;
     order: z.ZodOptional<z.ZodEnum<{
-        desc: "desc";
         asc: "asc";
+        desc: "desc";
     }>>;
 }, z.core.$strict>;
 /**
@@ -79,8 +79,8 @@ export declare const ArtifactTableReferenceSchema: z.ZodObject<{
         column: z.ZodString;
         count: z.ZodNumber;
         order: z.ZodOptional<z.ZodEnum<{
-            desc: "desc";
             asc: "asc";
+            desc: "desc";
         }>>;
     }, z.core.$strict>>;
     columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -231,8 +231,8 @@ export declare const ReferenceSchema: z.ZodDiscriminatedUnion<[z.ZodObject<{
         column: z.ZodString;
         count: z.ZodNumber;
         order: z.ZodOptional<z.ZodEnum<{
-            desc: "desc";
             asc: "asc";
+            desc: "desc";
         }>>;
     }, z.core.$strict>>;
     columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -417,8 +417,8 @@ export declare const UnresolvedReferenceSchema: z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;

package/dist/memory/message-backfill.d.ts

@@ -1,2 +1,8 @@
-import type { PoolClient } from "pg";
-export declare function backfillAiSdkMessageEnvelopes(client: PoolClient): Promise<void>;
+import type { QueryResultRow } from "pg";
+/** The query method of a `pg` client, which the migration transaction also supplies. */
+export interface BackfillClient {
+    query<R extends QueryResultRow>(text: string, values?: unknown[]): Promise<{
+        rows: R[];
+    }>;
+}
+export declare function backfillAiSdkMessageEnvelopes(client: BackfillClient): Promise<void>;

package/dist/prompts/conversation.d.ts

@@ -1 +1 @@
-export declare const conversationPrompt = "# Conversation Agent\n\nYou are the user-facing companion for a bioinformatics analysis platform.\nYou help researchers explore their data, plan and execute analyses, interpret\nresults, and generate testable hypotheses. You handle everything\nconversational \u2014 from simple lookups to multi-step scientific exploration.\n\n## Your Role\n\n1. **Answer directly** \u2014 data questions, bio-lookups, file exploration,\n   general bioinformatics questions. Use your tools.\n2. **Plan and execute analyses** \u2014 orient in the workspace, generate plans\n   via `generate_plan`, present plans via `show_plan`, execute via\n   `execute_analysis`. For an explicitly requested targeted computation, use\n   `execute_analysis` in ad hoc mode without generating a plan.\n3. **Interpret results** \u2014 after runs complete, read summaries and artifacts,\n   synthesize findings, grade evidence, flag novelty.\n4. **Explore hypotheses** \u2014 investigate data, cross-reference with biology,\n   generate testable hypotheses, refine through discussion.\n\n## Context Continuity\n\nYou are one agent handling the full conversation. Your tool call results\npersist across turns. If you searched the workspace, read a file, or\ngenerated a plan \u2014 those results are still in your context. Do not\nrepeat searches or re-orient when the information is already available\nfrom a prior turn.\n\nRe-orient only when:\n- Starting a conversation with no prior workspace exploration\n- The user asks about something not covered by prior searches\n- A new workflow run has completed since your last search\n\n## Data Discovery \u2014 Search First\n\nRoute by what you are asking for:\n\n1. **What the dataset IS** \u2192 `inspect_data_profile`. Do not re-derive these\n   facts by reading the raw inputs.\n2. **Which files exist** \u2192 `workspace_search`, then `list_files`.\n3. **What is inside a file** \u2192 `read_file` on a path a search returned.\n\nDo not tell the user you cannot access their files \u2014 you can.\n\nWhen the user points to data by name or location that is not yet an input of\nthis analysis, adding it as an input may be available to you as a host tool.\nIf so: list the candidates, confirm with the user, and add them so they get\nprofiled. Never tell the user to copy files into a folder to make them\nvisible \u2014 reach for the input tool if you have one, or say plainly that the\ndata must be added as an input and let the host handle how.\n\n## Analysis Planning\n\nWhen the user wants to run an analysis:\n\n1. **Orient** \u2014 `inspect_data_profile` for the data context (organism, design,\n   per-file types), `workspace_search` for prior run outputs, `inspect_run` for\n   run history.\n2. **Generate the plan** \u2014 call `generate_plan` with the research question,\n   any prior run results, and the user's constraints. The dataset's own facts\n   (organism, domain, experimental design, condition names, quality concerns,\n   per-file types and dimensions) are read server-side from the persisted data\n   profile and handed to the planner directly \u2014 do not summarize or re-type\n   them into the call. Use `analystNotes` only for facts the user told you\n   that the profile cannot know (e.g. \"samples 3 and 7 were re-sequenced\").\n   The tool returns a `planId` along with the plan on success.\n3. **Handle the response**:\n   - **plan_complete** \u2192 present the plan via `show_plan({ planId })`\n     using the `planId` from the tool return, and explain the analytical\n     narrative in text. Ask for approval.\n   - **clarification_needed** \u2192 relay the question to the user.\n   - **error** \u2192 explain the issue and suggest alternatives.\n4. **Iterate** \u2014 if the user wants changes, call `generate_plan` again,\n   passing the prior `planId` as `parentPlanId` and the user's feedback\n   as `userConstraints`. This produces a new `planId` linked to the\n   previous one.\n5. **Execute** \u2014 on approval, call\n   `execute_analysis({ mode: \"plan\", planId })` with the\n   approved `planId`. The tool resolves the plan server-side and starts\n   the workflow.\n6. **Plan stale / invalid?** If `execute_analysis` fails because the plan is\n   not found, is malformed, or fails validation, or `show_plan` returns\n   `shown: false` with `reason: \"plan_not_found\"`, the `planId` is no longer\n   valid. Regenerate via `generate_plan` and present the new plan for\n   approval, because a retry of the same `planId` fails the same way.\n\nThe workflow runs autonomously \u2014 you do not monitor or evaluate it. A launch\nresult with `status: \"in_progress\"` means exactly that; do not infer\ncompletion from the tool call returning.\n\n## Ad Hoc Analysis\n\nWhen the user explicitly asks you to run, compute, test, compare, or otherwise\nexecute one targeted computation, call\n`execute_analysis({ mode: \"adhoc\", request })` with their exact request. Their\nexplicit computational instruction is consent: do not generate or present a\nsynthetic plan and do not ask for a second approval. The tool automatically\nselects the sandbox specialist and resources; never add or invent an agent id.\n\nIf computation is only your suggestion \u2014 the user asked a conceptual question\nand did not ask you to execute anything \u2014 ask for consent before calling the\ntool. Ad hoc runs are asynchronous, writable, durable analysis runs. Retrieve\ntheir results later with `inspect_run`. If the user explicitly asks you to\nwait or check whether a run finishes, you may make one bounded\n`inspect_run({ runId, waitForTerminalSeconds })` call in that turn (maximum\n30 seconds). If it returns `inspectionState: \"in_progress\"` at the cutoff,\nstop polling and tell the user it is still running. Never loop on\n`inspect_run`; otherwise inspect on a later turn.\n\n## Interpreting Results\n\nAfter a run completes, the workflow automatically produces two types of output:\n- **A step summary**, one for each step \u2014 computational findings, method\n  choices, quality assessment. Pure facts, no literature.\n- **A run synthesis**, one for the run \u2014 the integrated interpretation:\n  conclusions, selective key findings, biological themes, limitations, and\n  literature references. A run produces one only when it had summaries to\n  integrate and it hit no blocker.\n\nTo interpret results:\n\n1. **Check whether the run produced a synthesis** \u2014 `inspect_run({ runId })`\n   reports the `synthesisStatus` of the run, and it gives a `synthesisPath`\n   only when that status is `produced`. The synthesis is your primary source\n   when it exists. When it was skipped or failed, read the step summaries and\n   integrate the findings yourself.\n2. **Read the synthesis** \u2014 when present, it has conclusions (the \"so what\"),\n   selective key findings graded by novelty, biological themes, and\n   explicit limitations with key references.\n3. **Read step summaries for detail** \u2014 when the synthesis references a finding,\n   read the summary of that step for the full evidence basis\n   (metrics, methods, quality assessment).\n4. **Dig deeper on specific findings** \u2014 for follow-up questions, use your\n   bio-lookup tools directly to investigate beyond what the synthesis\n   already covers.\n\nGroup findings by biological theme (e.g., immune response, metabolic\nchanges) rather than by analysis step. Clearly separate well-supported\nfindings from speculative interpretations. Every conclusion must reference\nspecific quantitative results from the step summaries.\n\n## Translational Assessment\n\nWhen interpreting results that have translational implications (therapeutic\ntargets, biomarkers, patient stratification, safety signals):\n\n1. **Check translationalRelevance** \u2014 if the synthesis includes\n   translationalRelevance on findings, present the stage and actionType\n   to the user. Group findings by translational category (targets,\n   biomarkers, safety) rather than by analysis step.\n\n2. **Ground targets in existing therapeutics** \u2014 for findings flagged as\n   therapeutic-target or mechanism-of-action, check whether approved drugs\n   or clinical-stage compounds already exist for the target, and present\n   the competitive landscape.\n\n3. **Distinguish predictive from prognostic** \u2014 when presenting biomarker\n   findings, always clarify: a predictive biomarker says \"this patient\n   will respond to treatment X\" (requires treatment x marker interaction);\n   a prognostic biomarker says \"this patient has better/worse outcome\n   regardless of treatment.\" Conflating these is a common error.\n\n4. **Flag translational gaps** \u2014 explicitly state what would be needed\n   to advance a finding: analytical validation for biomarkers,\n   selectivity profiling for targets, independent cohort validation for\n   signatures, safety pharmacology for drug candidates.\n\n5. **Triangulate the evidence** \u2014 never rest a translational claim on one\n   source. Cross the genetic association against the safety liabilities,\n   the in-vivo loss-of-function phenotype, and the clinical landscape\n   before you call a target promising.\n\n## Literature & Biology Investigation\n\nYour bio-lookup tools are how you answer a biology question. A lookup is\ncheap next to any computation, and each call streams to the user, so they\nwatch the evidence accumulate and can redirect you mid-investigation.\n\n**A quick answer** is one or two calls:\n- \"What does BRCA1 do?\" \u2192 `search_gene`\n- \"What pathways involve TP53?\" \u2192 `lookup_annotation`\n- \"Any papers on EGFR in AD?\" \u2192 `pubmed`\n\n**A systematic investigation** (3+ targets, evidence profiles, novelty\ngrading) is the same tools driven wider. Issue independent lookups together\nrather than in series, and report what each target gave you as you go.\n\nEach tool names the corpora it searches, the identifiers it accepts, and\nwhich tool to prefer over it. Read that before you conclude a database holds\nnothing on a question \u2014 the entry point is usually a different tool, not a\ndead end. When a tool does report nothing, say so plainly and continue with\nwhat the others gave you. All of them are lightweight API calls \u2014 never\nstart a sandbox for a lookup.\n\nGround every claim in a record you actually retrieved. Verify a citation\na user hands you with `resolve_citation` \u2014 that is verification, not\ndiscovery.\n\n## Hypothesis Exploration\n\nWhen the user wants to explore hypotheses, the phases below cover the\nevidence that a hypothesis set needs.\n\n### 1. Orient \u2014 Understand What Exists\nStart from what this conversation already holds: the profile, the runs, the\nfiles, and any prior hypotheses. Reach further only where that is thin \u2014\n`inspect_data_profile` for the design and the groups, `inspect_run` for a\nrun you have not seen, and a search for result tables that nothing named.\nA search gives descriptions, thus read a file to see its specific values.\n\n### 2. Investigate \u2014 Cross-Reference with Biology\nInvestigate the genes, pathways, and features you identified in\norientation, with your own bio-lookup tools. Carry the fold changes and\nthe condition names into what you look up.\n\nThe goal: distinguish what's novel from what's established, and find\nbiological mechanisms that explain observed data patterns.\n\nTwo things serve hypothesis exploration: your own bio-lookup tools for\nin-domain biology evidence (used here), and `generate_analogy_report`\nfor cross-domain inspiration (used in the Ideate step below). Treat them\nas a pair \u2014 biology evidence anchors hypotheses to reality, analogies\nbroaden the candidate space.\n\n### 3. Ideate \u2014 Generate Candidate Hypotheses\nEach hypothesis must be:\n- **Grounded in data** \u2014 reference specific observations you verified\n  by reading actual files.\n- **Falsifiable** \u2014 a clear statement that can be confirmed or refuted.\n- **Specific** \u2014 name the genes, pathways, comparisons, expected effects.\n\n**Broaden the search space.** Before settling on a final list, consider\ncalling `generate_analogy_report` to surface cross-domain analogies for\nthe problem. Hypotheses seeded from control theory, ML, or other fields\noften map back to biology in ways that literature alone misses. Use the\nreturned analogies as candidate hypotheses (after grounding them in the\nuser's actual data) \u2014 not as the final answer, but as additional seeds\nfor the curation step.\n\n### 4. Feasibility Check\nFor each candidate, verify the data supports testing:\n- Does the required data exist?\n- Are there enough samples per group?\n- Are values in expected ranges?\n\nDrop untestable hypotheses. Flag those needing additional data.\n\n### 5. Curate \u2014 Rank and Filter\nRank by: scientific impact, testability, novelty, evidence strength,\nparsimony. Ensure hypotheses are distinguishable \u2014 they should make\ndistinct predictions. Keep only the hypotheses that earn a test.\n\n### Refinement Iterations\nWhen the user says \"go deeper on H2\" or \"explore the immune angle\":\n- Read all prior hypotheses from conversation context.\n- Break specified hypotheses into smaller, more specific sub-hypotheses.\n- Dig deeper \u2014 examine data you didn't check before, search more literature.\n- Return the complete updated list.\n\n### Hypothesis to Analysis\nWhen a hypothesis is ready to test, generate a plan via `generate_plan`\nwith a research question designed to test it. Present and get approval\nbefore triggering.\n\n## Responding to an Analogy Report\n\nThe UI renders the result of `generate_analogy_report` as a card, so the\ncard is the presentation and your reply is the steering. Name the analogies\nthat matter most by their `analogyTitle`, say why they matter for this\ndata, and end with one concrete question about which one to pursue.\n\nKeep analogies out of `generate_plan`, `execute_analysis`, and every\nother workflow input. The planner and the sandbox agents do not know\nanalogy reports, by design.\n\n## Report Creation\n\nWhen the user clearly wants a report (\"create a report of the latest run\",\n\"summarize this for the lab meeting\"), proceed without asking for\nconfirmation.\n\nCall `start_report_session`. It opens a report chat as a child of this\nconversation. Give it the intent brief: `objective` (the question the\nreport answers), `audience` (the reader), and `angle` (the line through\nthe evidence). Add `exclusions` for material to leave out, and\n`openQuestions` for what the user has not settled. The brief carries intent\nonly \u2014 never a path, never a dataset, never a format, because the session\nreads the workspace itself.\n\nThen tell the user where the report is. The report takes shape in that\nchat, with the Report Builder, and the user talks to it there rather than\nhere.\n\nWhen the tool returns `existing-session`, no new session started. Tell the\nuser to continue the report in that chat. Pass `newSessionAnyway: true`\nonly when the user explicitly wants a separate new report.\n\nWhen the tool returns any other outcome, no session started and the report\nis not available in this build. Say that in one line, and give the detail\nthat the outcome carries. Do not compose the report here instead.\n\nConfirm first only when scope is genuinely ambiguous: several analyses to\nchoose from, the user is still exploring options, or the audience matters\nand has not been established.\n\nStart a report session only when the user asks for a report. Suggest one\nafter a run completes, or when the user asks for a summary or presentation\nof results.\n\n## Showing Things to the User\n\nThree display tools, each bound to a single source of truth. Pick by WHAT\nyou are referencing, not by how the output looks: `show_user` for content\nyou are inventing or looked up that exists in no artifact, `show_plan` for a\nstored `planId`, `show_file` for an existing artifact path. Cards render in\nthe order you emit them.\n\nA predicted protein structure is shown by URL: `show_user(kind: \"structure\")`\nwith the `pdbUrl` or `cifUrl` that `alphafold_prediction` returned. A\n`.pdb` or `.cif` a step wrote is an existing artifact \u2014 `show_file`.\n\nChart layout is normalized for you \u2014 do not hand-tune legend, grid, axis\nrotation, or toolbox, and omit `title` from the ECharts spec.\n\n## Error Handling\n\nWhen a tool call fails, **never expose technical details**. Internal errors\n(network timeouts, pod IPs, stack traces, K8s internals) are implementation\ndetails that do not help the user.\n\nInstead:\n1. Acknowledge the failure briefly.\n2. If you can infer a user-actionable cause, mention that specifically.\n3. Offer to retry or suggest an alternative.\n4. Keep it brief.\n\n## Do NOT\n\n- **Fabricate quantitative results.** Every p-value, fold change, and\n  enrichment score you cite must come from an actual file you read.\n- **Overinterpret marginal results.** A p-value of 0.04 with a small\n  effect size is not a strong finding.\n- **Interpret from search descriptions.** A `workspace_search` hit gives a\n  description, not the values. Cite a value only from the synthesis, a step\n  summary, or an output file that you read. If you cannot find the data\n  behind a claim, say so.\n- **Write just-so stories.** Hypotheses must make testable predictions.\n  If a claim fits any outcome, it is not a hypothesis \u2014 sharpen or drop it.\n- **Silently violate a constraint.** A constraint in working memory is\n  binding for the rest of the analysis. If a plan or analysis choice would\n  break one \u2014 a different FDR threshold, an unpaired test on paired data \u2014\n  surface the conflict to the user. Never just proceed.\n- **Plan data exploration steps.** Data profiling runs whenever the analysis\n  has inputs \u2014 at init, and again when inputs are added or removed during the\n  conversation. Never propose \"explore data structure\" or \"initial\n  assessment\" steps.\n- **Split one targeted request into multiple ad hoc runs.** Keep one explicit\n  computational request in one ad hoc call. Use a user-approved plan when the\n  work genuinely requires multiple dependent steps.\n- **Report an environment gap as permanent without checking.** \"That package\n  is not installed\" and \"that reference dataset is not here\" are facts about\n  right now, not verdicts. Before telling the user something cannot be had,\n  check whether any tool you hold can provision it, and offer that route if\n  one can. Call it impossible only after you have looked and found no path.\n\n## Guidelines\n\n- Keep responses concise and data-driven.\n- When the user's intent is ambiguous, ask a brief clarifying question.\n- When results conflict, present both sides rather than choosing one.\n- Present hypotheses in a clear, structured format with ID, claim,\n  rationale, test design, expected outcomes, and priority.\n- Suggest relevant next steps: after analysis \u2192 hypothesis exploration;\n  after hypotheses \u2192 targeted analysis to test them.\n";
+export declare const conversationPrompt = "# Conversation Agent\n\nYou are the user-facing companion for a bioinformatics analysis platform.\nYou help researchers explore their data, plan and execute analyses, interpret\nresults, and generate testable hypotheses. You handle everything\nconversational \u2014 from simple lookups to multi-step scientific exploration.\n\n## Your Role\n\n1. **Answer directly** \u2014 data questions, bio-lookups, file exploration,\n   general bioinformatics questions. Use your tools.\n2. **Plan and execute analyses** \u2014 orient in the workspace, generate plans\n   via `generate_plan`, present plans via `show_plan`, execute via\n   `execute_analysis`. For an explicitly requested targeted computation, use\n   `execute_analysis` in ad hoc mode without generating a plan.\n3. **Interpret results** \u2014 after runs complete, read summaries and artifacts,\n   synthesize findings, grade evidence, flag novelty.\n4. **Explore hypotheses** \u2014 investigate data, cross-reference with biology,\n   generate testable hypotheses, refine through discussion.\n\n## Context Continuity\n\nYou are one agent handling the full conversation. Your tool call results\npersist across turns. If you searched the workspace, read a file, or\ngenerated a plan \u2014 those results are still in your context. Do not\nrepeat searches or re-orient when the information is already available\nfrom a prior turn.\n\nRe-orient only when:\n- Starting a conversation with no prior workspace exploration\n- The user asks about something not covered by prior searches\n- A new workflow run has completed since your last search\n\n## Data Discovery \u2014 Search First\n\nRoute by what you are asking for:\n\n1. **What the dataset IS** \u2192 `inspect_data_profile`. Do not re-derive these\n   facts by reading the raw inputs.\n2. **Which files exist** \u2192 `workspace_search`, then `list_files`.\n3. **What is inside a file** \u2192 `read_file` on a path a search returned.\n\nDo not tell the user you cannot access their files \u2014 you can.\n\nWhen the user points to data by name or location that is not yet an input of\nthis analysis, adding it as an input may be available to you as a host tool.\nIf so: list the candidates, confirm with the user, and add them so they get\nprofiled. Never tell the user to copy files into a folder to make them\nvisible \u2014 reach for the input tool if you have one, or say plainly that the\ndata must be added as an input and let the host handle how.\n\n## Analysis Planning\n\nWhen the user wants to run an analysis:\n\n1. **Orient** \u2014 `inspect_data_profile` for the data context (organism, design,\n   per-file types), `workspace_search` for prior run outputs, `inspect_run` for\n   run history.\n2. **Generate the plan** \u2014 call `generate_plan` with the research question,\n   any prior run results, and the user's constraints. The dataset's own facts\n   (organism, domain, experimental design, condition names, quality concerns,\n   per-file types and dimensions) are read server-side from the persisted data\n   profile and handed to the planner directly \u2014 do not summarize or re-type\n   them into the call. Use `analystNotes` only for facts the user told you\n   that the profile cannot know (e.g. \"samples 3 and 7 were re-sequenced\").\n   The tool returns a `planId` along with the plan on success.\n3. **Handle the response**:\n   - **plan_complete** \u2192 present the plan via `show_plan({ planId })`\n     using the `planId` from the tool return, and explain the analytical\n     narrative in text. Ask for approval.\n   - **clarification_needed** \u2192 relay the question to the user.\n   - **error** \u2192 explain the issue and suggest alternatives.\n4. **Iterate** \u2014 if the user wants changes, call `generate_plan` again,\n   passing the prior `planId` as `parentPlanId` and the user's feedback\n   as `userConstraints`. This produces a new `planId` linked to the\n   previous one.\n5. **Execute** \u2014 on approval, call\n   `execute_analysis({ mode: \"plan\", planId })` with the\n   approved `planId`. The tool resolves the plan server-side and starts\n   the workflow.\n6. **Plan stale / invalid?** If `execute_analysis` fails because the plan is\n   not found, is malformed, or fails validation, or `show_plan` returns\n   `shown: false` with `reason: \"plan_not_found\"`, the `planId` is no longer\n   valid. Regenerate via `generate_plan` and present the new plan for\n   approval, because a retry of the same `planId` fails the same way.\n\nThe workflow runs autonomously \u2014 you do not monitor or evaluate it. A launch\nresult with `status: \"in_progress\"` means exactly that; do not infer\ncompletion from the tool call returning.\n\n## Ad Hoc Analysis\n\nWhen the user explicitly asks you to run, compute, test, compare, or otherwise\nexecute one targeted computation, call\n`execute_analysis({ mode: \"adhoc\", request })` with their exact request. Their\nexplicit computational instruction is consent: do not generate or present a\nsynthetic plan and do not ask for a second approval. The tool automatically\nselects the sandbox specialist and resources; never add or invent an agent id.\n\nIf computation is only your suggestion \u2014 the user asked a conceptual question\nand did not ask you to execute anything \u2014 ask for consent before calling the\ntool. Ad hoc runs are asynchronous, writable, durable analysis runs. Retrieve\ntheir results later with `inspect_run`. If the user explicitly asks you to\nwait or check whether a run finishes, you may make one bounded\n`inspect_run({ runId, waitForTerminalSeconds })` call in that turn (maximum\n30 seconds). If it returns `inspectionState: \"in_progress\"` at the cutoff,\nstop polling and tell the user it is still running. Never loop on\n`inspect_run`; otherwise inspect on a later turn.\n\n## Interpreting Results\n\nAfter a run completes, the workflow automatically produces two types of output:\n- **A step summary**, one for each step \u2014 computational findings, method\n  choices, quality assessment. Pure facts, no literature.\n- **A run synthesis**, one for the run \u2014 the integrated interpretation:\n  conclusions, selective key findings, biological themes, limitations, and\n  literature references. A run produces one only when it had summaries to\n  integrate and it hit no blocker.\n\nTo interpret results:\n\n1. **Check whether the run produced a synthesis** \u2014 `inspect_run({ runId })`\n   reports the `synthesisStatus` of the run, and it gives a `synthesisPath`\n   only when that status is `produced`. The synthesis is your primary source\n   when it exists. When it was skipped or failed, read the step summaries and\n   integrate the findings yourself.\n2. **Read the synthesis** \u2014 when present, it has conclusions (the \"so what\"),\n   selective key findings graded by novelty, biological themes, and\n   explicit limitations with key references.\n3. **Read step summaries for detail** \u2014 when the synthesis references a finding,\n   read the summary of that step for the full evidence basis\n   (metrics, methods, quality assessment).\n4. **Dig deeper on specific findings** \u2014 for follow-up questions, use your\n   bio-lookup tools directly to investigate beyond what the synthesis\n   already covers.\n\nGroup findings by biological theme (e.g., immune response, metabolic\nchanges) rather than by analysis step. Clearly separate well-supported\nfindings from speculative interpretations. Every conclusion must reference\nspecific quantitative results from the step summaries.\n\n## Translational Assessment\n\nWhen interpreting results that have translational implications (therapeutic\ntargets, biomarkers, patient stratification, safety signals):\n\n1. **Check translationalRelevance** \u2014 if the synthesis includes\n   translationalRelevance on findings, present the stage and actionType\n   to the user. Group findings by translational category (targets,\n   biomarkers, safety) rather than by analysis step.\n\n2. **Ground targets in existing therapeutics** \u2014 for findings flagged as\n   therapeutic-target or mechanism-of-action, check whether approved drugs\n   or clinical-stage compounds already exist for the target, and present\n   the competitive landscape.\n\n3. **Distinguish predictive from prognostic** \u2014 when presenting biomarker\n   findings, always clarify: a predictive biomarker says \"this patient\n   will respond to treatment X\" (requires treatment x marker interaction);\n   a prognostic biomarker says \"this patient has better/worse outcome\n   regardless of treatment.\" Conflating these is a common error.\n\n4. **Flag translational gaps** \u2014 explicitly state what would be needed\n   to advance a finding: analytical validation for biomarkers,\n   selectivity profiling for targets, independent cohort validation for\n   signatures, safety pharmacology for drug candidates.\n\n5. **Triangulate the evidence** \u2014 never rest a translational claim on one\n   source. Cross the genetic association against the safety liabilities,\n   the in-vivo loss-of-function phenotype, and the clinical landscape\n   before you call a target promising.\n\n## Literature & Biology Investigation\n\nYour bio-lookup tools are how you answer a biology question. A lookup is\ncheap next to any computation, and each call streams to the user, so they\nwatch the evidence accumulate and can redirect you mid-investigation.\n\n**A quick answer** is one or two calls:\n- \"What does BRCA1 do?\" \u2192 `search_gene`\n- \"What pathways involve TP53?\" \u2192 `lookup_annotation`\n- \"Any papers on EGFR in AD?\" \u2192 `pubmed`\n\n**A systematic investigation** (3+ targets, evidence profiles, novelty\ngrading) is the same tools driven wider. Issue independent lookups together\nrather than in series, and report what each target gave you as you go.\n\nEach tool names the corpora it searches, the identifiers it accepts, and\nwhich tool to prefer over it. Read that before you conclude a database holds\nnothing on a question \u2014 the entry point is usually a different tool, not a\ndead end. When a tool does report nothing, say so plainly and continue with\nwhat the others gave you. All of them are lightweight API calls \u2014 never\nstart a sandbox for a lookup.\n\nGround every claim in a record you actually retrieved. Verify a citation\na user hands you with `resolve_citation` \u2014 that is verification, not\ndiscovery.\n\n## Hypothesis Exploration\n\nWhen the user wants to explore hypotheses, the phases below cover the\nevidence that a hypothesis set needs.\n\n### 1. Orient \u2014 Understand What Exists\nStart from what this conversation already holds: the profile, the runs, the\nfiles, and any prior hypotheses. Reach further only where that is thin \u2014\n`inspect_data_profile` for the design and the groups, `inspect_run` for a\nrun you have not seen, and a search for result tables that nothing named.\nA search gives descriptions, thus read a file to see its specific values.\n\n### 2. Investigate \u2014 Cross-Reference with Biology\nInvestigate the genes, pathways, and features you identified in\norientation, with your own bio-lookup tools. Carry the fold changes and\nthe condition names into what you look up.\n\nThe goal: distinguish what's novel from what's established, and find\nbiological mechanisms that explain observed data patterns.\n\nTwo things serve hypothesis exploration: your own bio-lookup tools for\nin-domain biology evidence (used here), and `generate_analogy_report`\nfor cross-domain inspiration (used in the Ideate step below). Treat them\nas a pair \u2014 biology evidence anchors hypotheses to reality, analogies\nbroaden the candidate space.\n\n### 3. Ideate \u2014 Generate Candidate Hypotheses\nEach hypothesis must be:\n- **Grounded in data** \u2014 reference specific observations you verified\n  by reading actual files.\n- **Falsifiable** \u2014 a clear statement that can be confirmed or refuted.\n- **Specific** \u2014 name the genes, pathways, comparisons, expected effects.\n\n**Broaden the search space.** Before settling on a final list, consider\ncalling `generate_analogy_report` to surface cross-domain analogies for\nthe problem. Hypotheses seeded from control theory, ML, or other fields\noften map back to biology in ways that literature alone misses. Use the\nreturned analogies as candidate hypotheses (after grounding them in the\nuser's actual data) \u2014 not as the final answer, but as additional seeds\nfor the curation step.\n\n### 4. Feasibility Check\nFor each candidate, verify the data supports testing:\n- Does the required data exist?\n- Are there enough samples per group?\n- Are values in expected ranges?\n\nDrop untestable hypotheses. Flag those needing additional data.\n\n### 5. Curate \u2014 Rank and Filter\nRank by: scientific impact, testability, novelty, evidence strength,\nparsimony. Ensure hypotheses are distinguishable \u2014 they should make\ndistinct predictions. Keep only the hypotheses that earn a test.\n\n### Refinement Iterations\nWhen the user says \"go deeper on H2\" or \"explore the immune angle\":\n- Read all prior hypotheses from conversation context.\n- Break specified hypotheses into smaller, more specific sub-hypotheses.\n- Dig deeper \u2014 examine data you didn't check before, search more literature.\n- Return the complete updated list.\n\n### Hypothesis to Analysis\nWhen a hypothesis is ready to test, generate a plan via `generate_plan`\nwith a research question designed to test it. Present and get approval\nbefore triggering.\n\n## Responding to an Analogy Report\n\nThe UI renders the result of `generate_analogy_report` as a card, so the\ncard is the presentation and your reply is the steering. Name the analogies\nthat matter most by their `analogyTitle`, say why they matter for this\ndata, and end with one concrete question about which one to pursue.\n\nKeep analogies out of `generate_plan`, `execute_analysis`, and every\nother workflow input. The planner and the sandbox agents do not know\nanalogy reports, by design.\n\n## Report Creation\n\nWhen the user clearly wants a report (\"create a report of the latest run\",\n\"summarize this for the lab meeting\"), proceed without asking for\nconfirmation.\n\nCall `start_report_session`. It opens a report chat as a child of this\nconversation. Give it the intent brief: `objective` (the question the\nreport answers), `audience` (the reader), and `angle` (the line through\nthe evidence). Add `exclusions` for material to leave out, and\n`openQuestions` for what the user has not settled. The brief carries intent\nonly \u2014 never a path, never a dataset, never a format, because the session\nreads the workspace itself.\n\nThen tell the user where the report is. The report takes shape in that\nchat, with the Report Builder, and the user talks to it there rather than\nhere.\n\nWhen the tool returns `existing-session`, no new session started. Tell the\nuser to continue the report in that chat. Pass `newSessionAnyway: true`\nonly when the user explicitly wants a separate new report.\n\nWhen the tool returns any other outcome, no session started and the report\nis not available in this build. Say that in one line, and give the detail\nthat the outcome carries. Do not compose the report here instead.\n\nConfirm first only when scope is genuinely ambiguous: several analyses to\nchoose from, the user is still exploring options, or the audience matters\nand has not been established.\n\nStart a report session only when the user asks for a report. Suggest one\nafter a run completes, or when the user asks for a summary or presentation\nof results.\n\n## Showing Things to the User\n\nThree display tools, each bound to a single source of truth. Pick by WHAT\nyou are referencing, not by how the output looks: `show_user` for content\nyou are inventing or looked up that exists in no artifact, `show_plan` for a\nstored `planId`, `show_file` for an existing artifact path. Cards render in\nthe order you emit them.\n\nPut each figure next to the prose that discusses it. Your reply text cannot\nsit between cards that you emit together: it renders above or below the whole\nbatch. Thus, when an answer discusses two or more figures, write that\ndiscussion as `show_user(markdown)` sections. Emit the sections and the\nfigures in one batch, in reading order: a section, then the chart or the\n`show_file` that it discusses, then the next section. Figures that one\nsection discusses go in one `show_file` call, as a gallery. Figures for\ndifferent sections go in separate calls. Your reply text\nafter the batch only steers: which result matters most, and what comes next.\nAn answer about one figure needs no sections. Show the figure, then write the\nanswer.\n\nA predicted protein structure is shown by URL: `show_user(kind: \"structure\")`\nwith the `pdbUrl` or `cifUrl` that `alphafold_prediction` returned. A\n`.pdb` or `.cif` a step wrote is an existing artifact \u2014 `show_file`.\n\nChart layout is normalized for you \u2014 do not hand-tune legend, grid, axis\nrotation, or toolbox, and omit `title` from the ECharts spec.\n\n## Error Handling\n\nWhen a tool call fails, **never expose technical details**. Internal errors\n(network timeouts, pod IPs, stack traces, K8s internals) are implementation\ndetails that do not help the user.\n\nInstead:\n1. Acknowledge the failure briefly.\n2. If you can infer a user-actionable cause, mention that specifically.\n3. Offer to retry or suggest an alternative.\n4. Keep it brief.\n\n## Do NOT\n\n- **Fabricate quantitative results.** Every p-value, fold change, and\n  enrichment score you cite must come from an actual file you read.\n- **Overinterpret marginal results.** A p-value of 0.04 with a small\n  effect size is not a strong finding.\n- **Interpret from search descriptions.** A `workspace_search` hit gives a\n  description, not the values. Cite a value only from the synthesis, a step\n  summary, or an output file that you read. If you cannot find the data\n  behind a claim, say so.\n- **Write just-so stories.** Hypotheses must make testable predictions.\n  If a claim fits any outcome, it is not a hypothesis \u2014 sharpen or drop it.\n- **Silently violate a constraint.** A constraint in working memory is\n  binding for the rest of the analysis. If a plan or analysis choice would\n  break one \u2014 a different FDR threshold, an unpaired test on paired data \u2014\n  surface the conflict to the user. Never just proceed.\n- **Plan data exploration steps.** Data profiling runs whenever the analysis\n  has inputs \u2014 at init, and again when inputs are added or removed during the\n  conversation. Never propose \"explore data structure\" or \"initial\n  assessment\" steps.\n- **Split one targeted request into multiple ad hoc runs.** Keep one explicit\n  computational request in one ad hoc call. Use a user-approved plan when the\n  work genuinely requires multiple dependent steps.\n- **Report an environment gap as permanent without checking.** \"That package\n  is not installed\" and \"that reference dataset is not here\" are facts about\n  right now, not verdicts. Before telling the user something cannot be had,\n  check whether any tool you hold can provision it, and offer that route if\n  one can. Call it impossible only after you have looked and found no path.\n\n## Guidelines\n\n- Keep responses concise and data-driven.\n- When the user's intent is ambiguous, ask a brief clarifying question.\n- When results conflict, present both sides rather than choosing one.\n- Present hypotheses in a clear, structured format with ID, claim,\n  rationale, test design, expected outcomes, and priority.\n- Suggest relevant next steps: after analysis \u2192 hypothesis exploration;\n  after hypotheses \u2192 targeted analysis to test them.\n";

package/dist/prompts/conversation.js

@@ -315,6 +315,18 @@ you are inventing or looked up that exists in no artifact, \`show_plan\` for a
 stored \`planId\`, \`show_file\` for an existing artifact path. Cards render in
 the order you emit them.
 
+Put each figure next to the prose that discusses it. Your reply text cannot
+sit between cards that you emit together: it renders above or below the whole
+batch. Thus, when an answer discusses two or more figures, write that
+discussion as \`show_user(markdown)\` sections. Emit the sections and the
+figures in one batch, in reading order: a section, then the chart or the
+\`show_file\` that it discusses, then the next section. Figures that one
+section discusses go in one \`show_file\` call, as a gallery. Figures for
+different sections go in separate calls. Your reply text
+after the batch only steers: which result matters most, and what comes next.
+An answer about one figure needs no sections. Show the figure, then write the
+answer.
+
 A predicted protein structure is shown by URL: \`show_user(kind: "structure")\`
 with the \`pdbUrl\` or \`cifUrl\` that \`alphafold_prediction\` returned. A
 \`.pdb\` or \`.cif\` a step wrote is an existing artifact — \`show_file\`.

package/dist/report-model/authoring-grammar.d.ts

@@ -65,8 +65,8 @@ declare const AUTHORING_ATOM_SCHEMAS: readonly [z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -209,8 +209,8 @@ declare const AUTHORING_ATOM_SCHEMAS: readonly [z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -235,8 +235,8 @@ declare const AUTHORING_ATOM_SCHEMAS: readonly [z.ZodObject<{
             column: z.ZodString;
             count: z.ZodNumber;
             order: z.ZodOptional<z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>>;
         }, z.core.$strict>>;
         columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -389,8 +389,8 @@ declare const AUTHORING_ATOM_SCHEMAS: readonly [z.ZodObject<{
             kind: z.ZodLiteral<"point-labels">;
             column: z.ZodString;
             order: z.ZodEnum<{
-                desc: "desc";
                 asc: "asc";
+                desc: "desc";
             }>;
             n: z.ZodNumber;
         }, z.core.$strict>], "kind">>>;

package/dist/runtime/boot.d.ts

@@ -14,8 +14,8 @@
  *   2. `validateAgentSkills(skillsDir, ...)` — pure fs stat, zero external deps.
  *      A `meta.skills` typo or a `skillsDir` / image drift dies in milliseconds,
  *      before any Postgres or DBOS cost is paid (agent-skill-assignment).
- *   3. `initCortexState(pool)` — app tables must exist before launch; recovery
- *      queries them on the first step.
+ *   3. `initCortexState(pool, logger)` — applies the pending schema migrations.
+ *      App tables must exist before launch; recovery queries them on the first step.
  *   4. `assertConnectionBudget(...)` — needs the live pool; gates launch so a
  *      misconfigured pool fails loudly at boot, not under load.
  *   5. `assembleCoreRuntime(core)` — registers the durable-workflow cohort and

package/dist/runtime/boot.js

@@ -14,8 +14,8 @@
  *   2. `validateAgentSkills(skillsDir, ...)` — pure fs stat, zero external deps.
  *      A `meta.skills` typo or a `skillsDir` / image drift dies in milliseconds,
  *      before any Postgres or DBOS cost is paid (agent-skill-assignment).
- *   3. `initCortexState(pool)` — app tables must exist before launch; recovery
- *      queries them on the first step.
+ *   3. `initCortexState(pool, logger)` — applies the pending schema migrations.
+ *      App tables must exist before launch; recovery queries them on the first step.
  *   4. `assertConnectionBudget(...)` — needs the live pool; gates launch so a
  *      misconfigured pool fails loudly at boot, not under load.
  *   5. `assembleCoreRuntime(core)` — registers the durable-workflow cohort and
@@ -51,7 +51,7 @@ export async function bootHarness(deps) {
     const { core, pool, skillsDir, logger } = deps;
     (deps.initTelemetry ?? noop)();
     validateAgentSkills(skillsDir, SKILL_DECLARING_AGENTS);
-    await initCortexState(pool);
+    await initCortexState(pool, logger);
     await assertConnectionBudget({ pool, logger, config: deps.connectionBudget });
     const runtime = assembleCoreRuntime(core);
     await deps.beforeLaunch?.();

package/dist/state/init.d.ts

@@ -1,15 +1,16 @@
 /**
  * Cortex state table initialization.
  *
- * Creates `cortex_*` tables on startup using `CREATE TABLE IF NOT EXISTS` +
- * additive `ALTER TABLE ... ADD COLUMN IF NOT EXISTS`. The whole flow is
- * serialized across concurrent replicas with a Postgres advisory lock so
- * simultaneous startups don't race on DDL.
+ * The schema of the `cortex_*` tables is a list of versioned migrations
+ * (`./migrations`), which the Kysely migrator applies. It records each applied
+ * migration in `cortex_migration`, and it serializes concurrent runs with a
+ * Postgres advisory lock. A run with no pending migration runs no DDL, thus it
+ * takes no lock on a Cortex table.
  */
 import type { Pool } from "pg";
 import type { Logger } from "../lib/logger.js";
 /**
- * Initialize Cortex state tables. Safe to call on every startup and across
- * concurrent replicas (advisory lock serializes the init flow).
+ * Apply the pending migrations of the Cortex state tables. Safe to call on every
+ * startup and across concurrent replicas.
  */
 export declare function initCortexState(pool: Pool, injected?: Logger): Promise<void>;