from pathlib import Path

from apps.web.vue3 import main as web_main


REPO_ROOT = Path(__file__).resolve().parents[2]


def _index_html() -> str:
    return (REPO_ROOT / "apps/web/vue3/index.html").read_text(encoding="utf-8")


def test_ppi_reset_dialog_opens_gene_list_without_instruction_textarea():
    html = _index_html()
    assert 'title="PPI Reset 输入基因列表"' in html
    assert 'width="92%"' in html
    assert 'class="ppi-reset-dialog-body"' in html
    assert 'class="ppi-reset-table-wrap"' in html
    assert 'max-height:70vh' in html
    assert 'overflow:auto' in html
    assert 'v-model="ppiResetSearch"' in html
    assert 'class="ppi-reset-table"' in html
    assert "v-for=\"row in ppiResetFilteredRows\"" in html
    assert "{{ row.gene_id }}" in html
    assert "{{ row.source }}" in html
    assert "当前保留 {{ ppiResetKeptCount }} / {{ ppiResetRows.length }} 个 ID" in html
    assert 'v-model="ppiResetInstruction"' not in html


def test_ppi_alphafold_links_remain_in_file_list_and_use_table_preview():
    html = _index_html()
    assert ".ppi_alphafold2_links.tsv')) return false" not in html
    assert "AlphaFold DB/Fold2 单蛋白结构链接" not in html
    assert "if (stage?.name === 'ppi') return !isImageFile(name);" in html
    assert 'class="table-preview-table"' in html
    assert "v-for=\"(row, rowIdx) in tablePreviewFilteredRows\"" in html
    assert "当前显示 {{ tablePreviewFilteredRows.length }} / {{ tablePreviewRows.length }} 行" in html
    assert "openTablePreview(file)" in html
    assert "tablePreviewFilteredRows" in html


def test_ppi_result_action_opens_reset_dialog():
    html = _index_html()
    assert "isPpiResetIntent" in html
    assert "raw.includes('基因id')" in html
    assert '@click="openPpiResetDialog(stage)"' in html
    assert 'title="PPI Reset 输入基因列表"' in html


def test_ppi_reset_uses_current_stage_prefix_before_default_execution_prefix():
    html = _index_html()
    assert "const inferPpiPrefixFromStage = (stage)" in html
    assert "const ppiResetPrefix = ref('')" in html
    assert "inferPpiPrefixFromStage(stage) || params.prefix || executionPrefix('ppi')" in html
    assert "const prefixValue = ppiResetPrefix.value || params.prefix || executionPrefix('ppi')" in html
    assert "prefix: prefixValue" in html


def test_ppi_species_resolution_api_contract_exists():
    main_py = (REPO_ROOT / "apps/web/vue3/main.py").read_text(encoding="utf-8")
    assert "class PpiSpeciesResolutionRequest(BaseModel)" in main_py
    assert '@app.post("/api/ppi/species-resolution")' in main_py
    assert "resolve_ppi_species_resolution(" in main_py
    assert "targetSpecies: List[str]" in main_py
    assert "referenceSpecies: List[str]" in main_py
    assert "ignoreExistingOrtholog: bool = False" in main_py
    assert "ignore_existing_ortholog=bool(req.ignoreExistingOrtholog)" in main_py
    assert "requestedStages: List[str]" in main_py
    assert "requested_stages=req.requestedStages or []" in main_py
    assert '"reference_species": "referenceSpecies"' in main_py
    assert '"requested_stages": "requestedStages"' in main_py
    assert '"jobId": "job_id"' in main_py


def test_reference_bundle_download_api_contract_exists():
    main_py = (REPO_ROOT / "apps/web/vue3/main.py").read_text(encoding="utf-8")
    assert "class ReferenceBundleDownloadRequest(BaseModel)" in main_py
    assert '@app.post("/api/reference-bundle/download")' in main_py
    assert "download_reference_annotation_bundle(" in main_py
    assert '"species_code": "speciesCode"' in main_py
    assert '"taxon_id": "taxonId"' in main_py
    assert '"requested_stages": "requestedStages"' in main_py
    assert 'include_recommended=bool(payload.get("include_recommended"))' in main_py


def test_ppi_execute_path_runs_species_resolution_preflight_before_execute():
    html = _index_html()
    assert "const runPpiSpeciesResolutionPreflight = async" in html
    assert "fetch('/api/ppi/species-resolution'" in html
    assert "diagnostics.reference_recommendations" in html
    assert "requestedStages" in html
    assert "PPI/KaKs 前置数据检查" in html
    assert "Spinacia oleracea" not in html
    assert "const shouldRunPpiKaksPreflight =" in html
    assert "const currentIsDependencyOwner = ppiKaksDependencyStages.has(currentStageId) || ppiKaksDependencyStages.has(requestBody.stage)" in html
    assert "id: 'ppi_kaks_reference_status'" in html
    assert "PPI/KaKs reference data and Ortholog mapping required" in html


def test_ppi_kaks_temporary_breaker_is_disabled_and_stage_failure_keeps_scheduler_alive():
    html = _index_html()
    assert "const ppiKaksTemporaryCircuitBreakerEnabled = false;" in html
    assert "await ensureOrthologProducerForPpiKaks();" in html
    assert "executeStageWithConfirmation(stage" in html
    assert ".finally(() => scheduleCheck(0));" in html

    catch_start = html.index("                    } catch (err) {", html.index("const executeStageWithConfirmation = async"))
    catch_end = html.index("                    } finally {", catch_start)
    ordinary_failure = html[catch_start:catch_end]
    assert "stageExecutionStatus.value[stageId] = 'failed';" in ordinary_failure
    assert "console.error('[ERROR] Stage failed:', stageId, err);" in ordinary_failure

    scheduler_start = html.index("const executeStagesWithDependencies = async")
    scheduler_end = html.index("const NCBI_SPECIES_DEFAULTS", scheduler_start)
    scheduler = html[scheduler_start:scheduler_end]
    assert "return deps.some(dep => stageExecutionStatus.value[dep] === 'failed');" in scheduler
    assert "stageExecutionStatus.value[stageId] = 'failed';" in scheduler


def test_ortholog_scope_dialog_and_ppi_queue_preflight_are_wired():
    html = _index_html()
    assert "'ortholog', 'phylogeny'" in html
    assert "currentStageId === 'ortholog' && currentBatchIncludesPpiKaks" in html
    assert "ignoreExistingOrtholog: currentStageId === 'ortholog'" in html
    assert "allowNeedsOrtholog: currentStageId === 'ortholog'" in html
    assert "ppiHasNearReferenceBeforeArabidopsis" in html


def test_ppi_is_preflighted_first_and_kaks_is_deferred_to_its_confirmation():
    html = _index_html()
    assert "const ppiKaksDependencyStages = new Set(['ppi', 'kaks'])" in html
    assert "const ensurePpiKaksDependencyOwner = async (ownerStageId, stageParamsOverride = null) =>" in html
    assert "const ensureOrthologProducerForPpiKaks = async" in html
    assert "for (const ownerStageId of requestedStages)" in html
    assert "await ensurePpiKaksDependencyOwner(ownerStageId)" in html
    assert "const requestedStages = [ownerStageId];" in html
    assert "autoInsertedFor: requestedStages" in html
    assert ".filter(stageId => stageId === 'ppi')" in html
    assert "const prepareKaksSelectedReference = async" in html
    assert "await ensurePpiKaksDependencyOwner('kaks', stageParams)" in html
    assert "referencePolicySource: 'ppi_owner_ortholog_producer'" in html
    assert "referencePolicySource: 'kaks_owner_ortholog_producer'" in html
    assert "await ensureOrthologProducerForPpiKaks()" in html


def test_ppi_preflight_uses_current_stage_and_releases_direct_target_from_ortholog():
    html = _index_html()
    assert "const releaseDirectTargetPpiFromOrtholog = (resolution = {}) =>" in html
    assert "resolution?.decision !== 'ready_target_string'" in html
    assert "const requestedStages = currentIsDependencyOwner" in html
    assert "? [currentStageId]" in html
    assert "releaseDirectTargetPpiFromOrtholog(preflight.resolution);" in html


def test_ppi_needing_mapping_uses_hidden_internal_ortholog_producer():
    html = _index_html()
    start = html.index("const ensureOrthologStageForPpiKaks =")
    end = html.index("const ensurePpiKaksDependencyOwner =", start)
    producer = html[start:end]

    assert "rememberPpiKaksInternalOrthologProducer('ppi'" in producer
    assert "attachOrthologDependencyToOwners(requestedStages);" not in producer
    assert "nextStages.splice" not in producer
    assert "batchExecuteStages.value = nextStages" not in producer


def test_ppi_internal_ortholog_executes_without_visible_stage_scheduler():
    html = _index_html()
    start = html.index("const executePpiOwnedOrthologProducer =")
    end = html.index("const waitForPpiProducerDependency =", start)
    executor = html[start:end]

    assert "executeStageDirect('ortholog', producerParams)" in executor
    assert "executeStagesWithDependencies([producerStage]" not in executor
    assert "stageExecutionStatus.value.ortholog" not in executor


def test_kaks_confirmation_chooses_ppi_or_project_reference_and_mapping_owner():
    html = _index_html()

    assert 'v-model="confirmParams.kaksReferenceSource"' in html
    assert 'label="ppi"' in html
    assert 'label="project"' in html
    assert "orthologMappingOwner: usePpi ? 'ppi' : 'kaks'" in html
    assert "requestBody.orthologMappingOwner = stageParams.orthologMappingOwner" in html


def test_ppi_and_kaks_static_dependencies_hide_internal_ortholog():
    html = _index_html()
    catalog = (REPO_ROOT / "gfa_core/mas/stage_catalog.py").read_text(encoding="utf-8")
    main_py = (REPO_ROOT / "apps/web/vue3/main.py").read_text(encoding="utf-8")

    assert "'ppi': ['identify']," in html
    assert '"ppi": ["identify"],' in catalog
    assert '"ppi": ["identify"],' in main_py
    assert "'kaks': ['identify']," in html
    assert '"kaks": ["identify"],' in catalog
    assert '"kaks": ["identify"],' in main_py
    assert '"ortholog": ["identify"],' in catalog


def test_normal_full_gene_family_plan_excludes_ortholog_and_orders_ppi_before_kaks():
    main_py = (REPO_ROOT / "apps/web/vue3/main.py").read_text(encoding="utf-8")
    catalog = (REPO_ROOT / "gfa_core/mas/stage_catalog.py").read_text(encoding="utf-8")

    workflow_start = main_py.index("FULL_GENE_FAMILY_WORKFLOW_STAGES = [")
    workflow_end = main_py.index("]", workflow_start)
    workflow_block = main_py[workflow_start:workflow_end]
    assert '"ortholog"' not in workflow_block
    assert workflow_block.index('"ppi"') < workflow_block.index('"kaks"')

    context_start = main_py.index("def _downstream_gene_family_stages_for_context")
    context_end = main_py.index("def _resolve_contextual_gene_family_request", context_start)
    context_block = main_py[context_start:context_end]
    full_workflow_start = context_block.index("if _looks_like_gene_family_workflow_query(text):")
    full_workflow_end = context_block.index("return stages", full_workflow_start)
    full_workflow_block = context_block[full_workflow_start:full_workflow_end]
    assert '"ortholog"' not in full_workflow_block
    assert full_workflow_block.index('"ppi"') < full_workflow_block.index('"kaks"')

    normalize_start = main_py.index("def _normalize_full_gene_family_workflow_plan")
    normalize_end = main_py.index("def _", normalize_start + 4)
    normalize_block = main_py[normalize_start:normalize_end]
    assert 'if sid == "ortholog":' in normalize_block


def test_confirmed_full_workflow_recovers_original_user_request_from_history():
    history = [
        {"role": "user", "content": "执行基因家族分析"},
        {"role": "assistant", "content": "是否继续？"},
        {"role": "user", "content": "继续"},
    ]

    assert web_main._full_gene_family_workflow_query_text("继续", history) == "执行基因家族分析"
    assert web_main._full_gene_family_workflow_query_text("执行直系同源基因鉴定", []) == ""


def test_confirmed_full_workflow_removes_visible_ortholog_and_stale_kaks_dependency():
    stages = [
        "phylogeny", "motif", "domain", "structure", "combo", "promoter",
        "synteny", "interspecies_synteny", "karyotype", "pep", "ortholog", "kaks", "ppi",
    ]
    details = [web_main._stage_detail_defaults(stage) for stage in stages]
    next(item for item in details if item["id"] == "kaks")["dependencies"] = ["identify", "ortholog"]

    normalized_stages, normalized_details = web_main._normalize_full_gene_family_workflow_plan(
        message="执行基因家族分析",
        stage_ids=stages,
        stages_detail=details,
        plan_params={"targetSpecies": ["Ft"], "referenceSpecies": ["At"], "geneFamily": "SPL"},
        plan_prefix="Ft.SPL",
    )

    assert "ortholog" not in normalized_stages
    assert normalized_stages.index("ppi") < normalized_stages.index("kaks")
    detail_by_id = {item["id"]: item for item in normalized_details}
    assert detail_by_id["ppi"]["dependencies"] == ["identify"]
    assert detail_by_id["kaks"]["dependencies"] == ["identify"]
    assert detail_by_id["ppi"]["params"]["targetSpecies"] == ["Ft"]
    assert detail_by_id["ppi"]["params"]["referenceSpecies"] == []
    assert detail_by_id["ppi"]["params"]["scopeMode"] == "target_only"
    assert detail_by_id["ppi"]["params"]["analysisRoute"] == "single_species"
    assert detail_by_id["kaks"]["params"]["referenceSpecies"] == ["At"]


def test_deterministic_context_exit_applies_confirmed_full_workflow_contract():
    request = web_main.AgentPlanRequest(
        message="继续",
        prefix="Ft.SPL",
        history=[
            {"role": "user", "content": "执行基因家族分析"},
            {"role": "assistant", "content": "是否继续？"},
            {"role": "user", "content": "继续"},
        ],
        intent={"params": {"referenceSpecies": ["At"]}},
    )
    contextual_request = {
        "family": "SPL",
        "prefix": "Ft.SPL",
        "stages": [
            "phylogeny", "motif", "domain", "structure", "combo", "promoter",
            "synteny", "interspecies_synteny", "karyotype", "pep", "ortholog", "kaks", "ppi",
        ],
        "targetSpecies": ["Ft"],
        "referenceSpecies": ["At"],
        "comparativeSpecies": [],
        "scopeMode": "target_plus_reference",
        "requiresConfirmedSubfamily": True,
        "skipSubfamilyLabels": False,
        "subfamilyState": {"by_species": {"Ft": {"status": "confirmed"}}},
        "contextGate": {"status": "ready", "issues": []},
    }

    response = web_main._build_contextual_gene_family_plan_response(
        request,
        "test_confirmed_full_workflow",
        contextual_request,
    )

    assert response["mode"] == "deterministic_context"
    assert "ortholog" not in response["plan"]["stages"]
    assert response["plan"]["stages"].index("ppi") < response["plan"]["stages"].index("kaks")
    detail_by_id = {item["id"]: item for item in response["plan"]["stages_detail"]}
    assert detail_by_id["kaks"]["dependencies"] == ["identify"]


def test_kaks_request_carries_selected_ortholog_mapping_owner_to_backend():
    main_py = (REPO_ROOT / "apps/web/vue3/main.py").read_text(encoding="utf-8")

    assert 'orthologMappingOwner: str = ""' in main_py
    assert '"orthologMappingOwner": getattr(req, \'orthologMappingOwner\', \'\')' in main_py
    assert (
        'ortholog_mapping_owner=params.get("orthologMappingOwner") '
        'or params.get("ortholog_mapping_owner") or ""'
    ) in main_py

def test_ppi_plan_generation_never_inserts_static_ortholog_dependency():
    main_py = (REPO_ROOT / "apps/web/vue3/main.py").read_text(encoding="utf-8")
    catalog = (REPO_ROOT / "gfa_core/mas/stage_catalog.py").read_text(encoding="utf-8")

    assert '"ppi": ["identify", "ortholog"]' not in main_py
    assert '"ppi": ["identify", "ortholog"]' not in catalog

    context_start = main_py.index("def _downstream_gene_family_stages_for_context")
    context_end = main_py.index("def _resolve_contextual_gene_family_request", context_start)
    context = main_py[context_start:context_end]
    ppi_start = context.index('if any(token in text for token in ["ppi", "互作"]):')
    ppi_end = context.index('if any(token in text for token in ["表达", "expression", "rna"]):', ppi_start)
    ppi_block = context[ppi_start:ppi_end]
    assert 'stages.append("ppi")' in ppi_block
    assert 'stages.append("ortholog")' not in ppi_block
    assert 'elif stage_id in {"kaks", "ppi"} and "ortholog" in node_by_stage:' not in main_py


def test_ppi_preflight_recovered_reference_is_written_to_ppi_owner_only():
    html = _index_html()
    assert "const applyResolvedPpiReferenceToBatch = (resolution = {}, requestedStages = [], requestBody = {})" in html
    assert "const applyPpiOwnerSelectionToBatch = (ownerSelection = {}, requestBody = {})" in html
    assert "ppiReferenceTaxonId: taxonId" in html
    assert "ppiReferenceStorageKey: storageKey" in html
    assert "dependencyOwner: 'ppi'" in html
    assert "requestBody.ppiKaksReferenceSpecies = [resolvedRef]" not in html
    assert "const recoveredReferenceApplied = applyResolvedPpiReferenceToBatch(resolution, requestedStages, requestBody)" in html


def test_ready_preflight_propagates_recovered_reference_before_early_return():
    html = _index_html()
    start = html.index("const ensurePpiKaksDependencyOwner = async (ownerStageId, stageParamsOverride = null) =>")
    end = html.index("const ensureOrthologProducerForPpiKaks = async () =>", start)
    producer = html[start:end]
    propagation = "applyResolvedPpiReferenceToBatch(preflight.resolution, requestedStages, requestBody);"
    ready_branch = "if (preflight.resolution?.status !== 'needs_ortholog')"
    assert propagation in producer
    assert producer.index(propagation) < producer.index(ready_branch)


def test_ppi_kaks_plan_marks_reference_as_preliminary():
    html = _index_html()
    assert "参考物种：${listText(refs)}（仅作为初步推荐，执行前将确定技术参考物种）" in html


def test_initial_ppi_kaks_reference_dialog_offers_project_reference():
    html = _index_html()
    assert 'label="project_reference"' in html
    assert "confirmParams.ppiKaksProjectReferenceSpecies" in html
    assert "decision === 'project_reference'" in html
    assert "ppi_kaks_user_selected_project_reference" in html


def test_batch_confirmation_marks_both_ppi_kaks_reference_labels_as_preliminary():
    html = _index_html()
    start = html.index('v-if="!isBatchExecuting && batchExecuteParams && batchExecuteParams.geneFamilyScopeOptions"')
    end = html.index('v-if="(batchExecuteStages || []).some', start)
    batch_confirmation = html[start:end]
    assert "const batchIncludesPpiKaks = () =>" in html
    setup_return = html[html.index("                return {", html.index("onUnmounted(() =>")):]
    assert "batchIncludesPpiKaks," in setup_return
    assert "reference 参考物种{{ batchIncludesPpiKaks() ? '（仅作为初步推荐，执行前将确定技术参考物种）' : '' }}" in batch_confirmation
    assert "batchIncludesPpiKaks() ? 'reference 参考物种（仅作为初步推荐，执行前将确定技术参考物种）' : 'reference 参考物种（仅用于标签迁移）'" in batch_confirmation