synapse-react-client 4.0.45 → 4.0.47

package/dist/features/team/invitation/components/OpenInvitationsToUserCard.js.map

@@ -1 +1 @@
-{"version":3,"file":"OpenInvitationsToUserCard.js","names":[],"sources":["../../../../../src/features/team/invitation/components/OpenInvitationsToUserCard.tsx"],"sourcesContent":["import { displayToast } from '@/components/ToastMessage/ToastMessage'\nimport { UserBadge } from '@/components/UserCard/UserBadge'\nimport UserOrTeamBadge from '@/components/UserOrTeamBadge/UserOrTeamBadge'\nimport {\n  useAddMemberToTeam,\n  useDeleteMembershipInvitation,\n  useGetAllOpenMembershipInvitations,\n} from '@/synapse-queries/team/useTeamMembers'\nimport { useGetCurrentUserProfile } from '@/synapse-queries/user/useUserBundle'\nimport { ChatTwoTone } from '@mui/icons-material'\nimport { Card, CardProps, Collapse, Divider, Tooltip } from '@mui/material'\nimport Button from '@mui/material/Button'\nimport Stack from '@mui/material/Stack'\nimport Typography from '@mui/material/Typography'\nimport { MembershipInvitation } from '@sage-bionetworks/synapse-client/generated/models/index'\nimport { useRef } from 'react'\nimport TransitionGroup from 'react-transition-group/TransitionGroup'\nimport {\n  ACCEPT_TEAM_INVITATION_ERROR_MESSAGE,\n  ACCEPT_TEAM_INVITATION_SUCCESS_MESSAGE,\n  DECLINE_TEAM_INVITATION_ERROR_MESSAGE,\n} from '../utils/constants'\nimport styles from './OpenInvitationsToUserCard.module.scss'\n\nfunction InvitationRow(props: { invitation: MembershipInvitation }) {\n  const { invitation } = props\n\n  const { mutate: acceptInvitation, isPending: acceptIsPending } =\n    useAddMemberToTeam({\n      onSuccess: () => {\n        displayToast(ACCEPT_TEAM_INVITATION_SUCCESS_MESSAGE, 'success')\n      },\n      onError: error => {\n        displayToast(error.message, 'danger', {\n          title: ACCEPT_TEAM_INVITATION_ERROR_MESSAGE,\n        })\n      },\n    })\n  const { mutate: deleteMembershipInvitation, isPending: deleteIsPending } =\n    useDeleteMembershipInvitation({\n      onSuccess: () => {\n        displayToast('Invitation dismissed.', 'info')\n      },\n      onError: error => {\n        displayToast(error.message, 'danger', {\n          title: DECLINE_TEAM_INVITATION_ERROR_MESSAGE,\n        })\n      },\n    })\n\n  return (\n    <div key={invitation.id} className={styles.row}>\n      <span className={styles.teamName}>\n        <UserOrTeamBadge principalId={invitation.teamId} />\n      </span>\n      <div className={styles.invitationMessage}>\n        {invitation.message && (\n          <>\n            <Tooltip\n              title={\n                <>\n                  Message from{' '}\n                  <UserBadge\n                    userId={invitation.createdBy}\n                    showFullName\n                    showCardOnHover={false}\n                    disableLink\n                  />\n                </>\n              }\n            >\n              <ChatTwoTone sx={{ color: 'grey.700' }} />\n            </Tooltip>\n            <Typography variant=\"body2\" color=\"text.secondary\">\n              {invitation.message}\n            </Typography>\n          </>\n        )}\n      </div>\n      <Button\n        variant=\"contained\"\n        color=\"primary\"\n        loading={acceptIsPending}\n        disabled={deleteIsPending}\n        onClick={() => {\n          acceptInvitation({\n            teamId: invitation.teamId!,\n            userId: invitation.inviteeId!,\n          })\n        }}\n      >\n        Join\n      </Button>\n      <Button\n        variant=\"outlined\"\n        loading={deleteIsPending}\n        disabled={acceptIsPending}\n        onClick={() => {\n          deleteMembershipInvitation({\n            membershipInvitation: invitation,\n          })\n        }}\n      >\n        Decline\n      </Button>\n    </div>\n  )\n}\n\ntype OpenInvitationsToUserCardProps = {\n  cardProps?: CardProps\n}\n\n/**\n * Shows a card of the open team membership invitations for the current user, if any exist. If no invitations exist, nothing is shown.\n */\nexport default function OpenInvitationsToUserCard(\n  props: OpenInvitationsToUserCardProps,\n) {\n  const { cardProps } = props\n  const { data: currentUser } = useGetCurrentUserProfile()\n  const { data: openInvitations, isLoading } =\n    useGetAllOpenMembershipInvitations(currentUser?.ownerId!, {\n      enabled: Boolean(currentUser?.ownerId),\n    })\n\n  // Keep track of the maximum number of invitations seen so that if the list of invitations goes down to 0 we can still show the section (with a message indicating there are no invitations) instead of hiding the section entirely.\n  // This is to prevent jarring changes in the UI if a user accepts/declines an invitation and the section disappears entirely.\n  const maxSeenInvitationsRef = useRef(0)\n  maxSeenInvitationsRef.current = Math.max(\n    maxSeenInvitationsRef.current,\n    openInvitations?.length ?? 0,\n  )\n  if (\n    maxSeenInvitationsRef.current == 0 &&\n    (isLoading || !openInvitations || openInvitations.length === 0)\n  ) {\n    return null\n  }\n\n  return (\n    <Card {...cardProps}>\n      <Typography variant=\"headline3\" gutterBottom>\n        Pending Team Invitations\n      </Typography>\n      <Typography variant=\"body1\" gutterBottom>\n        You have been invited to join the following team(s). 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+{"version":3,"file":"OpenInvitationsToUserCard.js","names":[],"sources":["../../../../../src/features/team/invitation/components/OpenInvitationsToUserCard.tsx"],"sourcesContent":["import { displayToast } from '@/components/ToastMessage/ToastMessage'\nimport { UserBadge } from '@/components/UserCard/UserBadge'\nimport UserOrTeamBadge from '@/components/UserOrTeamBadge/UserOrTeamBadge'\nimport {\n  useAddMemberToTeam,\n  useDeleteMembershipInvitation,\n  useGetAllOpenMembershipInvitations,\n} from '@/synapse-queries/team/useTeamMembers'\nimport { useGetCurrentUserProfile } from '@/synapse-queries/user/useUserBundle'\nimport ChatTwoTone from '@mui/icons-material/ChatTwoTone'\nimport { Card, CardProps, Collapse, Divider, Tooltip } from '@mui/material'\nimport Button from '@mui/material/Button'\nimport Stack from '@mui/material/Stack'\nimport Typography from '@mui/material/Typography'\nimport { MembershipInvitation } from '@sage-bionetworks/synapse-client/generated/models/index'\nimport { useRef } from 'react'\nimport TransitionGroup from 'react-transition-group/TransitionGroup'\nimport {\n  ACCEPT_TEAM_INVITATION_ERROR_MESSAGE,\n  ACCEPT_TEAM_INVITATION_SUCCESS_MESSAGE,\n  DECLINE_TEAM_INVITATION_ERROR_MESSAGE,\n} from '../utils/constants'\nimport styles from './OpenInvitationsToUserCard.module.scss'\n\nfunction InvitationRow(props: { invitation: MembershipInvitation }) {\n  const { invitation } = props\n\n  const { mutate: acceptInvitation, isPending: acceptIsPending } =\n    useAddMemberToTeam({\n      onSuccess: () => {\n        displayToast(ACCEPT_TEAM_INVITATION_SUCCESS_MESSAGE, 'success')\n      },\n      onError: error => {\n        displayToast(error.message, 'danger', {\n          title: ACCEPT_TEAM_INVITATION_ERROR_MESSAGE,\n        })\n      },\n    })\n  const { mutate: deleteMembershipInvitation, isPending: deleteIsPending } =\n    useDeleteMembershipInvitation({\n      onSuccess: () => {\n        displayToast('Invitation dismissed.', 'info')\n      },\n      onError: error => {\n        displayToast(error.message, 'danger', {\n          title: DECLINE_TEAM_INVITATION_ERROR_MESSAGE,\n        })\n      },\n    })\n\n  return (\n    <div key={invitation.id} className={styles.row}>\n      <span className={styles.teamName}>\n        <UserOrTeamBadge principalId={invitation.teamId} />\n      </span>\n      <div className={styles.invitationMessage}>\n        {invitation.message && (\n          <>\n            <Tooltip\n              title={\n                <>\n                  Message from{' '}\n                  <UserBadge\n                    userId={invitation.createdBy}\n                    showFullName\n                    showCardOnHover={false}\n                    disableLink\n                  />\n                </>\n              }\n            >\n              <ChatTwoTone sx={{ color: 'grey.700' }} />\n            </Tooltip>\n            <Typography variant=\"body2\" color=\"text.secondary\">\n              {invitation.message}\n            </Typography>\n          </>\n        )}\n      </div>\n      <Button\n        variant=\"contained\"\n        color=\"primary\"\n        loading={acceptIsPending}\n        disabled={deleteIsPending}\n        onClick={() => {\n          acceptInvitation({\n            teamId: invitation.teamId!,\n            userId: invitation.inviteeId!,\n          })\n        }}\n      >\n        Join\n      </Button>\n      <Button\n        variant=\"outlined\"\n        loading={deleteIsPending}\n        disabled={acceptIsPending}\n        onClick={() => {\n          deleteMembershipInvitation({\n            membershipInvitation: invitation,\n          })\n        }}\n      >\n        Decline\n      </Button>\n    </div>\n  )\n}\n\ntype OpenInvitationsToUserCardProps = {\n  cardProps?: CardProps\n}\n\n/**\n * Shows a card of the open team membership invitations for the current user, if any exist. If no invitations exist, nothing is shown.\n */\nexport default function OpenInvitationsToUserCard(\n  props: OpenInvitationsToUserCardProps,\n) {\n  const { cardProps } = props\n  const { data: currentUser } = useGetCurrentUserProfile()\n  const { data: openInvitations, isLoading } =\n    useGetAllOpenMembershipInvitations(currentUser?.ownerId!, {\n      enabled: Boolean(currentUser?.ownerId),\n    })\n\n  // Keep track of the maximum number of invitations seen so that if the list of invitations goes down to 0 we can still show the section (with a message indicating there are no invitations) instead of hiding the section entirely.\n  // This is to prevent jarring changes in the UI if a user accepts/declines an invitation and the section disappears entirely.\n  const maxSeenInvitationsRef = useRef(0)\n  maxSeenInvitationsRef.current = Math.max(\n    maxSeenInvitationsRef.current,\n    openInvitations?.length ?? 0,\n  )\n  if (\n    maxSeenInvitationsRef.current == 0 &&\n    (isLoading || !openInvitations || openInvitations.length === 0)\n  ) {\n    return null\n  }\n\n  return (\n    <Card {...cardProps}>\n      <Typography variant=\"headline3\" gutterBottom>\n        Pending Team Invitations\n      </Typography>\n      <Typography variant=\"body1\" gutterBottom>\n        You have been invited to join the following team(s). New content may be\n        visible to you after you accept a team invitation.\n      </Typography>\n      {openInvitations && openInvitations.length > 0 ? (\n        <Stack\n          component={TransitionGroup}\n          divider={<Divider flexItem />}\n          spacing={2}\n          mt={2}\n        >\n          {openInvitations.map(invitation => (\n            <Collapse key={invitation.id}>\n              <InvitationRow invitation={invitation} />\n            </Collapse>\n          ))}\n        </Stack>\n      ) : (\n        <Typography\n          variant=\"body1Italic\"\n          align=\"center\"\n          color=\"text.secondary\"\n          mt={2}\n        >\n          You have no pending team invitations.\n        </Typography>\n      )}\n    </Card>\n  )\n}\n"],"mappings":";;;;;;;;;;;;;;;;AAwBA,SAAS,EAAc,GAA6C;CAClE,IAAM,EAAE,kBAAe,GAEjB,EAAE,QAAQ,GAAkB,WAAW,MAC3C,EAAmB;EACjB,iBAAiB;GACf,EAAa,GAAwC,SAAS;EAChE;EACA,UAAS,MAAS;GAChB,EAAa,EAAM,SAAS,UAAU,EACpC,OAAO,EACT,CAAC;EACH;CACF,CAAC,GACG,EAAE,QAAQ,GAA4B,WAAW,MACrD,EAA8B;EAC5B,iBAAiB;GACf,EAAa,yBAAyB,MAAM;EAC9C;EACA,UAAS,MAAS;GAChB,EAAa,EAAM,SAAS,UAAU,EACpC,OAAO,EACT,CAAC;EACH;CACF,CAAC;CAEH,OACE,kBAAC,OAAD;EAAyB,WAAW,EAAO;YAA3C;GACE,kBAAC,QAAD;IAAM,WAAW,EAAO;cACtB,kBAAC,GAAD,EAAiB,aAAa,EAAW,OAAS,CAAA;GAC9C,CAAA;GACN,kBAAC,OAAD;IAAK,WAAW,EAAO;cACpB,EAAW,WACV,kBAAA,GAAA,EAAA,UAAA,CACE,kBAAC,GAAD;KACE,OACE,kBAAA,GAAA,EAAA,UAAA;MAAE;MACa;MACb,kBAAC,GAAD;OACE,QAAQ,EAAW;OACnB,cAAA;OACA,iBAAiB;OACjB,aAAA;MACD,CAAA;KACD,EAAA,CAAA;eAGJ,kBAAC,GAAD,EAAa,IAAI,EAAE,OAAO,WAAW,EAAI,CAAA;IAClC,CAAA,GACT,kBAAC,GAAD;KAAY,SAAQ;KAAQ,OAAM;eAC/B,EAAW;IACF,CAAA,CACZ,EAAA,CAAA;GAED,CAAA;GACL,kBAAC,GAAD;IACE,SAAQ;IACR,OAAM;IACN,SAAS;IACT,UAAU;IACV,eAAe;KACb,EAAiB;MACf,QAAQ,EAAW;MACnB,QAAQ,EAAW;KACrB,CAAC;IACH;cACD;GAEO,CAAA;GACR,kBAAC,GAAD;IACE,SAAQ;IACR,SAAS;IACT,UAAU;IACV,eAAe;KACb,EAA2B,EACzB,sBAAsB,EACxB,CAAC;IACH;cACD;GAEO,CAAA;EACL;IAtDK,EAAW,EAsDhB;AAET;AASA,SAAwB,EACtB,GACA;CACA,IAAM,EAAE,iBAAc,GAChB,EAAE,MAAM,MAAgB,EAAyB,GACjD,EAAE,MAAM,GAAiB,iBAC7B,EAAmC,GAAa,SAAU,EACxD,SAAS,EAAQ,GAAa,QAChC,CAAC,GAIG,IAAwB,EAAO,CAAC;CAYtC,OAXA,EAAsB,UAAU,KAAK,IACnC,EAAsB,SACtB,GAAiB,UAAU,CAC7B,GAEE,EAAsB,WAAW,MAChC,KAAa,CAAC,KAAmB,EAAgB,WAAW,KAEtD,OAIP,kBAAC,GAAD;EAAM,GAAI;YAAV;GACE,kBAAC,GAAD;IAAY,SAAQ;IAAY,cAAA;cAAa;GAEjC,CAAA;GACZ,kBAAC,GAAD;IAAY,SAAQ;IAAQ,cAAA;cAAa;GAG7B,CAAA;GACX,KAAmB,EAAgB,SAAS,IAC3C,kBAAC,GAAD;IACE,WAAW;IACX,SAAS,kBAAC,GAAD,EAAS,UAAA,GAAU,CAAA;IAC5B,SAAS;IACT,IAAI;cAEH,EAAgB,KAAI,MACnB,kBAAC,GAAD,EAAA,UACE,kBAAC,GAAD,EAA2B,cAAa,CAAA,EAChC,GAFK,EAAW,EAEhB,CACX;GACI,CAAA,IAEP,kBAAC,GAAD;IACE,SAAQ;IACR,OAAM;IACN,OAAM;IACN,IAAI;cACL;GAEW,CAAA;EAEV;;AAEV"}

package/dist/mocks/cohortBuilder/cohortBuilderMockProfiles.d.ts

@@ -0,0 +1,53 @@
+import { AggregateCountSuppressionStrategy } from '@sage-bionetworks/synapse-client/generated/models/AggregateCountSuppressionStrategy';
+import { FacetPostProcessingConfig } from '@sage-bionetworks/synapse-client/generated/models/FacetPostProcessingConfig';
+/**
+ * Best-guess Cohort Builder 2.0 source layout, expressed as the columns the two
+ * VirtualTables expose. The participant-perspective VT groups MATERIAL by
+ * participant; the data-perspective VT groups MATERIAL by file/dataset reference.
+ * Data attributes keep the same column name in both VTs (a STRING_LIST in the
+ * participant VT, a scalar in MATERIAL and the data VT) so one filter tree can be
+ * applied to both as a defining condition.
+ */
+/** Relative frequency of each value, used by the synthetic data generator. */
+export type WeightedValues = Readonly<Record<string, number>>;
+export type MockParticipantAttribute = {
+    name: string;
+    values: WeightedValues;
+    isQuasiIdentifier: boolean;
+};
+export type MockAssay = {
+    assay: string;
+    dataType: string;
+    fileFormats: readonly string[];
+    /** Portal-specific data attributes (e.g. specimenType, tissue) and their possible values. */
+    extraAttributes: Readonly<Record<string, readonly string[]>>;
+};
+export type MockStudy = {
+    name: string;
+    participantCount: number;
+    /** FILE studies map participants to individual files; DATASET studies map every participant to every study dataset. */
+    mapping: 'FILE' | 'DATASET';
+    assays: readonly MockAssay[];
+};
+export type CohortBuilderMockProfile = {
+    portalName: string;
+    participantIdPrefix: string;
+    participantsVirtualTableId: string;
+    dataVirtualTableId: string;
+    /** First synthetic entity ID assigned to a file or dataset reference. */
+    firstReferenceEntityId: number;
+    participantAttributes: readonly MockParticipantAttribute[];
+    extraDataAttributeNames: readonly string[];
+    studies: readonly MockStudy[];
+    suppressionThreshold: number;
+    countSuppressionStrategy: AggregateCountSuppressionStrategy;
+    facetPostProcessingConfig: FacetPostProcessingConfig;
+};
+export declare const PARTICIPANT_ID_COLUMN_NAME = "individualId";
+export declare const STUDY_COLUMN_NAME = "study";
+export declare const DATA_REFERENCE_COLUMN_NAME = "dataReference";
+export declare const REFERENCE_TYPE_COLUMN_NAME = "referenceType";
+export declare const CORE_DATA_ATTRIBUTE_NAMES: readonly ["dataType", "assay", "fileFormat"];
+export declare const ELITE_MOCK_PROFILE: CohortBuilderMockProfile;
+export declare const ADKP_MOCK_PROFILE: CohortBuilderMockProfile;
+//# sourceMappingURL=cohortBuilderMockProfiles.d.ts.map

package/dist/mocks/cohortBuilder/cohortBuilderMockProfiles.d.ts.map

@@ -0,0 +1 @@
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package/dist/mocks/cohortBuilder/cohortBuilderMockProfiles.js

@@ -0,0 +1,391 @@
+//#region src/mocks/cohortBuilder/cohortBuilderMockProfiles.ts
+var e = "individualId", t = "study", n = "dataReference", r = "referenceType", i = [
+	"dataType",
+	"assay",
+	"fileFormat"
+], a = {
+	false: 85,
+	true: 15
+}, o = {
+	portalName: "ELITE",
+	participantIdPrefix: "ELITE-SYN",
+	participantsVirtualTableId: "syn90000001",
+	dataVirtualTableId: "syn90000002",
+	firstReferenceEntityId: 901e5,
+	participantAttributes: [
+		{
+			name: "sex",
+			values: {
+				Female: 58,
+				Male: 41,
+				Unknown: 1
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "ageRange",
+			values: {
+				"20-24": 1,
+				"25-29": 1,
+				"30-34": 1,
+				"35-39": 2,
+				"40-44": 2,
+				"45-49": 3,
+				"50-54": 4,
+				"55-59": 5,
+				"60-64": 6,
+				"65-69": 7,
+				"70-74": 8,
+				"75-79": 9,
+				"80-84": 10,
+				"85-89": 11,
+				"90-94": 12,
+				"95-99": 9,
+				"100-104": 5,
+				"105-109": .4,
+				">109": .1
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "race",
+			values: {
+				White: 78,
+				"Black or African American": 9,
+				Asian: 6,
+				"American Indian or Alaska Native": .3,
+				"More than one race": 3,
+				Unknown: 4
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "ethnicity",
+			values: {
+				"Not Hispanic or Latino": 90,
+				"Hispanic or Latino": 7,
+				Unknown: 3
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "apoeGenotype",
+			values: {
+				"e2/e2": .7,
+				"e2/e3": 12,
+				"e2/e4": 2,
+				"e3/e3": 61,
+				"e3/e4": 21,
+				"e4/e4": 2
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "familyStudyParticipant",
+			values: {
+				false: 60,
+				true: 40
+			},
+			isQuasiIdentifier: !1
+		},
+		{
+			name: "hasDementia",
+			values: a,
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "hasDiabetes",
+			values: a,
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "hasCardiovascularDisease",
+			values: {
+				false: 70,
+				true: 30
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "mortalityStatus",
+			values: {
+				Living: 55,
+				Deceased: 45
+			},
+			isQuasiIdentifier: !1
+		}
+	],
+	extraDataAttributeNames: ["specimenType"],
+	studies: [
+		{
+			name: "LLFS",
+			participantCount: 1200,
+			mapping: "DATASET",
+			assays: [
+				{
+					assay: "WGS",
+					dataType: "genomicVariants",
+					fileFormats: ["VCF"],
+					extraAttributes: { specimenType: ["blood"] }
+				},
+				{
+					assay: "SomaScan",
+					dataType: "proteomics",
+					fileFormats: ["CSV"],
+					extraAttributes: { specimenType: ["plasma"] }
+				},
+				{
+					assay: "LC-MS",
+					dataType: "metabolomics",
+					fileFormats: ["CSV"],
+					extraAttributes: { specimenType: ["plasma"] }
+				}
+			]
+		},
+		{
+			name: "NECS",
+			participantCount: 500,
+			mapping: "FILE",
+			assays: [{
+				assay: "WGS",
+				dataType: "genomicVariants",
+				fileFormats: ["CRAM", "VCF"],
+				extraAttributes: { specimenType: ["blood", "saliva"] }
+			}, {
+				assay: "RNAseq",
+				dataType: "geneExpression",
+				fileFormats: ["FASTQ", "BAM"],
+				extraAttributes: { specimenType: ["blood"] }
+			}]
+		},
+		{
+			name: "LonGenity",
+			participantCount: 700,
+			mapping: "FILE",
+			assays: [{
+				assay: "methylationArray",
+				dataType: "epigenetics",
+				fileFormats: ["IDAT"],
+				extraAttributes: { specimenType: ["blood"] }
+			}, {
+				assay: "SomaScan",
+				dataType: "proteomics",
+				fileFormats: ["CSV"],
+				extraAttributes: { specimenType: ["plasma"] }
+			}]
+		},
+		{
+			name: "ILO",
+			participantCount: 300,
+			mapping: "FILE",
+			assays: [{
+				assay: "scRNAseq",
+				dataType: "geneExpression",
+				fileFormats: ["FASTQ", "H5AD"],
+				extraAttributes: { specimenType: ["PBMC"] }
+			}, {
+				assay: "metagenomics",
+				dataType: "genomicVariants",
+				fileFormats: ["FASTQ"],
+				extraAttributes: { specimenType: [
+					"blood",
+					"plasma",
+					"PBMC",
+					"saliva"
+				] }
+			}]
+		}
+	],
+	suppressionThreshold: 20,
+	countSuppressionStrategy: "EXCLUDE_ROW",
+	facetPostProcessingConfig: {
+		algorithm: "ROUNDING",
+		parameters: {
+			concreteType: "org.sagebionetworks.repo.model.FacetRoundingParameters",
+			roundTo: 5
+		}
+	}
+}, s = {
+	portalName: "AD Knowledge Portal",
+	participantIdPrefix: "ADKP-SYN",
+	participantsVirtualTableId: "syn90000011",
+	dataVirtualTableId: "syn90000012",
+	firstReferenceEntityId: 902e5,
+	participantAttributes: [
+		{
+			name: "sex",
+			values: {
+				female: 62,
+				male: 38
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "ageDeathRange",
+			values: {
+				"<70": 6,
+				"70-74": 6,
+				"75-79": 10,
+				"80-84": 18,
+				"85-89": 25,
+				"90+": 35
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "race",
+			values: {
+				White: 85,
+				"Black or African American": 8,
+				Asian: 2,
+				"More than one race": 1,
+				Unknown: 4
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "isHispanic",
+			values: {
+				false: 93,
+				true: 5,
+				Unknown: 2
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "apoeGenotype",
+			values: {
+				22: 1,
+				23: 12,
+				24: 2,
+				33: 58,
+				34: 24,
+				44: 3
+			},
+			isQuasiIdentifier: !0
+		},
+		{
+			name: "diagnosis",
+			values: {
+				control: 30,
+				"Alzheimer's Disease": 45,
+				MCI: 20,
+				"frontotemporal dementia": .5,
+				other: 4.5
+			},
+			isQuasiIdentifier: !1
+		},
+		{
+			name: "braak",
+			values: {
+				"Stage 0": 3,
+				"Stage I": 8,
+				"Stage II": 12,
+				"Stage III": 20,
+				"Stage IV": 25,
+				"Stage V": 22,
+				"Stage VI": 10
+			},
+			isQuasiIdentifier: !1
+		},
+		{
+			name: "amyCerad",
+			values: {
+				None: 25,
+				Sparse: 15,
+				Moderate: 25,
+				Frequent: 35
+			},
+			isQuasiIdentifier: !1
+		}
+	],
+	extraDataAttributeNames: ["tissue"],
+	studies: [
+		{
+			name: "ROSMAP",
+			participantCount: 900,
+			mapping: "FILE",
+			assays: [
+				{
+					assay: "rnaSeq",
+					dataType: "geneExpression",
+					fileFormats: ["fastq", "bam"],
+					extraAttributes: { tissue: ["dorsolateral prefrontal cortex"] }
+				},
+				{
+					assay: "snrnaSeq",
+					dataType: "geneExpression",
+					fileFormats: ["fastq", "h5ad"],
+					extraAttributes: { tissue: ["dorsolateral prefrontal cortex"] }
+				},
+				{
+					assay: "wholeGenomeSeq",
+					dataType: "genomicVariants",
+					fileFormats: ["cram", "vcf"],
+					extraAttributes: { tissue: ["dorsolateral prefrontal cortex"] }
+				}
+			]
+		},
+		{
+			name: "MSBB",
+			participantCount: 300,
+			mapping: "FILE",
+			assays: [{
+				assay: "rnaSeq",
+				dataType: "geneExpression",
+				fileFormats: ["fastq", "bam"],
+				extraAttributes: { tissue: [
+					"dorsolateral prefrontal cortex",
+					"temporal cortex",
+					"cerebellum",
+					"parahippocampal gyrus"
+				] }
+			}, {
+				assay: "TMT quantitation",
+				dataType: "proteomics",
+				fileFormats: ["raw", "csv"],
+				extraAttributes: { tissue: ["parahippocampal gyrus"] }
+			}]
+		},
+		{
+			name: "MayoRNAseq",
+			participantCount: 250,
+			mapping: "FILE",
+			assays: [{
+				assay: "rnaSeq",
+				dataType: "geneExpression",
+				fileFormats: ["fastq", "bam"],
+				extraAttributes: { tissue: ["temporal cortex", "cerebellum"] }
+			}]
+		},
+		{
+			name: "DiverseCohorts",
+			participantCount: 400,
+			mapping: "DATASET",
+			assays: [{
+				assay: "rnaSeq",
+				dataType: "geneExpression",
+				fileFormats: ["bam"],
+				extraAttributes: { tissue: ["dorsolateral prefrontal cortex"] }
+			}, {
+				assay: "snATACSeq",
+				dataType: "epigenetics",
+				fileFormats: ["tsv"],
+				extraAttributes: { tissue: ["dorsolateral prefrontal cortex"] }
+			}]
+		}
+	],
+	suppressionThreshold: 20,
+	countSuppressionStrategy: "EXCLUDE_ROW",
+	facetPostProcessingConfig: {
+		algorithm: "NOISE",
+		parameters: {
+			concreteType: "org.sagebionetworks.repo.model.FacetNoiseParameters",
+			epsilon: 1
+		}
+	}
+};
+//#endregion
+export { s as ADKP_MOCK_PROFILE, i as CORE_DATA_ATTRIBUTE_NAMES, n as DATA_REFERENCE_COLUMN_NAME, o as ELITE_MOCK_PROFILE, e as PARTICIPANT_ID_COLUMN_NAME, r as REFERENCE_TYPE_COLUMN_NAME, t as STUDY_COLUMN_NAME };
+
+//# sourceMappingURL=cohortBuilderMockProfiles.js.map

package/dist/mocks/cohortBuilder/cohortBuilderMockProfiles.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"cohortBuilderMockProfiles.js","names":[],"sources":["../../../src/mocks/cohortBuilder/cohortBuilderMockProfiles.ts"],"sourcesContent":["import { AggregateCountSuppressionStrategy } from '@sage-bionetworks/synapse-client/generated/models/AggregateCountSuppressionStrategy'\nimport { FacetPostProcessingConfig } from '@sage-bionetworks/synapse-client/generated/models/FacetPostProcessingConfig'\n\n/**\n * Best-guess Cohort Builder 2.0 source layout, expressed as the columns the two\n * VirtualTables expose. The participant-perspective VT groups MATERIAL by\n * participant; the data-perspective VT groups MATERIAL by file/dataset reference.\n * Data attributes keep the same column name in both VTs (a STRING_LIST in the\n * participant VT, a scalar in MATERIAL and the data VT) so one filter tree can be\n * applied to both as a defining condition.\n */\n\n/** Relative frequency of each value, used by the synthetic data generator. */\nexport type WeightedValues = Readonly<Record<string, number>>\n\nexport type MockParticipantAttribute = {\n  name: string\n  values: WeightedValues\n  isQuasiIdentifier: boolean\n}\n\nexport type MockAssay = {\n  assay: string\n  dataType: string\n  fileFormats: readonly string[]\n  /** Portal-specific data attributes (e.g. specimenType, tissue) and their possible values. */\n  extraAttributes: Readonly<Record<string, readonly string[]>>\n}\n\nexport type MockStudy = {\n  name: string\n  participantCount: number\n  /** FILE studies map participants to individual files; DATASET studies map every participant to every study dataset. */\n  mapping: 'FILE' | 'DATASET'\n  assays: readonly MockAssay[]\n}\n\nexport type CohortBuilderMockProfile = {\n  portalName: string\n  participantIdPrefix: string\n  participantsVirtualTableId: string\n  dataVirtualTableId: string\n  /** First synthetic entity ID assigned to a file or dataset reference. */\n  firstReferenceEntityId: number\n  participantAttributes: readonly MockParticipantAttribute[]\n  extraDataAttributeNames: readonly string[]\n  studies: readonly MockStudy[]\n  suppressionThreshold: number\n  countSuppressionStrategy: AggregateCountSuppressionStrategy\n  facetPostProcessingConfig: FacetPostProcessingConfig\n}\n\nexport const PARTICIPANT_ID_COLUMN_NAME = 'individualId'\nexport const STUDY_COLUMN_NAME = 'study'\nexport const DATA_REFERENCE_COLUMN_NAME = 'dataReference'\nexport const REFERENCE_TYPE_COLUMN_NAME = 'referenceType'\nexport const CORE_DATA_ATTRIBUTE_NAMES = [\n  'dataType',\n  'assay',\n  'fileFormat',\n] as const\n\nconst TRUE_FALSE_RARE: WeightedValues = { false: 85, true: 15 }\nconst TRUE_FALSE_COMMON: WeightedValues = { false: 60, true: 40 }\n\n// ADM-8371: 5-year bins with a censored top bin.\nconst ELITE_AGE_RANGES: WeightedValues = {\n  '20-24': 1,\n  '25-29': 1,\n  '30-34': 1,\n  '35-39': 2,\n  '40-44': 2,\n  '45-49': 3,\n  '50-54': 4,\n  '55-59': 5,\n  '60-64': 6,\n  '65-69': 7,\n  '70-74': 8,\n  '75-79': 9,\n  '80-84': 10,\n  '85-89': 11,\n  '90-94': 12,\n  '95-99': 9,\n  '100-104': 5,\n  '105-109': 0.4,\n  '>109': 0.1,\n}\n\nconst ELITE_BLOOD_SPECIMENS = ['blood', 'plasma', 'PBMC', 'saliva'] as const\n\nexport const ELITE_MOCK_PROFILE: CohortBuilderMockProfile = {\n  portalName: 'ELITE',\n  participantIdPrefix: 'ELITE-SYN',\n  participantsVirtualTableId: 'syn90000001',\n  dataVirtualTableId: 'syn90000002',\n  firstReferenceEntityId: 90100000,\n  participantAttributes: [\n    {\n      name: 'sex',\n      values: { Female: 58, Male: 41, Unknown: 1 },\n      isQuasiIdentifier: true,\n    },\n    { name: 'ageRange', values: ELITE_AGE_RANGES, isQuasiIdentifier: true },\n    {\n      name: 'race',\n      values: {\n        White: 78,\n        'Black or African American': 9,\n        Asian: 6,\n        'American Indian or Alaska Native': 0.3,\n        'More than one race': 3,\n        Unknown: 4,\n      },\n      isQuasiIdentifier: true,\n    },\n    {\n      name: 'ethnicity',\n      values: {\n        'Not Hispanic or Latino': 90,\n        'Hispanic or Latino': 7,\n        Unknown: 3,\n      },\n      isQuasiIdentifier: true,\n    },\n    {\n      name: 'apoeGenotype',\n      values: {\n        'e2/e2': 0.7,\n        'e2/e3': 12,\n        'e2/e4': 2,\n        'e3/e3': 61,\n        'e3/e4': 21,\n        'e4/e4': 2,\n      },\n      isQuasiIdentifier: true,\n    },\n    {\n      name: 'familyStudyParticipant',\n      values: TRUE_FALSE_COMMON,\n      isQuasiIdentifier: false,\n    },\n    { name: 'hasDementia', values: TRUE_FALSE_RARE, isQuasiIdentifier: true },\n    { name: 'hasDiabetes', values: TRUE_FALSE_RARE, isQuasiIdentifier: true },\n    {\n      name: 'hasCardiovascularDisease',\n      values: { false: 70, true: 30 },\n      isQuasiIdentifier: true,\n    },\n    {\n      name: 'mortalityStatus',\n      values: { Living: 55, Deceased: 45 },\n      isQuasiIdentifier: false,\n    },\n  ],\n  extraDataAttributeNames: ['specimenType'],\n  studies: [\n    {\n      name: 'LLFS',\n      participantCount: 1200,\n      mapping: 'DATASET',\n      assays: [\n        {\n          assay: 'WGS',\n          dataType: 'genomicVariants',\n          fileFormats: ['VCF'],\n          extraAttributes: { specimenType: ['blood'] },\n        },\n        {\n          assay: 'SomaScan',\n          dataType: 'proteomics',\n          fileFormats: ['CSV'],\n          extraAttributes: { specimenType: ['plasma'] },\n        },\n        {\n          assay: 'LC-MS',\n          dataType: 'metabolomics',\n          fileFormats: ['CSV'],\n          extraAttributes: { specimenType: ['plasma'] },\n        },\n      ],\n    },\n    {\n      name: 'NECS',\n      participantCount: 500,\n      mapping: 'FILE',\n      assays: [\n        {\n          assay: 'WGS',\n          dataType: 'genomicVariants',\n          fileFormats: ['CRAM', 'VCF'],\n          extraAttributes: { specimenType: ['blood', 'saliva'] },\n        },\n        {\n          assay: 'RNAseq',\n          dataType: 'geneExpression',\n          fileFormats: ['FASTQ', 'BAM'],\n          extraAttributes: { specimenType: ['blood'] },\n        },\n      ],\n    },\n    {\n      name: 'LonGenity',\n      participantCount: 700,\n      mapping: 'FILE',\n      assays: [\n        {\n          assay: 'methylationArray',\n          dataType: 'epigenetics',\n          fileFormats: ['IDAT'],\n          extraAttributes: { specimenType: ['blood'] },\n        },\n        {\n          assay: 'SomaScan',\n          dataType: 'proteomics',\n          fileFormats: ['CSV'],\n          extraAttributes: { specimenType: ['plasma'] },\n        },\n      ],\n    },\n    {\n      name: 'ILO',\n      participantCount: 300,\n      mapping: 'FILE',\n      assays: [\n        {\n          assay: 'scRNAseq',\n          dataType: 'geneExpression',\n          fileFormats: ['FASTQ', 'H5AD'],\n          extraAttributes: { specimenType: ['PBMC'] },\n        },\n        {\n          assay: 'metagenomics',\n          dataType: 'genomicVariants',\n          fileFormats: ['FASTQ'],\n          extraAttributes: { specimenType: ELITE_BLOOD_SPECIMENS },\n        },\n      ],\n    },\n  ],\n  suppressionThreshold: 20,\n  countSuppressionStrategy: 'EXCLUDE_ROW',\n  facetPostProcessingConfig: {\n    algorithm: 'ROUNDING',\n    parameters: {\n      concreteType: 'org.sagebionetworks.repo.model.FacetRoundingParameters',\n      roundTo: 5,\n    },\n  },\n}\n\nconst ADKP_BRAIN_TISSUES = [\n  'dorsolateral prefrontal cortex',\n  'temporal cortex',\n  'cerebellum',\n  'parahippocampal gyrus',\n] as const\n\nexport const ADKP_MOCK_PROFILE: CohortBuilderMockProfile = {\n  portalName: 'AD Knowledge Portal',\n  participantIdPrefix: 'ADKP-SYN',\n  participantsVirtualTableId: 'syn90000011',\n  dataVirtualTableId: 'syn90000012',\n  firstReferenceEntityId: 90200000,\n  participantAttributes: [\n    {\n      name: 'sex',\n      values: { female: 62, male: 38 },\n      isQuasiIdentifier: true,\n    },\n    {\n      name: 'ageDeathRange',\n      values: {\n        '<70': 6,\n        '70-74': 6,\n        '75-79': 10,\n        '80-84': 18,\n        '85-89': 25,\n        '90+': 35,\n      },\n      isQuasiIdentifier: true,\n    },\n    {\n      name: 'race',\n      values: {\n        White: 85,\n        'Black or African American': 8,\n        Asian: 2,\n        'More than one race': 1,\n        Unknown: 4,\n      },\n      isQuasiIdentifier: true,\n    },\n    {\n      name: 'isHispanic',\n      values: { false: 93, true: 5, Unknown: 2 },\n      isQuasiIdentifier: true,\n    },\n    {\n      name: 'apoeGenotype',\n      values: { '22': 1, '23': 12, '24': 2, '33': 58, '34': 24, '44': 3 },\n      isQuasiIdentifier: true,\n    },\n    {\n      name: 'diagnosis',\n      values: {\n        control: 30,\n        \"Alzheimer's Disease\": 45,\n        MCI: 20,\n        'frontotemporal dementia': 0.5,\n        other: 4.5,\n      },\n      isQuasiIdentifier: false,\n    },\n    {\n      name: 'braak',\n      values: {\n        'Stage 0': 3,\n        'Stage I': 8,\n        'Stage II': 12,\n        'Stage III': 20,\n        'Stage IV': 25,\n        'Stage V': 22,\n        'Stage VI': 10,\n      },\n      isQuasiIdentifier: false,\n    },\n    {\n      name: 'amyCerad',\n      values: { None: 25, Sparse: 15, Moderate: 25, Frequent: 35 },\n      isQuasiIdentifier: false,\n    },\n  ],\n  extraDataAttributeNames: ['tissue'],\n  studies: [\n    {\n      name: 'ROSMAP',\n      participantCount: 900,\n      mapping: 'FILE',\n      assays: [\n        {\n          assay: 'rnaSeq',\n          dataType: 'geneExpression',\n          fileFormats: ['fastq', 'bam'],\n          extraAttributes: { tissue: ['dorsolateral prefrontal cortex'] },\n        },\n        {\n          assay: 'snrnaSeq',\n          dataType: 'geneExpression',\n          fileFormats: ['fastq', 'h5ad'],\n          extraAttributes: { tissue: ['dorsolateral prefrontal cortex'] },\n        },\n        {\n          assay: 'wholeGenomeSeq',\n          dataType: 'genomicVariants',\n          fileFormats: ['cram', 'vcf'],\n          extraAttributes: { tissue: ['dorsolateral prefrontal cortex'] },\n        },\n      ],\n    },\n    {\n      name: 'MSBB',\n      participantCount: 300,\n      mapping: 'FILE',\n      assays: [\n        {\n          assay: 'rnaSeq',\n          dataType: 'geneExpression',\n          fileFormats: ['fastq', 'bam'],\n          extraAttributes: { tissue: ADKP_BRAIN_TISSUES },\n        },\n        {\n          assay: 'TMT quantitation',\n          dataType: 'proteomics',\n          fileFormats: ['raw', 'csv'],\n          extraAttributes: { tissue: ['parahippocampal gyrus'] },\n        },\n      ],\n    },\n    {\n      name: 'MayoRNAseq',\n      participantCount: 250,\n      mapping: 'FILE',\n      assays: [\n        {\n          assay: 'rnaSeq',\n          dataType: 'geneExpression',\n          fileFormats: ['fastq', 'bam'],\n          extraAttributes: { tissue: ['temporal cortex', 'cerebellum'] },\n        },\n      ],\n    },\n    {\n      name: 'DiverseCohorts',\n      participantCount: 400,\n      mapping: 'DATASET',\n      assays: [\n        {\n          assay: 'rnaSeq',\n          dataType: 'geneExpression',\n          fileFormats: ['bam'],\n          extraAttributes: { tissue: ['dorsolateral prefrontal cortex'] },\n        },\n        {\n          assay: 'snATACSeq',\n          dataType: 'epigenetics',\n          fileFormats: ['tsv'],\n          extraAttributes: { tissue: ['dorsolateral prefrontal cortex'] },\n        },\n      ],\n    },\n  ],\n  suppressionThreshold: 20,\n  countSuppressionStrategy: 'EXCLUDE_ROW',\n  facetPostProcessingConfig: {\n    algorithm: 'NOISE',\n    parameters: {\n      concreteType: 'org.sagebionetworks.repo.model.FacetNoiseParameters',\n      epsilon: 1.0,\n    },\n  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package/dist/mocks/cohortBuilder/cohortBuilderMockQueryEngine.d.ts

@@ -0,0 +1,41 @@
+import { BelowThresholdErrorResponse } from '@sage-bionetworks/synapse-client/generated/models/BelowThresholdErrorResponse';
+import { ColumnModel } from '@sage-bionetworks/synapse-client/generated/models/ColumnModel';
+import { ErrorResponse } from '@sage-bionetworks/synapse-client/generated/models/ErrorResponse';
+import { QueryResultBundle } from '@sage-bionetworks/synapse-client/generated/models/QueryResultBundle';
+import { RowSuppressionErrorResponse } from '@sage-bionetworks/synapse-client/generated/models/RowSuppressionErrorResponse';
+import { QueryBundleRequest } from '@sage-bionetworks/synapse-types';
+import { CohortBuilderSyntheticData } from './cohortBuilderSyntheticData';
+/**
+ * Which access tier the mocked caller has on the participants source:
+ * - `FULL`: the caller met the access requirement (exact results, rows allowed).
+ * - `AGGREGATE_ONLY`: authenticated but unapproved (count gate, post-processed
+ *   facets, no participant rows).
+ */
+export type CohortBuilderAccess = 'FULL' | 'AGGREGATE_ONLY';
+export type CohortBuilderMockErrorBody = ErrorResponse | BelowThresholdErrorResponse | RowSuppressionErrorResponse;
+export type CohortBuilderMockQueryResult = {
+    status: 200;
+    body: QueryResultBundle;
+} | {
+    status: number;
+    body: CohortBuilderMockErrorBody;
+};
+export declare const MOCK_BELOW_THRESHOLD_HTTP_STATUS = 403;
+export declare const MOCK_ROW_SUPPRESSED_HTTP_STATUS = 403;
+/** Column models of both VirtualTables, derived from the synthetic data's profile. */
+export declare function getCohortBuilderColumnModels(data: CohortBuilderSyntheticData): {
+    participants: ColumnModel[];
+    dataReferences: ColumnModel[];
+};
+/** The stack default of `org.sagebionetworks.table.query.cohort.max.values`. */
+export declare const MOCK_MAX_COHORT_VALUES = 10000;
+export type CohortBuilderMockQueryOptions = {
+    /** Maximum number of distinct values in one cohort. Defaults to {@link MOCK_MAX_COHORT_VALUES}. */
+    maxCohortValues?: number;
+};
+/**
+ * Emulates a Cohort Builder 2.0 table query against synthetic data, returning
+ * either a QueryResultBundle or the error the backend would return.
+ */
+export declare function runCohortBuilderMockQuery(data: CohortBuilderSyntheticData, request: QueryBundleRequest, access: CohortBuilderAccess, options?: CohortBuilderMockQueryOptions): CohortBuilderMockQueryResult;
+//# sourceMappingURL=cohortBuilderMockQueryEngine.d.ts.map

package/dist/mocks/cohortBuilder/cohortBuilderMockQueryEngine.d.ts.map

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