Organizations

An organization (or org) is a DNAnexus entity that is used to associate a group of users. The administrators of an org can manage account creation, configure permissions in the context of the org as well as the projects owned by the org, and oversee billing. All storage and compute costs associated with an org are invoiced to a single billing account designated by the org administrators. Additionally, data objects and projects may be shared with orgs as an entity.

Org Membership Status

A user may be a member of an org at one of two membership statuses:

  1. ADMIN
  2. MEMBER

An org ADMIN is granted all possible permissions in the org and may perform org administrative functions (e.g. adding/removing users or modifying org policies). An org MEMBER, on the other hand, is granted only a subset of the possible permissions in the org and has no administrative power in the org.

Org Permission Flags

Org permission flags, configurable by user, dictate the allowable actions for each user in an org. The following permission flags exist:

  • allowBillableActivities boolean Whether or not the user can perform certain activities that would incur charges for the org. Users with this flag set to true may create projects and apps billed to the org and download files while billing the data transfer costs to the org, as well as view the org's pricing model (and view the cost of any projects or jobs billed to the org).
  • projectAccess string The maximum project permission that the user will be granted to projects shared with the org (must be one of "ADMINISTER", "CONTRIBUTE", "UPLOAD", "VIEW", or "NONE")
  • appAccess boolean Whether or not the user can access and run apps shared with the org

Org ADMINs have all possible permissions in the org; that is, org ADMINs receive the following set of permission flags:

  • { allowBillableActivities: true, projectAccess: "ADMINISTER", appAccess: true }

Org MEMBERs, on the other hand, will receive the following set of permission flags, by default:

  • { allowBillableActivities: false, projectAccess: "CONTRIBUTE", appAccess: true }

The permission flags for org MEMBERs can be configured at any point by any org ADMIN (/org-xxxx/setMemberAccess).

Org Policies

Org policies, configurable by org, dictate many different behaviors when the org interacts with other entities. The following policies exist:

  • memberListVisibility string (default "ADMIN" in /org/new) The org membership status required to be able to view the membership status and permission flags in effect for any other member of the org (via /org-xxxx/findMembers). Must be one of "ADMIN", "MEMBER", or "PUBLIC". If "PUBLIC", then any DNAnexus user may view the membership status and permission flags in effect for any member of the org.
  • restrictProjectTransfer string (default "MEMBER" in /org/new) The org membership status required to be able to change the billing account of a project (via /project-xxxx/update or /project-xxxx/transfer) that is billed to this org. Must be one of "ADMIN" or "MEMBER". If "ADMIN", then only org ADMINs may change the billing account of an org-billed project; if "MEMBER", then any org member may do so.

List of API Methods

Organization API Methods

Related API Methods

API Method Specifications

API method: /org/new

Specification

Creates a new organization. Upon success, the requesting user will become the one and only ADMIN of the organization. The organization's handle and name will be visible to the public.

Inputs

  • handle string A case-insensitively unique handle for the org (i.e. the chosen handle must not already be in use by any other user or org). An org handle:

    • must start with an alpha character (uppercase or lowercase)
    • must be at least 3 characters long
    • may contain alphanumeric characters (uppercase and lowercase), periods, and underscores

    The lowercase of handle will be appended to "org-" to form the ID of this org.

  • name string A descriptive name for the organization

  • policies mapping (optional) A set of organization policies to override the corresponding default policies. Policies that are not included will inherit the system default policies. See org policies for more information

  • nonce string (optional) Unique identifier for this request. Ensures that even if multiple requests fail and are retried, only a single org is created. For more information, see Nonces.

Outputs

  • id string ID of the newly created organization ("org-" + handle)

Errors

  • InvalidInput
    • A nonce was reused in a request but some of the other inputs had changed signifying a new and different request
    • A nonce may not exceed 128 bytes
  • InvalidState
    • The handle of the org case-insensitively matches that of an existing org or user, or of a previously destroyed org
  • PermissionDenied
    • The requesting user does not have a full scope token

API method: /org-xxxx/describe

Specification

Describes an organization. The output may be restricted if this is invoked by a non-member user; the exact subset of fields that will be returned is defined by the organization's policies.

Inputs

  • defaultFields boolean (optional, default false if fields is supplied, true otherwise) whether to include the default set of fields in the output (the default fields are described in the "Outputs" section below). The selections are overridden by any fields explicitly named in fields
  • fields mapping (optional) include or exclude fields from the output. These selections override the settings in defaultFields
    • key Desired output field (see the "Outputs" section below for valid values)
    • value boolean Whether to include the field

The following options are deprecated (and will not be respected if fields is present):

  • pendingTransfers boolean (optional, default false) If true, returns a list of project IDs which the org has been invited to be the billing account for

Outputs

  • id string The organization ID

The following fields are included by default (but can be disabled using fields or defaultFields):

  • class string The string "org"
  • handle string The organization handle, as originally provided to /org/new
  • name string The descriptive name of the organization

The following field (included by default) is available if the org's memberListVisibility policy is set to 'PUBLIC' or if the memberListVisibility policy is any other value, the requesting user is a MEMBER of the org, and a full scope token is supplied.

  • admins array of strings The IDs of users who are ADMINs of the organization

The remaining keys are only available if a full scope token is supplied

The following fields (included by default) are available if the requesting user is a member of the org:

  • level string Membership level of the requesting user in the org
  • allowBillableActivities boolean Whether the requesting user can perform billable activities on behalf of the org (see here for more information)
  • projectAccess string The maximum project permission the requesting user is granted via the org to projects explicitly shared with the org (see here for more information)
  • appAccess boolean Whether the requesting user can access and run apps shared with the org (see here for more information)
  • policies mapping Organization-wide policies
  • pendingBillingInformation mapping or null A mapping containing billing information that will go into effect once the accounts payable contact agrees to and confirms the billing information, or null if there is no pending billing information
  • estSpendingLimitLeft number or null Estimated number of dollars left before new activities billed to the org are locked down; the value null indicates that there is no spending limit currently imposed on the account. Note that this value may also be negative to indicate that the org has exceeded the spending limit (it may continue to become more negative if jobs are still running or any projects with a nonzero amount of storage are still billed to the org).
  • phiFeaturesEnabled boolean Whether PHI features have been enabled for the account
  • defaultRegion string The default region in which newly created projects billed to this org will reside (may be overriden at project creation time). For more information about regions, see Regions.
  • permittedRegions array of strings The regions in which this org is permitted to create projects. For more information about regions, see Regions.

The following fields (included by default) are available if the requesting user is a MEMBER of the org and billing information has been confirmed for this billing account:

  • billingInformation mapping The confirmed billing contact information to which invoices will be sent

The following fields (included by default) are available if the requesting user is a member of the org with allowBillableActivities permission:

  • computeCharges number Running total of compute charges (in dollars) for the account
  • storageCharges number Running total of storage charges (in dollars) for the account
  • storageChargesComputedAt timestamp Effective time at which storageCharges was computed
  • dataEgressCharges number Running total of data egress charges (in dollars) for the account

The following fields are only returned if the corresponding field in the fields input is set to true, the user is a member of the org with allowBillableActivities permission, and billing information has been confirmed for this billing account:

  • pricingModelsByRegion mapping Contains information about the pricing models that are in effect for the org (applied to projects whose billTo is this org). The mapping has one entry for each region in the permittedRegions of the org:

    • key region, e.g. "aws:us-east-1"
    • value mapping the pricing model that is applied in this region

      • storageRatePerGBMonth number Storage rate (in dollars per GB-month) for ordinary (non-archival) storage in this region
      • computeRatesPerHour mapping Contains compute rates for each instance type the account is permitted to use in this region. For a list of available instance types, see: Instance Types
        • key Instance type name
        • value number Rate (in dollars per instance-hour)
      • ipRates mapping Rate for data leaving DNAnexus from this region to specific destination IP ranges (specified in CIDR notation). If an IP is in more than one specified range, the rate is given by the most specific matching IP range. The key "0.0.0.0/0" will always exist and contain the default rate
        • key IP range (specified in CIDR notation)
        • value number Rate (in dollars per GB) leaving DNAnexus to that IP range

      The following field will be present only if the org has the phiFeaturesEnabled field set to true:

      • computeRatesPerHourPHI mapping Contains compute rates for each instance type the account is permitted to use in this region, applied only to projects that have the containsPHI flag set
        • key Instance type name
        • value number Rate (in dollars per instance-hour) for this instance type

The following fields are only returned if the corresponding field in the fields input is set to true and the requesting user is an ADMIN of the org:

  • pendingTransfers list of strings List of project IDs which the org has been invited to be the billing account for
  • userCreationFeaturesEnabled boolean Whether ADMINs of this org may provision a new account for another user

Errors

API method: /org-xxxx/update

Specification

Updates information about an organization. The requesting user must be an ADMIN of the organization.

Inputs

  • name string (optional) A descriptive name for the organization
  • policies mapping (optional) A set of organization policies to override the existing policies. Policies that are not included in the mapping will not be updated. See org policies for more information
  • defaultRegion string (optional) The default region in which all newly created projects billed to this org will reside (may be overriden at project creation time). For more information about regions, see Regions.

Outputs

  • id string ID of the organization

Errors

  • InvalidInput
    • defaultRegion is not in the org's permittedRegions
  • PermissionDenied
    • The requesting user is not an ADMIN of the organization
    • The requesting user does not have a full scope token

API method: /org-xxxx/invite

Specification

Invites a user to become a member of the organization. The invitation will be sent to an existing user or email address.

Inputs

  • invitee string User ID or email address of the user that will be invited to the organization with a membership status of level
  • level string (optional, default "MEMBER") Membership status that the invitee will receive (one of "MEMBER" or "ADMIN")
  • message string (optional) A message to the recipient invitee
  • suppressEmailNotification boolean (optional, default false) If true, will not send an email notification to the invitee

If level is "MEMBER", then the following optional org permission flags (see here for more information) may be included:

  • allowBillableActivities boolean (optional, default false) Whether the invitee can perform billable activities on behalf of the org.
  • appAccess boolean (optional, default true) Whether the user can access and run apps shared with the org
  • projectAccess string (optional, default "CONTRIBUTE") The maximum project permission the invitee will be granted via the org to projects explicitly shared with the org (one of "ADMINISTER", "CONTRIBUTE", "UPLOAD", "VIEW", or "NONE")

Outputs

  • id string Invite ID, or null if the invite did not need to be created (i.e. invitee already has at least the requested permission)
  • state string State of the invite

Errors

  • ResourceNotFound
    • invitee is not an existing user or is not a valid email address
  • PermissionDenied
    • The requesting user is not an ADMIN of the organization
    • The requesting user does not have a full scope token.

API method: /org-xxxx/setMemberAccess

Specification

Modifies the organization membership statuses and/or permission flags for members of the organization. To add new users to the organization, please refer to /org-xxxx/invite.

When switching the membership status of a user from "ADMIN" to "MEMBER", the permission flags are required.

For an existing user who is a "MEMBER" and will remain a "MEMBER", the specified permission flags will be set, and those that are unspecified will be unaffected.

When switching the membership status of a user from "MEMBER" to "ADMIN", the permission flags are prohibited.

This method will attempt to make all possible modifications; if some modifications cannot be made on some users in the input (e.g. because those users are not members of the organization), the modifications for all remaining users will still be made and an InvalidState error will be thrown. Note that this behavior does not apply to other errors.

Inputs

  • The input to /org-xxxx/setMemberAccess will be a mapping with the following key-value pairs:

    • key User ID
    • value mapping A mapping of organization membership status and permission flags to set for the corresponding user

      Includes the following key-value pairs:

      • level string One of "MEMBER" or "ADMIN"

      The following fields are required if level is "MEMBER" and the corresponding user currently has a membership status of "ADMIN", prohibited if level is "ADMIN", and optional otherwise:

      • allowBillableActivities boolean (optional) Whether the corresponding user can perform billable activities on behalf of the org
      • appAccess boolean (optional) Whether the corresponding user will be able to access or run apps shared with the org
      • projectAccess string (optional) The maximum project permission the corresponding user will be granted via the org to projects explicitly shared with the org (one of "ADMINISTER", "CONTRIBUTE", "UPLOAD", "VIEW", or "NONE")

Outputs

  • id string ID of the organization

Errors

  • InvalidInput
    • The requesting user specified himself in the input
  • InvalidState
    • At least one of the users is neither a MEMBER nor an ADMIN of the organization
  • PermissionDenied
    • The requesting user is not an ADMIN of the organization
    • The requesting user does not have a full scope token

API method: /org-xxxx/findProjects

Specification

Lists projects that are billed to the org (and optionally describes those projects). Only ADMINs of the org are permitted to perform this operation.

The ordering of the returned projects is:

  • Descending by last modified time stamp, and then
  • Ascending by ID

This behaves similarly to /system/findProjects

Inputs

  • name string or mapping (optional) If a string, then the exact case-sensitive name that the resulting projects must have. If a mapping, then then may include any subset of the following key-value pairs:
    • regexp string (mutually exclusive with glob; required if glob is not present) A PCRE regular expression that must be matched by the name of all resulting projects
    • flags string (optional if regexp is present, prohibited otherwise) Currently, this field may only be "i", which denotes that case-insensitive matching will be performed with the regexp
    • glob string (mutually exclusive with regexp; required if regexp is not present) A wildcard pattern that must be matched by the name of all resulting projects. The valid wildcard patterns are '*' (0 or more characters) and '?' (1 character)
  • id array of strings (optional) If specified, the resulting projects must have project IDs among this list of IDs. The array may contain no more than 1000 elements
  • tags string or mapping (optional) Defined by the grammar below, representing the tag(s) that all resulting projects must have
    • tags ::= < string >
    • tags ::= { "$and": tagsArray }
    • tags ::= { "$or": tagsArray }
    • tagsArray ::= [ ]
    • tagsArray ::= [tags, ...]
  • properties mapping (optional) Defined by the grammar below. If specified, each matching resulting project must have the specified properties. Each "key" is a property name, and each "value" may either be a string (meaning that the key must have the specified value) or the boolean true (meaning that the specified key must be present but may have any value)
    • constraint ::= { key: value, ... }
    • constraint ::= { "$and": constraintArray }
    • constraint ::= { "$or": constraintArray }
    • constraintArray ::= [ ]
    • constraintArray ::= [constraint, ...]
  • region string or array of strings (optional) If a string, then the result set will contain only projects whose region matches the string. If an array, then the result set will contain only projects whose region is one of the specified strings.
  • public boolean (optional) If true, then only public projects will be included in the result set. If false, then no public project will be included.
  • created mapping (optional) If at least one of the following keys is specified, the resulting projects must have been created in the indicated time frame. If not specified, there will be no constraint on project creation time. If a created hash does not contain at least one of the following keys, an error will be thrown.
    • after timestamp (optional) If specified, only return results created at or after this time
    • before timestamp (optional) If specified, only return results created at or before this time
  • describe boolean or mapping (optional, default false) False indicates that no extra metadata will be retrieved with the results. A mapping represents the input that will be used to call /project-xxxx/describe on each of the returned projects; true indicates the empty mapping input.
  • starting string (optional) Continue a previous query that had reached its limit; the value that was returned as next in the previous query's output should be provided here
  • limit int (optional, default 1000; max 1000) Maximum number of projects that will be returned
  • containsPHI boolean (optional) If set to true, only projects that contain PHI data will be retrieved. If set to false, only projects that do not contain PHI data will be retrieved.

Outputs

  • results array of mappings List of results, each with the following fields:

    • id string ID of the resulting project
    • public boolean Whether or not the project is public
    • level string The explicit project permission the requesting user has to the corresponding project; may be "NONE"

    If describe was true or a mapping:

    • describe mapping The output of the corresponding project's describe method. Note that this mapping may contain the key level with a corresponding value of "NONE" (unlike the output of /system/findProjects)
  • next string or null If null, then all results were reported in results. If a string, then it represents the next result that could not be returned because limit results have already been returned. This value should be supplied to starting in a subsequent query if more results are desired

Errors

  • PermissionDenied
    • The requesting user is not an ADMIN of the organization
    • The requesting user does not have a full scope token

API method: /org-xxxx/findApps

Specification

Lists all apps that are billed to the org; the ordering of results is arbitrary. Only ADMINs of the org are permitted to perform this operation.

This operation behaves similarly to /system/findApps, except that, by default, it returns all apps billed to the org, regardless of whether the app has been published, or whether the requesting user is either a developer or on the authorized users list.

Note that org ADMINS can call /app-xxxx/addDeveloper on any app returned by this route.

Inputs

  • name string or mapping (optional) If a string, the exact case-sensitive name that the results must have. If a mapping, then it can have a subset of the following fields:
    • regexp string (mutually exclusive with glob; required if glob is not present) A PCRE regular expression that the name of all results must match
    • flags string (optional; can only be present if regexp is present) Currently this field can only have value "i", which denotes that case-insensitive matching should be performed with the regular expression
    • glob string (mutually exclusive with regexp; required if regexp is not present) A wildcard pattern that the name of all results must match. The valid wildcard characters are '*' (0 or more characters) and '?' (1 character).
  • category string (optional) A category an app must be tagged with
  • allVersions boolean (optional, default false) Whether to remove the restriction that only app versions tagged with "default" are returned
  • published boolean (optional) If true, only published apps are returned; if false, only unpublished apps are returned, if not supplied, published and unpublished apps are returned.
  • createdBy string (optional) ID of the user who created the app
  • developer string (optional) ID of a developer the app must have
  • authorizedUser string (optional) One of a userID, an orgID or the string "PUBLIC", that must exist in each app's authorizedUsers list
  • modified mapping (optional) If at least one of the following keys is specified, the resulting apps must have been last modified in the indicated time frame. If not specified, there will be no constraint on when the app was last modified. If a modified hash does not contain at least one of the following keys, an error will be thrown.
    • after timestamp (optional) If specified, only return results that were last modified at or after this time
    • before timestamp (optional) If specified, only return results that were last modified at or before this time
  • created mapping (optional) If at least one of the following keys is specified, the resulting apps must have been created in the indicated time frame. If not specified, there will be no constraint on app creation time. If a created hash does not contain at least one of the following keys, an error will be thrown.
    • after timestamp (optional) If specified, only return results created at or after this time
    • before timestamp (optional) If specified, only return results created at or before this time
  • describe boolean or mapping (optional, default false) False indicates that no extra metadata should be retrieved with the results. A mapping represents the input that would be used for calling /app-xxxx/describe on each of the returned results; a value of true is equivalent to the empty hash input.
  • starting mapping (optional) Continue a previous query that had reached its limit; the value that was returned as next in the query's output should be provided here
  • limit int (optional, default 1000) Maximum number of results that may be returned; must be between 1 and 1000 (inclusive)

Outputs

  • results array of mappings List of results, each with the following fields:

    • id string ID of the app

    If describe was set to true or a mapping:

    • describe mapping The output of the result's corresponding describe method
  • next mapping or null If null, all results were reported in results. If a mapping, represents the next result that could not be returned because limit results have already been returned. This value should be passed directly to starting in a subsequent query if more results are desired.

Errors

  • PermissionDenied
    • The requesting user is not an ADMIN of the organization
    • The requesting user does not have a full scope token

API method: /org-xxxx/removeMember

Specification

Removes the specified user from the org. The requesting user may remove any org member, including himself, from the org. By default, this operation additionally revokes all permissions that the specified user has to projects and/or apps that are billed to the org (please see /project-xxxx/decreasePermissions, /app-xxxx[/yyyy]/removeDevelopers, and /app-xxxx[/yyyy]/removeAuthorizedUsers for more information). Upon completion, the specified user may no longer perform any action that can incur charges to the org.

The requesting user must be an ADMIN of the org, but he does not need to have ADMINISTER permission to projects, or developer access to apps, whose permissions may be modified as a result of this operation.

If the requesting user is removing another member from the org, then the requesting user may be granted elevated permissions to projects and/or apps from which the specified user will be removed in order to prevent any resources that are billed to the org from becoming orphaned. In other words, the requesting user will be granted ADMINISTER permission to a project if the specified user is the sole user in the project with ADMINISTER permission; similarly, the requesting user will only be granted developer access to an app if the specified user is the sole developer of the app. No elevated permissions will be granted if the requesting user is removing himself from the org.

If the specified user is not a member of the org at the time of invocation, then all permissions that the specified user has, at that time, to projects and/or apps that are billed to the org will remain untouched.

Inputs

  • user string ID of the user to remove from the org
  • revokeProjectPermissions boolean (optional, default true) whether or not to revoke all explicit permissions granted to user to projects billed to the org. The requesting ADMIN does not need to have ADMINISTER permission to projects billed to the org that will be modified as a result of this operation.
  • revokeAppPermissions boolean (optional, default true) whether or not to revoke all explicit developer and authorized accesses granted to user to apps billed to the org. The requesting ADMIN does not need to have developer access to apps billed to the org that will be modified as a result of this operation.

Outputs

  • id string ID of the manipulated org
  • projects mapping mapping with the following key-value pairs
    • key ID of the project to which the specified user was revoked explicit permission
    • value boolean whether or not the requesting administrator was granted ADMINISTER permission to the corresponding project
  • apps mapping mapping with the following key-value pairs
    • key name of the app to which the specified user was revoked all explicit accesses
    • value boolean whether or not the requesting administrator was granted developer access to the corresponding app

Errors

  • InvalidState
    • The requesting user may not remove himself if he is the only ADMIN in the org
  • PermissionDenied
    • Must have full scope auth token
    • Must be an ADMIN of the org

API method: /org-xxxx/findMembers

Specification

Finds all members of the org, subject to the contraints specified by the requesting user.

The requesting user may be required to have a certain minimum org membership level in order to perform this operation; see memberListVisibility for more information. To bypass the minimum org membership level restriction and view the membership information of oneself, please invoke /org-xxxx/describe.

The ordering of the returned members is ascending by ID.

Inputs

  • level string (optional) Restrict results to members with the specified membership level; must be one of "MEMBER" or "ADMIN"
  • id array of strings (optional) If specified, the resulting list of members must have user IDs among this list of IDs. The array may contain no more than 1000 elements.
  • describe boolean or mapping (optional, default false) False indicates that no extra metadata will be retrieved with the results; true represents the empty mapping input. A mapping represents the input that will be used to describe each of the members in the result set; see /user-xxxx/describe for more information.
  • starting mapping (optional) Continue a previous query that had reached its limit; the non-null value that was returned as next in that query's output should be provided here.
  • limit int (optional, default 1000; max 1000) Maximum number of members that may be returned

Outputs

  • results array of mappings List of results, each with the following fields:

    • id string ID of the org member
    • level string Membership level of the member in this org
    • allowBillableActivities boolean Whether or not the corresponding member can perform billable activities on behalf of the org (see here for more information)
    • projectAccess string The maximum project permission the corresponding member is granted via the org to projects explicitly shared with this org
    • appAccess boolean Whether or not the corresponding member can access and run apps shared with this org

    If describe was true or a mapping:

    • describe mapping Metadata about the org member; the output will be equivalent to that of /user-xxxx/describe, with the exception that the extra keys will not be present if the requesting user is also the member being described. The mapping will contain a subset of the following keys:
      • id
      • class
      • first
      • last
      • middle
      • handle
  • next mapping or null If null, all results were reported in results. If a mapping, represents the next result that could not be returned because limit results have already been returned. This value should be passed directly to starting in a subsequent query if more results are desired.

Errors

  • PermissionDenied
    • The requesting user does not have a sufficient org membership level; see memberListVisibility for more information. /org-xxxx/describe may be invoked to view the requesting user's own org membership information.
    • Must have full scope auth token

API method: /org-xxxx/destroy

Specification

Destroys the specified org. All members will be removed from the organization. Any project or app permissions granted to the org will be revoked.

Inputs

  • None

Outputs

  • id string ID of the organization

Errors

  • InvalidState
    • There are existing projects and/or apps billed to this org
  • PermissionDenied
    • The requesting user must be an ADMIN of the org
    • Must have full scope auth token

Last edited by Thanh-Ha Nguyen, 2017-04-12 04:40:03

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