Data Biosphere Data Store CLI Client

This repository is a pip-installable command line interface (CLI) and Python library (API) for interacting with the Data Biosphere Data Storage System (DSS), also called the data store.

Currently the dbio package supports interaction with the data store for uploading, downloading, and fetching information about data in the data store.

The Data Biosphere CLI is compatible with Python versions 3.5+.

Installation

pip install dbio-cli.

Usage

Documentation on readthedocs.io:

To see the list of commands you can use, type dbio --help.

Configuration management

The Data Biosphere CLI supports ingesting configuration from a configurable array of sources. Each source is a JSON file. Configuration sources that follow the first source update the configuration using recursive dictionary merging. Sources are enumerated in the following order (i.e., in order of increasing priority):

  • Site-wide configuration source, /etc/dbio/config.json
  • User configuration source, ~/.config/dbio/config.json
  • Any sources listed in the colon-delimited variable DBIO_CONFIG_FILE
  • Command line options

Array merge operators: When loading a chain of configuration sources, the Data Biosphere CLI uses recursive dictionary merging to combine the sources. Additionally, when the original config value is a list, the package supports array manipulation operators, which let you extend and modify arrays defined in underlying configurations. See https://github.com/kislyuk/tweak#array-merge-operators for a list of these operators.

Service to Service Authorization

Google service credentials must be whitelisted before they will authenticate with the Data Biosphere CLI.

Set the environment variable GOOGLE_APPLICATION_CREDENTIALS to the path of your Google service credentials file to authenticate.

One can also use: dbio dss login.

See Google service credentials for more information about service accounts. Use the Google Cloud IAM web console to manage service accounts.

Development

To develop on the CLI, first run pip install -r requirements-dev.txt. You can install your locally modified copy of the dbio package by running make install in the repository root directory.

To use the command line interface with a local or test DSS, first run dbio (or scripts/dbio if you want to use the package in-place from the repository root directory). This will create the file ~/.config/dbio/config.json, which you can modify to update the value of DSSClient.swagger_url to point to the URL of the Swagger definition served by your DSS deployment. Lastly, the CLI enforces HTTPS connection to the DSS API. If you are connecting to a local DSS, make this change in dbio/util/__init__.py in the SwaggerClient object:

scheme = "http"

To use the Python interface with a local or test DSS, pass the URL of the Swagger definition to the DSSClient constructor via the swagger_url parameter:

client = DSSClient(swagger_url="https://dss.example.com/v1/swagger.json")

You can also layer a minimal config file on top of the default config.json using the DBIO_CONFIG_FILE environment variable, for example:

export SWAGGER_URL="https://dss.dev.ucsc-cgp-redwood.org/v1/swagger.json"
jq -n .DSSClient.swagger_url=env.SWAGGER_URL > ~/.config/dbio/config.staging.json
export DBIO_CONFIG_FILE=~/.config/dbio/config.staging.json

Testing

Before you run tests, first run dbio dss login. This will open a browser where you can log in to authenticate with Google. Use an email address from one of the whitelisted domains (in DSS_SUBSCRIPTION_AUTHORIZED_DOMAINS_ARRAY from here).

Then make test.

Primary CI testing is through Travis CI on the Gitlab toilspark instance.

Bugs

Please report bugs, issues, feature requests, etc. in the DataBiosphere/data-store-cli repository on GitHub.

Security Policy

Please email reports about any security related issues you find to team-redwood-group@ucsc.edu. Use a descriptive subject line for your report email. In addition, please include the following information along with your report:

  • Your name and affiliation (if any).
  • A description of the technical details of the vulnerabilities, to help us reproduce your findings.
  • An explanation of who can exploit this vulnerability, and what they gain when doing so (an attack scenario).
  • Whether this vulnerability is public or known to third parties. If so, please provide details.

License

Licensed under the terms of the MIT License.

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CLI documentation

Human Cell Atlas Command Line Interface

For general help, run {prog} help. For help with individual commands, run {prog} <command> --help.

usage: dbio [-h] [--version] [--log-level {INFO,CRITICAL,WARNING,ERROR,DEBUG}]
            {clear-dbio-cache,help,dss,auth} ...

Named Arguments

--version show program’s version number and exit
--log-level

Possible choices: INFO, CRITICAL, WARNING, ERROR, DEBUG

[‘DEBUG’, ‘INFO’, ‘WARNING’, ‘ERROR’, ‘CRITICAL’]

Default: “INFO”

Sub-commands:

clear-dbio-cache

Clear the cached DataBiosphere API definitions. This can help resolve errors communicating with the API.

dbio clear-dbio-cache [-h]
help

Print help message

dbio help [-h]
dss

Interact with the Data Storage System

dbio dss [-h]
         {get-bundles-all,get-bundles-checkout,delete-bundle,get-bundle,patch-bundle,put-bundle,post-bundles-checkout,get-collections,put-collection,delete-collection,get-collection,patch-collection,get-events,get-event,get-file,head-file,put-file,post-search,get-subscriptions,put-subscription,delete-subscription,get-subscription,login,logout,upload,download,download-manifest,create-version,download-collection}
         ...
Sub-commands:
get-bundles-all

Lists all the bundles available in the data-store, responses will be returned in a paginated format, at most 500 values shall be returned at a time. Tombstoned bundles will be omitted from the list of bundles available.

dbio dss get-bundles-all [-h] --replica {aws,gcp} [--prefix PREFIX]
                         [--token TOKEN] [--per-page PER_PAGE]
                         [--search-after SEARCH_AFTER] [--no-paginate]
Named Arguments
--replica

Possible choices: aws, gcp

Replica to fetch from.

--prefix Used to specify the beginning of a particular bundle UUID. Capitalized letters will be lower-cased as is done when users submit a uuid (all uuids have lower-cased letters upon ingestion into the dss). Characters other than letters, numbers, and dashes are not allowed and will error. The specified character(s) will return all available bundle uuids starting with that character(s).
--token Token to manage retries. End users constructing queries should not set this parameter.
--per-page Max number of results to return per page.
--search-after Search-After-Context. An internal state pointer parameter for use with pagination. This parameter is referenced by the Link header as described in the “Pagination” section. The API client should not need to set this parameter directly; it should instead directly fetch the URL given in the Link header.
--no-paginate

Do not automatically page the responses

Default: True
get-bundles-checkout

Use this route with the checkout_job_id identifier returned by POST /bundles/{uuid}/checkout.

dbio dss get-bundles-checkout [-h] --replica {aws,gcp} --checkout-job-id
                              CHECKOUT_JOB_ID
Named Arguments
--replica

Possible choices: aws, gcp

Replica to fetch from.

--checkout-job-id
 A RFC4122-compliant ID for the checkout job request.
delete-bundle

Delete the bundle with the given UUID. This deletion is applied across replicas.

dbio dss delete-bundle [-h] --reason REASON --uuid UUID --replica {aws,gcp}
                       [--version VERSION]
Named Arguments
--reason User-friendly reason for the bundle or timestamp-specfic bundle deletion.
--uuid A RFC4122-compliant ID for the bundle.
--replica

Possible choices: aws, gcp

Replica to write to.

--version Timestamp of bundle creation in DSS_VERSION format.
get-bundle

Given a bundle UUID, return the latest version of that bundle. If the version is provided, that version of the bundle is returned instead.

dbio dss get-bundle [-h] --uuid UUID [--version VERSION] --replica {aws,gcp}
                    [--directurls DIRECTURLS] [--presignedurls PRESIGNEDURLS]
                    [--token TOKEN] [--per-page PER_PAGE]
                    [--start-at START_AT] [--no-paginate]
Named Arguments
--uuid Bundle unique ID.
--version Timestamp of bundle creation in DSS_VERSION format.
--replica

Possible choices: aws, gcp

Replica to fetch from.

--directurls

When set to true, the response will contain API-specific URLs that are tied to the specified replica, for example gs://bucket/object or s3://bucket/object

This parameter is mutually exclusive with the presigned urls parameter. The use of presigned URLs is recommended for data access. Cloud native URLs are currently provided for a limited set of use cases and may not be provided in the future. If cloud native URLs are required, please contact the data store team regarding the credentials necessary to use them.

--presignedurls
 Include presigned URLs in the response. This is mutually exclusive with the directurls parameter.
--token Token to manage retries. End users constructing queries should not set this parameter.
--per-page Max number of results to return per page.
--start-at An internal state pointer parameter for use with pagination. This parameter is referenced by the Link header as described in the “Pagination” section. The API client should not need to set this parameter directly; it should instead directly fetch the URL given in the Link header.
--no-paginate

Do not automatically page the responses

Default: True
patch-bundle

Add or remove files from a bundle. A specific version of the bundle to update must be provided, and a new version will be written. Bundle manifests exceeding 20,000 files will not be included in the Elasticsearch index document.

dbio dss patch-bundle [-h] [--add-files ADD_FILES]
                      [--remove-files REMOVE_FILES] --uuid UUID --replica
                      {aws,gcp} --version VERSION
Named Arguments
--add-files List of new files to add to the bundle. File names must be unique.
--remove-files List of files to remove from the bundle. Files must match exactly to be removed. Files not found in the bundle are ignored.
--uuid A RFC4122-compliant ID of the bundle to update.
--replica

Possible choices: aws, gcp

Replica to update the bundle on. Updates are propagated to other replicas.

--version Timestamp of the bundle to update in DSS_VERSION format format (required).
put-bundle

Create a new version of a bundle with a given UUID. The list of file UUID and versions to be included must be provided.

dbio dss put-bundle [-h] --creator-uid CREATOR_UID --files FILES [FILES ...]
                    --uuid UUID --version VERSION --replica {aws,gcp}
Named Arguments
--creator-uid User ID who is creating this bundle.
--files This is a list of dictionaries describing each of the files. Each dictionary includes the fields: - The “uuid” of a file already previously uploaded with “PUT file/{uuid}”. - The “version” timestamp of the file. - The “name” of the file. This can be most anything, and is the name the file will have when downloaded. - The “indexed” field, which specifies whether a file should be indexed or not. Bundle manifests exceeding 20,000 files will not be included in the Elasticsearch index document. Example representing 2 files with dummy values: [{‘uuid’: ‘ce55fd51-7833-469b-be0b-5da88ebebfcd’, ‘version’: ‘2017-06-16T193604.240704Z’, ‘name’: ‘dinosaur_dna.fa’, ‘indexed’: False}, {‘uuid’: ‘ae55fd51-7833-469b-be0b-5da88ebebfca’, ‘version’: ‘0303-04-23T193604.240704Z’, ‘name’: ‘dragon_dna.fa’, ‘indexed’: False}]
--uuid A RFC4122-compliant ID for the bundle.
--version Timestamp of bundle creation in DSS_VERSION format.
--replica

Possible choices: aws, gcp

Replica to write to.
post-bundles-checkout

Initiate asynchronous checkout of a bundle. The response JSON contains a field, checkout_job_id, that can be used to query the status of the checkout via the GET /bundles/checkout/{checkout_job_id} API method. FIXME: document the error code returned when the bundle or specified version does not exist. TODO: After some time period, the data will be removed. TBD: This could be based on initial checkout time or last access time.

dbio dss post-bundles-checkout [-h] [--destination DESTINATION]
                               [--email EMAIL] --uuid UUID [--version VERSION]
                               --replica {aws,gcp}
Named Arguments
--destination User-owned destination storage bucket.
--email An email address to send status updates to.
--uuid A RFC4122-compliant ID for the bundle.
--version Timestamp of file creation in DSS_VERSION format. If this is not provided, the latest version is returned.
--replica

Possible choices: aws, gcp

Replica to fetch from.
get-collections

Return a list of a user’s collections. Collections are sets of links to files, bundles, other collections, or fragments of JSON metadata files. Each entry in the input set of links is checked for referential integrity (the link target must exist in the replica referenced). Up to 1000 items can be referenced in a new collection, or added or removed using PATCH /collections. New collections are private to the authenticated user. Collection items are de-duplicated (if an identical item is given multiple times, it will only be added once). Collections are replicated across storage replicas similarly to files and bundles.

dbio dss get-collections [-h] [--per-page PER_PAGE] [--start-at START_AT]
                         [--no-paginate]
Named Arguments
--per-page Max number of results to return per page.
--start-at An internal state pointer parameter for use with pagination. This parameter is referenced by the Link header as described in the “Pagination” section. The API client should not need to set this parameter directly; it should instead directly fetch the URL given in the Link header.
--no-paginate

Do not automatically page the responses

Default: True
put-collection

Create a new collection. Collections are sets of links to files, bundles, other collections, or fragments of JSON metadata files. Each entry in the input set of links is checked for referential integrity (the link target must exist in the replica referenced). Up to 1000 items can be referenced in a new collection, or added or removed using PATCH /collections. New collections are private to the authenticated user. Collection items are de-duplicated (if an identical item is given multiple times, it will only be added once). Collections are replicated across storage replicas similarly to files and bundles.

dbio dss put-collection [-h] --contents CONTENTS [CONTENTS ...] --description
                        DESCRIPTION --details DETAILS --name NAME --replica
                        {aws,gcp} --uuid UUID --version VERSION
Named Arguments
--contents A list of objects describing links to files, bundles, other collections, and metadata fragments that are part of the collection.
--description A long description of the collection, formatted in Markdown.
--details Supplementary JSON metadata for the collection.
--name A short name identifying the collection.
--replica

Possible choices: aws, gcp

Replica to write to.

--uuid A RFC4122-compliant ID for the collection.
--version Timestamp of collection creation in DSS_VERSION format.
delete-collection

Delete a collection.

dbio dss delete-collection [-h] --uuid UUID --replica {aws,gcp}
Named Arguments
--uuid A RFC4122-compliant ID for the collection.
--replica

Possible choices: aws, gcp

Replica to delete from.
get-collection

Given a collection UUID, return the associated collection object.

dbio dss get-collection [-h] --uuid UUID --replica {aws,gcp}
                        [--version VERSION]
Named Arguments
--uuid A RFC4122-compliant ID for the collection.
--replica

Possible choices: aws, gcp

Replica to fetch from.

--version Timestamp of collection creation in DSS_VERSION format. If this is not provided, the latest version is returned.
patch-collection

Add or remove items from a collection. A specific version of the collection to update must be provided, and a new version will be written.

dbio dss patch-collection [-h] [--add-contents ADD_CONTENTS]
                          [--description DESCRIPTION] [--details DETAILS]
                          [--name NAME] [--remove-contents REMOVE_CONTENTS]
                          --uuid UUID --replica {aws,gcp} --version VERSION
Named Arguments
--add-contents List of new items to add to the collection. Items are de-duplicated (if an identical item is already present in the collection or given multiple times, it will only be added once).
--description New description for the collection.
--details New details for the collection.
--name New name for the collection.
--remove-contents
 List of items to remove from the collection. Items must match exactly to be removed. Items not found in the collection are ignored.
--uuid A RFC4122-compliant ID of the collection to update.
--replica

Possible choices: aws, gcp

Replica to update the collection on. Updates are propagated to other replicas.

--version Timestamp of the collection to update in DSS_VERSION format format (required).
get-events

Return urls where event data is available, with manifest of contents.

dbio dss get-events [-h] [--from-date FROM_DATE] [--to-date TO_DATE] --replica
                    {aws,gcp} [--per-page PER_PAGE] [--token TOKEN]
                    [--no-paginate]
Named Arguments
--from-date Timestamp to begin replaying events, in DSS_VERSION format. If this is not provided, replay from the earliest event.
--to-date Timestamp to stop replaying events, in DSS_VERSION format. If this is not provided, replay to the latest event.
--replica

Possible choices: aws, gcp

Replica to fetch from.

--per-page Max number of results to return per page.
--token Token to manage retries. End users constructing queries should not set this parameter.
--no-paginate

Do not automatically page the responses

Default: True
get-event

Given a bundle UUID and version, return the bundle metadata document.

dbio dss get-event [-h] --uuid UUID --version VERSION --replica {aws,gcp}
Named Arguments
--uuid Bundle unique ID.
--version Timestamp of bundle creation in DSS_VERSION format.
--replica

Possible choices: aws, gcp

Replica to fetch from.
get-file

Given a file UUID, return the latest version of that file. If the version is provided, that version of the file is returned instead. Headers will contain the data store metadata for the file. This endpoint returns a HTTP redirect to another HTTP endpoint with the file contents. NOTE When using the DataBiosphere DSS CLI, this will stream the file to stdout and may need to be piped. For example, dbio dss get-file --uuid UUID --replica aws > result.txt

dbio dss get-file [-h] --uuid UUID --replica {aws,gcp} [--version VERSION]
                  [--token TOKEN] [--directurl DIRECTURL]
                  [--content-disposition CONTENT_DISPOSITION]
Named Arguments
--uuid A RFC4122-compliant ID for the file.
--replica

Possible choices: aws, gcp

Replica to fetch from.

--version Timestamp of file creation in DSS_VERSION format. If this is not provided, the latest version is returned.
--token Token to manage retries. End users constructing queries should not set this parameter.
--directurl

When set to true, the response will contain API-specific URLs that are tied to the specified replica, for example gs://bucket/object or s3://bucket/object

The use of presigned URLs is recommended for data access. Cloud native URLs are currently provided for a limited set of use cases and may not be provided in the future. If cloud native URLs are required, please contact the data store team regarding the credentials necessary to use them.

--content-disposition
 

Optional and does not work when directurl=true (only works with the default presigned url response).

If this parameter is provided, the response from fetching the returned presigned url will include the specified Content-Disposition header.

This can be useful to indicate to a browser that a file should be downloaded rather than opened in a new tab, and can also supply the original filename in the response. Example:

content_disposition="attachment; filename=data.json"
head-file

Given a file UUID, return the metadata for the latest version of that file. If the version is provided, that version’s metadata is returned instead. The metadata is returned in the headers.

dbio dss head-file [-h] --uuid UUID --replica {aws,gcp} [--version VERSION]
Named Arguments
--uuid A RFC4122-compliant ID for the file.
--replica

Possible choices: aws, gcp

Replica to fetch from.

--version Timestamp of file creation in DSS_VERSION format. If this is not provided, the latest version is returned.
put-file

Create a new version of a file with a given UUID. The contents of the file are provided by the client by reference using a cloud object storage URL. The file on the cloud object storage service must have metadata set listing the file checksums and content-type. The metadata fields required are:

  • dss-sha256: SHA-256 checksum of the file
  • dss-sha1: SHA-1 checksum of the file
  • dss-s3_etag: S3 ETAG checksum of the file. See https://stackoverflow.com/q/12186993 for the general algorithm for how checksum is calculated. For files smaller than 64MB, this is the MD5 checksum of the file. For files larger than 64MB but smaller than 640,000MB, we use 64MB chunks. For files larger than 640,000MB, we use a chunk size equal to the total file size divided by 10000, rounded up to the nearest MB. MB, in this section, refers to 1,048,576 bytes. Note that 640,000MB is not the same as 640GB!
  • dss-crc32c: CRC-32C checksum of the file
dbio dss put-file [-h] --creator-uid CREATOR_UID --source-url SOURCE_URL
                  --uuid UUID --version VERSION
Named Arguments
--creator-uid User ID who is creating this file.
--source-url Cloud bucket URL for source data. Example is “s3://bucket_name/serious_dna.fa” .
--uuid A RFC4122-compliant ID for the file.
--version Timestamp of file creation in DSS_VERSION format. If this is not provided, the latest version is returned.
post-search

Accepts Elasticsearch JSON query and returns matching bundle identifiers Index Design: The metadata seach index is implemented as a document-oriented database using Elasticsearch. The index stores all information relevant to a bundle within each bundle document, largely eliminating the need for object-relational mapping. This design is optimized for queries that filter the data.

To illustrate this concept, say our index stored information on three entities, foo, bar, and baz. A foo can have many bars and bars can have many bazes. If we were to index bazes in a document-oriented design, the information on the foo a bar comes from and the bazes it contains are combined into a single document. A example sketch of this is shown below in JSON-schema.

{
  "definitions": {
    "bar": {
      "type": "object",
      "properties": {
        "uuid": {
          "type": "string",
          "format": "uuid"
        },
        "foo": {
          "type": "object",
          "properties": {
            "uuid": {
              "type": "string",
              "format": "uuid"
            },
            ...
          }
        },
        "bazes": {
          "type": "array",
          "items": {
            "type": "string",
            "format": "uuid"
          }
        },
        ...
      }
    }
  }
}

This closely resembles the structure of DSS bundle documents: projects have many bundles and bundles have many files. Each bundle document is a concatenation of the metadata on the project it belongs to and the files it contains. Limitations to Index Design: There are limitations to the design of DSS’s metadata search index. A few important ones are listed below.

  • Joins between bundle metadata must be conducted client-side
  • Querying is schema-specific; fields or values changed between schema version will break queries that use those fields and values
  • A new search index must be built for each schema version
  • A lot of metadata is duplicated between documents
dbio dss post-search [-h] --es-query ES_QUERY [--output-format {summary,raw}]
                     --replica {aws,gcp} [--per-page PER_PAGE]
                     [--search-after SEARCH_AFTER] [--no-paginate]
Named Arguments
--es-query Elasticsearch query
--output-format
 

Possible choices: summary, raw

Specifies the output format. The default format, summary, is a list of UUIDs for bundles that match the query. Set this parameter to raw to get the verbatim JSON metadata for bundles that match the query. When using output_format raw the per_page size is limit to no more than 10 to avoid excessively large response sizes.

--replica

Possible choices: aws, gcp

Replica to search.

--per-page Max number of results to return per page. When using output_format raw the per_page size is limit to no more than 10 to avoid excessively large response sizes.
--search-after Search-After-Context. An internal state pointer parameter for use with pagination. This parameter is referenced by the Link header as described in the “Pagination” section. The API client should not need to set this parameter directly; it should instead directly fetch the URL given in the Link header.
--no-paginate

Do not automatically page the responses

Default: True
get-subscriptions

Return a list of associated subscriptions.

dbio dss get-subscriptions [-h] --replica {aws,gcp}
                           [--subscription-type {elasticsearch,jmespath}]
Named Arguments
--replica

Possible choices: aws, gcp

Replica to fetch from.

--subscription-type
 

Possible choices: elasticsearch, jmespath

Type of subscriptions to fetch (elasticsearch or jmespath).
put-subscription

Register an HTTP endpoint that is to be notified when a given event occurs. Each user is allowed 100 subscriptions, a limit that may be increased in the future. Concerns about notification service limitations should be routed to the DSS development team.

dbio dss put-subscription [-h] [--attachments ATTACHMENTS] --callback-url
                          CALLBACK_URL
                          [--encoding {application/json,multipart/form-data}]
                          [--es-query ES_QUERY] [--form-fields FORM_FIELDS]
                          [--hmac-key-id HMAC_KEY_ID]
                          [--hmac-secret-key HMAC_SECRET_KEY]
                          [--jmespath-query JMESPATH_QUERY]
                          [--method {POST,PUT}]
                          [--payload-form-field PAYLOAD_FORM_FIELD] --replica
                          {aws,gcp}
Named Arguments
--attachments

The set of bundle metadata items to be included in the payload of a notification request to a subscription endpoint. Each property in this object represents an attachment to the notification payload. Each attachment will be a child property of the attachments property of the payload. The name of such a child property can be chosen freely provided it does not start with an underscore. For example, if the subscription is

{
  "attachments": {
    "taxon": {
      "type": "jmespath",
      "expression": "files.biomaterial_json.biomaterials[].content.biomaterial_core.ncbi_taxon_id[]"
    }
  }
}

the corresponding notification payload will contain the following entry

"attachments": {
  "taxon": [9606, 9606]
}

If a general error occurs during the processing of attachments, the notification will be sent with attachments containing only the reserved _errors attachment containing a string describing the error. If an error occurs during the processing of a specific attachment, the notification will be sent with all successfully processed attachments and additionally the _errors attachment containing an object with one property for each failed attachment. For example,

"attachments": {
  "taxon": [9606, 9606]
  "_errors" {
    "biomaterial": "Some error occurred"
  }
}

The value of the attachments property must be less than or equal to 128 KiB in size when serialized to JSON and encoded as UTF-8. If it is not, the notification will be sent with “attachments”: { “_errors”: “Attachments too large (131073 bytes)” }

--callback-url The subscriber’s URL. An HTTP request is made to the specified URL for every attempt to deliver a notification to the subscriber. If the HTTP response code is 2XX, the delivery attempt is considered successful. Otherwise, more attempts will be made with an exponentially increasing delay between attempts, until an attempt is successful or the a maximum number of attempts is reached. Occasionally, duplicate notifications may be sent. It is up to the receiver of the notification to tolerate duplicate notifications.
--encoding

Possible choices: application/json, multipart/form-data

The MIME type describing the encoding of the request body * application/json - the HTTP request body is the notification payload as JSON * multipart/form-data - the HTTP request body is a list of form fields, each consisting of a name and a corresponding value. See https://tools.ietf.org/html/rfc7578 for details on this encoding. The actual notification payload will be placed as JSON into a field of the name specified via payload_form_field.

--es-query An Elasticsearch query for restricting the set of bundles for which the subscriber is notified. The subscriber will only be notified for newly indexed bundles that match the given query. If this parameter is present the subscription will be of type elasticsearch, otherwise it will be of type jmespath.
--form-fields

A collection of static form fields to be supplied in the request body, alongside the actual notification payload. The value of each field must be a string. For example, if the subscriptions has this property set to {"foo" : "bar"}, the corresponding notification HTTP request body will consist of a multipart frame with two frames,

----------------2769baffc4f24cbc83ced26aa0c2f712
Content-Disposition: form-data; name="foo"
bar
----------------2769baffc4f24cbc83ced26aa0c2f712
Content-Disposition: form-data; name="payload"
{"transaction_id": "301c9079-3b20-4311-a131-bcda9b7f08ba", "subscription_id": ...

Since the type of this property is object, multi-valued fields are not supported. This property is ignored unless encoding is multipart/form-data.

--hmac-key-id An optional key ID to use with hmac_secret_key.
--hmac-secret-key
 The key for signing requests to the subscriber’s URL. The signature will be constructed according to https://tools.ietf.org/html/draft-cavage-http-signatures and transmitted in the HTTP Authorization header.
--jmespath-query
 An JMESPath query for restricting the set of bundles for which the subscriber is notified. The subscriber will only be notified for new bundles that match the given query. If es_query is specified, the subscription will be of type elasticsearch. If es_query is not present, the subscription will be of type jmespath
--method

Possible choices: POST, PUT

The HTTP request method to use when delivering a notification to the subscriber.

--payload-form-field
 The name of the form field that will hold the notification payload when the request is made. If the default name of the payload field collides with that of a field in form_fields, this porperty can be used to rename the payload and avoid the collision. This property is ignored unless encoding is multipart/form-data.
--replica

Possible choices: aws, gcp

Replica to write to.
delete-subscription

Delete a registered event subscription. The associated query will no longer trigger a callback if a matching document is added to the system.

dbio dss delete-subscription [-h] --uuid UUID --replica {aws,gcp}
                             [--subscription-type {elasticsearch,jmespath}]
Named Arguments
--uuid A RFC4122-compliant ID for the subscription.
--replica

Possible choices: aws, gcp

Replica to delete from.

--subscription-type
 

Possible choices: elasticsearch, jmespath

type of subscriptions to fetch (elasticsearch or jmespath)
get-subscription

Given a subscription UUID, return the associated subscription.

dbio dss get-subscription [-h] --uuid UUID --replica {aws,gcp}
                          [--subscription-type {elasticsearch,jmespath}]
Named Arguments
--uuid A RFC4122-compliant ID for the subscription.
--replica

Possible choices: aws, gcp

Replica to fetch from.

--subscription-type
 

Possible choices: elasticsearch, jmespath

type of subscriptions to fetch (elasticsearch or jmespath)
login

This command may open a browser window to ask for your consent to use web service authentication credentials.

Use –remote if using the CLI in a remote environment

dbio dss login [-h] [--access-token ACCESS_TOKEN] [--remote]
Named Arguments
--access-token Default: “”
--remote Default: False
logout

Clear sphinx-build dss authentication credentials previously configured with sphinx-build dss login.

dbio dss logout [-h]
upload

Upload a directory of files from the local filesystem and create a bundle containing the uploaded files. This method requires the use of a client-controlled object storage bucket to stage the data for upload.

dbio dss upload [-h] --src-dir SRC_DIR --replica REPLICA --staging-bucket
                STAGING_BUCKET [--timeout-seconds TIMEOUT_SECONDS]
                [--no-progress] [--bundle-uuid BUNDLE_UUID]
Named Arguments
--src-dir file path to a directory of files to upload to the replica.
--replica the replica to upload to. The supported replicas are: aws for Amazon Web Services, and gcp for Google Cloud Platform. [aws, gcp]
--staging-bucket
 a client controlled AWS S3 storage bucket to upload from.
--timeout-seconds
 

the time to wait for a file to upload to replica.

Default: 1200

--no-progress

if set, will not report upload progress. Note that even if this flag is not set, progress will not be reported if the logging level is higher than INFO or if the session is not interactive.

Default: False

--bundle-uuid
download

Download a bundle and save it to the local filesystem as a directory.

By default, all data and metadata files are downloaded. To disable the downloading of data, use the –no-data flag if using the CLI or pass the no_data=True argument if calling the download() API method. Likewise, to disable the downloading of metadata, use the –no-metadata flag for the CLI or pass the no_metadata=True argument if calling the download() API method.

If a retryable exception occurs, we wait a bit and retry again. The delay increases each time we fail and decreases each time we successfully read a block. We set a quota for the number of failures that goes up with every successful block read and down with each failure.

dbio dss download [-h] --bundle-uuid BUNDLE_UUID --replica REPLICA
                  [--version VERSION] [--download-dir DOWNLOAD_DIR]
                  [--metadata-filter METADATA_FILTER [METADATA_FILTER ...]]
                  [--data-filter DATA_FILTER [DATA_FILTER ...]]
                  [--no-metadata] [--no-data] [--num-retries NUM_RETRIES]
                  [--min-delay-seconds MIN_DELAY_SECONDS]
Named Arguments
--bundle-uuid The uuid of the bundle to download
--replica the replica to download from. The supported replicas are: aws for Amazon Web Services, and gcp for Google Cloud Platform. [aws, gcp]
--version

The version to download, else if not specified, download the latest. The version is a timestamp of bundle creation in RFC3339

Default: “”

--download-dir

The directory into which to download

Default: “”

--metadata-filter
 

One or more shell patterns against which all metadata files in the bundle will be matched case-sensitively. A file is considered a metadata file if the indexed property in the manifest is set. If and only if a metadata file matches any of the patterns in metadata_files will it be downloaded.

Default: (‘*’,)

--data-filter

One or more shell patterns against which all data files in the bundle will be matched case-sensitively. A file is considered a data file if the indexed property in the manifest is not set. The file will be downloaded only if a data file matches any of the patterns in data_files will it be downloaded.

Default: (‘*’,)

--no-metadata

Exclude metadata files. Cannot be set when –metadata-filter is also set.

Default: False

--no-data

Exclude data files. Cannot be set when –data-filter is also set.

Default: False

--num-retries

The initial quota of download failures to accept before exiting due to failures. The number of retries increase and decrease as file chucks succeed and fail.

Default: 10

--min-delay-seconds
 

The minimum number of seconds to wait in between retries.

Default: 0.25
download-manifest

Files are always downloaded to a cache / filestore directory called ‘.dbio’. This directory is created in the current directory where download is initiated. A copy of the manifest used is also written to the current directory. This manifest has an added column that lists the paths of the files within the ‘.dbio’ filestore.

The default layout is none. In this layout all of the files are downloaded to the filestore and the recommended way of accessing the files in by parsing the manifest copy that’s written to the download directory.

The bundle layout still downloads all of files to the filestore. For each bundle mentioned in the manifest a directory is created. All relevant metadata files for each bundle are linked into these directories in addition to relevant data files mentioned in the manifest.

Each row in the manifest represents one file in DSS. The manifest must have a header row. The header row must declare the following columns:

  • bundle_uuid - the UUID of the bundle containing the file in DSS.
  • bundle_version - the version of the bundle containing the file in DSS.
  • file_name - the name of the file as specified in the bundle.
  • file_uuid - the UUID of the file in the DSS.
  • file_sha256 - the SHA-256 hash of the file.
  • file_size - the size of the file.

The TSV may have additional columns. Those columns will be ignored. The ordering of the columns is insignificant because the TSV is required to have a header row.

This download format will serve as the main storage format for downloaded files. If a user specifies a different format for download (coming in the future) the files will first be downloaded in this format, then hard-linked to the user’s preferred format.

dbio dss download-manifest [-h] --manifest MANIFEST --replica REPLICA
                           [--layout LAYOUT] [--no-metadata] [--no-data]
                           [--num-retries NUM_RETRIES]
                           [--min-delay-seconds MIN_DELAY_SECONDS]
                           [--download-dir DOWNLOAD_DIR]
Named Arguments
--manifest The path to a TSV (tab-separated values) file listing files to download. If the directory for download already contains the manifest, the manifest will be overwritten to include a column with paths into the filestore.
--replica The replica from which to download. The supported replicas are: aws for Amazon Web Services, and gcp for Google Cloud Platform. [aws, gcp]
--layout

The layout of the downloaded files. Currently two options are supported, ‘none’ (the default), and ‘bundle’.

Default: “none”

--no-metadata

Exclude metadata files. Cannot be set when –metadata-filter is also set.

Default: False

--no-data

Exclude data files. Cannot be set when –data-filter is also set.

Default: False

--num-retries

The initial quota of download failures to accept before exiting due to failures. The number of retries increase and decrease as file chucks succeed and fail.

Default: 10

--min-delay-seconds
 

The minimum number of seconds to wait in between retries for downloading any file

Default: 0.25

--download-dir

The directory into which to download

Default: “”
create-version

Prints a timestamp that can be used for versioning

dbio dss create-version [-h]
download-collection

Download a bundle and save it to the local filesystem as a directory.

dbio dss download-collection [-h] --uuid UUID --replica REPLICA
                             [--version VERSION] [--download-dir DOWNLOAD_DIR]
Named Arguments
--uuid The uuid of the collection to download
--replica the replica to download from. The supported replicas are: aws for Amazon Web Services, and gcp for Google Cloud Platform. [aws, gcp]
--version The version to download, else if not specified, download the latest. The version is a timestamp of bundle creation in RFC3339
--download-dir

The directory into which to download

Default: “”
auth

Interact with the authorization and authentication system.

dbio auth [-h]
          {get-login,get-logout,get-openid-configuration,get-jwks.json,get-oauth-authorize,post-oauth-revoke,post-oauth-token,get-oauth-userinfo,post-oauth-userinfo,get-echo,post-v1-policies-evaluate,get-v1-users,post-v1-user,get-v1-user,put-v1-user,get-v1-user-owns,get-v1-user-groups,put-v1-user-group,get-v1-user-roles,put-v1-user-role,put-v1-user-policy,get-v1-groups,post-v1-group,get-v1-group,delete-v1-group,get-v1-group-roles,put-v1-group-role,get-v1-group-users,put-v1-group-user,put-v1-group-policy,get-v1-roles,post-v1-role,get-v1-role,delete-v1-role,put-v1-role-policy,get-v1-resources,get-v1-resource,post-v1-resource,delete-v1-resource,get-v1-resource-actions,put-v1-resource-action,delete-v1-resource-actions,get-v1-resource-policies,get-v1-resource-policy,post-v1-resource-policy,put-v1-resource-policy,delete-v1-resource-policy,get-v1-resource-ids,get-v1-resource-id,post-v1-resource-id,delete-v1-resource-id,get-v1-resource-id-members,put-v1-resource-id-member,login,logout}
          ...
Sub-commands:
get-login

Send the user agent to an identity provider selector and generate a user account to establish the user’s identity. This is a redirect endpoint.

dbio auth get-login [-h] --redirect-uri REDIRECT_URI [--state STATE]
Named Arguments
--redirect-uri Where to redirect to once login is complete.
--state An opaque parameter that is returned back to the redirect_uri.
get-logout

Logout the user from current sessions with the OIDC provider. You can log the users out from a specific application if the you know the client_id for the application. Otherwise the user will be logged out of the default application by oauth2_config.

dbio auth get-logout [-h] [--client-id CLIENT_ID]
Named Arguments
--client-id
get-openid-configuration

This endpoint is part of OIDC, see documentation at Provider Config

dbio auth get-openid-configuration [-h] --host HOST
Named Arguments
--host Must be auth.ucsc.ucsc-cgp-redwood.org.
get-jwks.json

Provide the public key used to sign all JWTs minted by the OIDC provider. See JSON Web Key Set for more info.

dbio auth get-jwks.json [-h]
get-oauth-authorize

This endpoint is part of OIDC and is used to redirect to an openid provider. See Auth Request

dbio auth get-oauth-authorize [-h] [--redirect-uri REDIRECT_URI]
                              [--state STATE] [--client-id CLIENT_ID]
                              [--scope SCOPE] [--respone-type RESPONE_TYPE]
                              [--nonce NONCE] [--prompt PROMPT]
Named Arguments
--redirect-uri
--state
--client-id
--scope
--respone-type
--nonce
--prompt
post-oauth-revoke

Revokes a refresh token from a client making all future token refresh requests fail.

dbio auth post-oauth-revoke [-h] --client-id CLIENT_ID --token TOKEN
Named Arguments
--client-id
--token The refresh token to revoke.
post-oauth-token

This endpoint is part of OIDC and is used to redirect to an openid provider. See Token Endpoint, and Refresh Tokens

dbio auth post-oauth-token [-h]
get-oauth-userinfo

This endpoint is part of OIDC and is used to redirect to an openid provider. See User Info

dbio auth get-oauth-userinfo [-h]
post-oauth-userinfo

This endpoint is part of OIDC and is used to redirect to an openid provider. See User Info

dbio auth post-oauth-userinfo [-h]
get-echo

Echoes the response back.

dbio auth get-echo [-h]
post-v1-policies-evaluate

Given a set of principals, actions, and resources, return a set of access control decisions.

dbio auth post-v1-policies-evaluate [-h] --principal PRINCIPAL --action ACTION
                                    [ACTION ...] --resource RESOURCE
                                    [RESOURCE ...]
Named Arguments
--principal Attested user identifier.
--action The action the principal is attempting to perform.
--resource The resource the principal will perform the action against.
get-v1-users

Paginate through all users.

dbio auth get-v1-users [-h] [--next-token NEXT_TOKEN] [--per-page PER_PAGE]
                       [--no-paginate]
Named Arguments
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
post-v1-user

Create a new user with the specified groups, roles, and iam policy.

dbio auth post-v1-user [-h] --user-id USER_ID [--groups GROUPS]
                       [--roles ROLES] [--policy POLICY]
Named Arguments
--user-id Used to identify users, groups, and roles.
--groups
--roles
--policy A resource policy, used for controlling access to a resource.
get-v1-user

Retrieve information about the user’s status and the policies attached.

dbio auth get-v1-user [-h] --user-id USER_ID
Named Arguments
--user-id User ID (email).
put-v1-user

Enable or disable a user. A disabled user will return false for all evaluations with that user as principal.

dbio auth put-v1-user [-h] --user-id USER_ID --status STATUS
Named Arguments
--user-id User ID (email).
--status
get-v1-user-owns

Paginate through a list of resources owned by a user.

dbio auth get-v1-user-owns [-h] --user-id USER_ID [--next-token NEXT_TOKEN]
                           [--per-page PER_PAGE] --resource-type RESOURCE_TYPE
                           [--no-paginate]
Named Arguments
--user-id User ID (email).
--next-token
--per-page
--resource-type
 
--no-paginate

Do not automatically page the responses

Default: True
get-v1-user-groups

Paginate through a list of groups of which a user is a member.

dbio auth get-v1-user-groups [-h] --user-id USER_ID [--next-token NEXT_TOKEN]
                             [--per-page PER_PAGE] [--no-paginate]
Named Arguments
--user-id User ID (email).
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
put-v1-user-group

Modify group(s) in which a user is a member.

dbio auth put-v1-user-group [-h] [--groups GROUPS] --user-id USER_ID --action
                            ACTION
Named Arguments
--groups
--user-id User ID (email).
--action
get-v1-user-roles

Paginate through all roles attached to a user.

dbio auth get-v1-user-roles [-h] --user-id USER_ID [--next-token NEXT_TOKEN]
                            [--per-page PER_PAGE] [--no-paginate]
Named Arguments
--user-id User ID (email).
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
put-v1-user-role

Modify the role(s) attached to a user.

dbio auth put-v1-user-role [-h] [--roles ROLES] --user-id USER_ID --action
                           ACTION
Named Arguments
--roles
--user-id User ID (email).
--action
put-v1-user-policy

Modify or add the user’s IAM policy.

dbio auth put-v1-user-policy [-h] [--policy POLICY] --user-id USER_ID
Named Arguments
--policy A resource policy, used for controlling access to a resource.
--user-id User ID (email).
get-v1-groups

Paginate through all groups.

dbio auth get-v1-groups [-h] [--next-token NEXT_TOKEN] [--per-page PER_PAGE]
                        [--no-paginate]
Named Arguments
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
post-v1-group

Create a new group, attach an IAM policy, and assign roles.

dbio auth post-v1-group [-h] [--group-id GROUP_ID] [--policy POLICY]
                        [--roles ROLES]
Named Arguments
--group-id Used to identify users, groups, and roles.
--policy A resource policy, used for controlling access to a resource.
--roles
get-v1-group

Get properties of a group, including the group’s IAM policy.

dbio auth get-v1-group [-h] --group-id GROUP_ID
Named Arguments
--group-id The name of the group.
delete-v1-group

Remove all users, policies, and roles from the group, and delete the group.

dbio auth delete-v1-group [-h] --group-id GROUP_ID
Named Arguments
--group-id The name of the group.
get-v1-group-roles

Paginate through all roles assigned to the group.

dbio auth get-v1-group-roles [-h] --group-id GROUP_ID
                             [--next-token NEXT_TOKEN] [--per-page PER_PAGE]
                             [--no-paginate]
Named Arguments
--group-id The name of the group.
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
put-v1-group-role

Modify the role(s) assigned to a group.

dbio auth put-v1-group-role [-h] [--roles ROLES] --group-id GROUP_ID --action
                            ACTION
Named Arguments
--roles
--group-id The name of the group.
--action
get-v1-group-users

Paginate through all users in a group.

dbio auth get-v1-group-users [-h] --group-id GROUP_ID
                             [--next-token NEXT_TOKEN] [--per-page PER_PAGE]
                             [--no-paginate]
Named Arguments
--group-id The name of the group.
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
put-v1-group-user

Modify the user(s) assigned to a group.

dbio auth put-v1-group-user [-h] [--users USERS] --group-id GROUP_ID --action
                            ACTION
Named Arguments
--users
--group-id The name of the group.
--action
put-v1-group-policy

Modify or create a policy attached to a group.

dbio auth put-v1-group-policy [-h] [--policy POLICY] --group-id GROUP_ID
Named Arguments
--policy A resource policy, used for controlling access to a resource.
--group-id The name of the group.
get-v1-roles

Paginate through all roles.

dbio auth get-v1-roles [-h] [--next-token NEXT_TOKEN] [--per-page PER_PAGE]
                       [--no-paginate]
Named Arguments
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
post-v1-role

Create a new role and attach a IAM policy.

dbio auth post-v1-role [-h] --role-id ROLE_ID --policy POLICY
Named Arguments
--role-id Used to identify users, groups, and roles.
--policy A resource policy, used for controlling access to a resource.
get-v1-role

Get properties of a role.

dbio auth get-v1-role [-h] --role-id ROLE_ID
Named Arguments
--role-id The name of the role.
delete-v1-role

Remove the role from all users and groups, and finally delete the role.

dbio auth delete-v1-role [-h] --role-id ROLE_ID
Named Arguments
--role-id The name of the role.
put-v1-role-policy

Modify the IAM policy attached to the role.

dbio auth put-v1-role-policy [-h] [--policy POLICY] --role-id ROLE_ID
Named Arguments
--policy A resource policy, used for controlling access to a resource.
--role-id The name of the role.
get-v1-resources

List available resource types

dbio auth get-v1-resources [-h] [--next-token NEXT_TOKEN]
                           [--per-page PER_PAGE] [--no-paginate]
Named Arguments
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
get-v1-resource

List all resources for this resource type

dbio auth get-v1-resource [-h] --resource-type-name RESOURCE_TYPE_NAME
                          [--next-token NEXT_TOKEN] [--per-page PER_PAGE]
                          [--no-paginate]
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
post-v1-resource

Create a new resource type.

dbio auth post-v1-resource [-h] [--owner-policy OWNER_POLICY]
                           [--actions ACTIONS] --resource-type-name
                           RESOURCE_TYPE_NAME
Named Arguments
--owner-policy A resource policy, used for controlling access to a resource.
--actions
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
delete-v1-resource

Delete an existing resource type if there are no ids of that resource type stored.

dbio auth delete-v1-resource [-h] --resource-type-name RESOURCE_TYPE_NAME
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
get-v1-resource-actions

List all actions for this resource type.

dbio auth get-v1-resource-actions [-h] --resource-type-name RESOURCE_TYPE_NAME
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
put-v1-resource-action

Add a new action for a resource type.

dbio auth put-v1-resource-action [-h] [--actions ACTIONS] --resource-type-name
                                 RESOURCE_TYPE_NAME
Named Arguments
--actions
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
delete-v1-resource-actions

Delete an existing action for a resource type.

dbio auth delete-v1-resource-actions [-h] [--actions ACTIONS]
                                     --resource-type-name RESOURCE_TYPE_NAME
Named Arguments
--actions
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
get-v1-resource-policies

List the available policies for this resource type.

dbio auth get-v1-resource-policies [-h] --resource-type-name
                                   RESOURCE_TYPE_NAME
                                   [--next-token NEXT_TOKEN]
                                   [--per-page PER_PAGE] [--no-paginate]
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
get-v1-resource-policy

Retrieve information about resource policy.

dbio auth get-v1-resource-policy [-h] --resource-type-name RESOURCE_TYPE_NAME
                                 --policy-name POLICY_NAME
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--policy-name
post-v1-resource-policy

Add a new resource policy. This makes the resource policy available for all resources of that type . Once added, the new resource policy can be applied to members by using PUT /v1/resource/{resource_type_name}/id/{resource_id}/members

dbio auth post-v1-resource-policy [-h] --policy POLICY
                                  [--policy-type {ResourcePolicy,IAMPolicy}]
                                  --resource-type-name RESOURCE_TYPE_NAME
                                  --policy-name POLICY_NAME
Named Arguments
--policy A resource policy, used for controlling access to a resource.
--policy-type Possible choices: ResourcePolicy, IAMPolicy
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--policy-name
put-v1-resource-policy

Modify an existing resource policy. This will affect all members that use this resource policy to access a {resource_type_name}/{resource_ids}.

dbio auth put-v1-resource-policy [-h] [--policy POLICY] --resource-type-name
                                 RESOURCE_TYPE_NAME --policy-name POLICY_NAME
Named Arguments
--policy A resource policy, used for controlling access to a resource.
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--policy-name
delete-v1-resource-policy

Delete an existing resource policy. This will affect all members that use this resource policy to access a {resource_type_name}/{resource_ids}.

dbio auth delete-v1-resource-policy [-h] --resource-type-name
                                    RESOURCE_TYPE_NAME --policy-name
                                    POLICY_NAME
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--policy-name
get-v1-resource-ids

List ids of all resources matching the specified resource type.

dbio auth get-v1-resource-ids [-h] --resource-type-name RESOURCE_TYPE_NAME
                              [--next-token NEXT_TOKEN] [--per-page PER_PAGE]
                              [--no-paginate]
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
get-v1-resource-id

Check if a resource of type resource_type_name with id resource_id exist.

dbio auth get-v1-resource-id [-h] --resource-type-name RESOURCE_TYPE_NAME
                             --resource-id RESOURCE_ID
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--resource-id The id of the resource.
post-v1-resource-id

Create a new resource.

dbio auth post-v1-resource-id [-h] --resource-type-name RESOURCE_TYPE_NAME
                              --resource-id RESOURCE_ID
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--resource-id The id of the resource.
delete-v1-resource-id

Delete a resource.

dbio auth delete-v1-resource-id [-h] --resource-type-name RESOURCE_TYPE_NAME
                                --resource-id RESOURCE_ID
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--resource-id The id of the resource.
get-v1-resource-id-members

List all members that have access to this resource. Members include users, and groups with any level of access to this resource.

dbio auth get-v1-resource-id-members [-h] --resource-type-name
                                     RESOURCE_TYPE_NAME --resource-id
                                     RESOURCE_ID [--next-token NEXT_TOKEN]
                                     [--per-page PER_PAGE] [--no-paginate]
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--resource-id The id of the resource.
--next-token
--per-page
--no-paginate

Do not automatically page the responses

Default: True
put-v1-resource-id-member

Give a principal access defined by {policy_name} to {resource_type_name}/{resource_id}.

dbio auth put-v1-resource-id-member [-h] --resource-type-name
                                    RESOURCE_TYPE_NAME --resource-id
                                    RESOURCE_ID
Named Arguments
--resource-type-name
 The name of a type of resources to which a resource policy can be applied.
--resource-id The id of the resource.
login

This command may open a browser window to ask for your consent to use web service authentication credentials.

Use –remote if using the CLI in a remote environment

dbio auth login [-h] [--access-token ACCESS_TOKEN] [--remote]
Named Arguments
--access-token Default: “”
--remote Default: False
logout

Clear sphinx-build auth authentication credentials previously configured with sphinx-build auth login.

dbio auth logout [-h]

Links: Index / Module Index / Search Page

API documentation

Data Storage System

class dbio.dss.DSSClient(*args, **kwargs)[source]

DataBiosphere Data Storage System API HTTP Semantics: The DSS API requires clients to follow certain HTTP protocol semantics that may require extra configuration in your HTTP client. The reference CLI and SDK (https://dbio.readthedocs.io/) is pre-configured to do this. If writing your own client, please note the following:

301 redirects: Some DSS API routes may return one or more HTTP 301 redirects, including potentially redirects to themselves (combined with the Retry-After delay described below). The client must follow these redirects to obtain the resource requested.

Retry-After header: Some DSS API routes may use the Retry-After header in combination with HTTP 301 or 500 series response codes. The client must follow the HTTP specification and wait the designated time period before continuing with the next request.

General retry logic: If you are building an application that will issue high numbers of API requests, you should be prepared for the possibility that a small fraction of requests fails due to network or server errors. In these situations, the HTTP client should follow best practice HTTP retry semantics. For example, clients may be configured to retry 5 times while waiting for an exponential number of seconds (1, 2, 4, 8, 16 seconds) upon encountering any 500 series response code, connect or read timeout.

The following Python code demonstrates an example configuration of the popular Requests library per the above guidance:

import requests, requests.packages.urllib3.util.retry
class RetryPolicy(requests.packages.urllib3.util.retry.Retry):
    def __init__(self, retry_after_status_codes={301}, **kwargs):
        super(RetryPolicy, self).__init__(**kwargs)
        self.RETRY_AFTER_STATUS_CODES = frozenset(retry_after_status_codes | retry.Retry.RETRY_AFTER_STATUS_CODES)

retry_policy = RetryPolicy(read=5, status=5, status_forcelist=frozenset({500, 502, 503, 504}))
s = requests.Session()
a = requests.adapters.HTTPAdapter(max_retries=retry_policy)
s.mount('https://', a)
print(s.get("https://dss.dev.ucsc-cgp-redwood.org").content)

Subscriptions: DSS supports webhook subscriptions for data events like bundle creation and deletion. Webhooks are callbacks to a public HTTPS endpoint provided by your application. When an event matching your subscription occurs, DSS will send a push notification (via an HTTPS POST or PUT request), giving your application an up-to-date stream of system activity. Subscriptions are delivered with the payload format

{
  'transaction_id': {uuid},
  'subscription_id': {uuid},
  'event_type': "CREATE"|"TOMBSTONE"|"DELETE",  # JMESPath subscriptions only
  'match': {
    'bundle_uuid': {uuid},
    'bundle_version': {version},
  }
  'jmespath_query': {jmespath_query},  # JMESPath subscriptions only
  'es_query': {es_query},  # Elasticsearch subscriptions only
  'attachments': {
    "attachment_name_1": {value},
    "attachment_name_1": {value},
    ...
    "_errors": [...]
  }
}

Special String Formats: DSS_VERSION: a timestamp that generally follows RFC3339 format guide. However there are a few differences. DSS_VERSION must always be in UTC time, ‘:’ are removed from the time, and the fractional seconds extends to 6 decimal places. Using the first example found here, the RFC3339 version would be 1985-04-12T23:20:50.52Z while the DSS_VERSION would be 1985-04-12T232050.520000Z Pagination: The DSS API supports pagination in a manner consistent with the GitHub API, which is based on RFC 5988. When the results of an API call exceed the page size specified, the HTTP response will contain a Link header of the following form: Link: <https://dss.dev.ucsc-cgp-redwood.org/v1/search?replica=aws&per_page=100&search_after=123>; rel="next". The URL in the header refers to the next page of the results to be fetched; if no Link rel="next" URL is included, then all results have been fetched. The client should recognize and parse the Link header appropriately according to RFC 5988, and retrieve the next page if requested by the user, or if all results are being retrieved.

clear_cache()

Clear the cached API definitions for a component. This can help resolve errors communicating with the API.

create_version()[source]

Prints a timestamp that can be used for versioning

classmethod delete_bundle(client, reason: str = None, uuid: str = None, replica: str = None, version: Optional[str] = None)

Delete a bundle or a specific bundle version

Parameters:
  • reason (<class 'str'>) – User-friendly reason for the bundle or timestamp-specfic bundle deletion.
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the bundle.
  • replica (<class 'str'>) – Replica to write to.
  • version (typing.Union[str, NoneType]) – Timestamp of bundle creation in DSS_VERSION format.

Delete the bundle with the given UUID. This deletion is applied across replicas.

classmethod delete_collection(client, uuid: str = None, replica: str = None)

Delete a collection.

Parameters:
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the collection.
  • replica (<class 'str'>) – Replica to delete from.

Delete a collection.

classmethod delete_subscription(client, uuid: str = None, replica: str = None, subscription_type: Optional[str] = 'jmespath')

Delete an event subscription.

Parameters:
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the subscription.
  • replica (<class 'str'>) – Replica to delete from.
  • subscription_type (typing.Union[str, NoneType]) – type of subscriptions to fetch (elasticsearch or jmespath)

Delete a registered event subscription. The associated query will no longer trigger a callback if a matching document is added to the system.

download(bundle_uuid, replica, version='', download_dir='', metadata_filter=('*', ), data_filter=('*', ), no_metadata=False, no_data=False, num_retries=10, min_delay_seconds=0.25)[source]

Download a bundle and save it to the local filesystem as a directory.

Parameters:
  • bundle_uuid (str) – The uuid of the bundle to download
  • replica (str) – the replica to download from. The supported replicas are: aws for Amazon Web Services, and gcp for Google Cloud Platform. [aws, gcp]
  • version (str) – The version to download, else if not specified, download the latest. The version is a timestamp of bundle creation in RFC3339
  • download_dir (str) – The directory into which to download
  • metadata_filter (iterable) – One or more shell patterns against which all metadata files in the bundle will be matched case-sensitively. A file is considered a metadata file if the indexed property in the manifest is set. If and only if a metadata file matches any of the patterns in metadata_files will it be downloaded.
  • data_filter (iterable) – One or more shell patterns against which all data files in the bundle will be matched case-sensitively. A file is considered a data file if the indexed property in the manifest is not set. The file will be downloaded only if a data file matches any of the patterns in data_files will it be downloaded.
  • no_metadata – Exclude metadata files. Cannot be set when –metadata-filter is also set.
  • no_data – Exclude data files. Cannot be set when –data-filter is also set.
  • num_retries (int) – The initial quota of download failures to accept before exiting due to failures. The number of retries increase and decrease as file chucks succeed and fail.
  • min_delay_seconds (float) – The minimum number of seconds to wait in between retries.

Download a bundle and save it to the local filesystem as a directory.

By default, all data and metadata files are downloaded. To disable the downloading of data, use the –no-data flag if using the CLI or pass the no_data=True argument if calling the download() API method. Likewise, to disable the downloading of metadata, use the –no-metadata flag for the CLI or pass the no_metadata=True argument if calling the download() API method.

If a retryable exception occurs, we wait a bit and retry again. The delay increases each time we fail and decreases each time we successfully read a block. We set a quota for the number of failures that goes up with every successful block read and down with each failure.

download_collection(uuid, replica, version=None, download_dir='')[source]

Download a bundle and save it to the local filesystem as a directory.

Parameters:
  • uuid (str) – The uuid of the collection to download
  • replica (str) – the replica to download from. The supported replicas are: aws for Amazon Web Services, and gcp for Google Cloud Platform. [aws, gcp]
  • version (str) – The version to download, else if not specified, download the latest. The version is a timestamp of bundle creation in RFC3339
  • download_dir (str) – The directory into which to download

Download a bundle and save it to the local filesystem as a directory.

download_manifest(manifest, replica, layout='none', no_metadata=False, no_data=False, num_retries=10, min_delay_seconds=0.25, download_dir='')[source]

Process the given manifest file in TSV (tab-separated values) format and download the files referenced by it.

Parameters:
  • layout (str) – The layout of the downloaded files. Currently two options are supported, ‘none’ (the default), and ‘bundle’.
  • manifest (str) – The path to a TSV (tab-separated values) file listing files to download. If the directory for download already contains the manifest, the manifest will be overwritten to include a column with paths into the filestore.
  • replica (str) – The replica from which to download. The supported replicas are: aws for Amazon Web Services, and gcp for Google Cloud Platform. [aws, gcp]
  • no_metadata – Exclude metadata files. Cannot be set when –metadata-filter is also set.
  • no_data – Exclude data files. Cannot be set when –data-filter is also set.
  • num_retries (int) – The initial quota of download failures to accept before exiting due to failures. The number of retries increase and decrease as file chucks succeed and fail.
  • min_delay_seconds (float) – The minimum number of seconds to wait in between retries for downloading any file
  • download_dir (str) – The directory into which to download

Files are always downloaded to a cache / filestore directory called ‘.dbio’. This directory is created in the current directory where download is initiated. A copy of the manifest used is also written to the current directory. This manifest has an added column that lists the paths of the files within the ‘.dbio’ filestore.

The default layout is none. In this layout all of the files are downloaded to the filestore and the recommended way of accessing the files in by parsing the manifest copy that’s written to the download directory.

The bundle layout still downloads all of files to the filestore. For each bundle mentioned in the manifest a directory is created. All relevant metadata files for each bundle are linked into these directories in addition to relevant data files mentioned in the manifest.

Each row in the manifest represents one file in DSS. The manifest must have a header row. The header row must declare the following columns:

  • bundle_uuid - the UUID of the bundle containing the file in DSS.
  • bundle_version - the version of the bundle containing the file in DSS.
  • file_name - the name of the file as specified in the bundle.
  • file_uuid - the UUID of the file in the DSS.
  • file_sha256 - the SHA-256 hash of the file.
  • file_size - the size of the file.

The TSV may have additional columns. Those columns will be ignored. The ordering of the columns is insignificant because the TSV is required to have a header row.

This download format will serve as the main storage format for downloaded files. If a user specifies a different format for download (coming in the future) the files will first be downloaded in this format, then hard-linked to the user’s preferred format.

expired_token()

Return True if we have an active session containing an expired (or nearly expired) token.

classmethod get_bundle(client, uuid: str = None, version: Optional[str] = None, replica: str = None, directurls: Optional[str] = None, presignedurls: Optional[str] = None, token: Optional[str] = None, per_page: Optional[str] = 500, start_at: Optional[str] = None)

Retrieve a bundle given a UUID and optionally a version.

Pagination

This method supports pagination. Use DSSClient.get_bundle.iterate(**kwargs) to create a generator that yields all results, making multiple requests over the wire if necessary:

for result in DSSClient.get_bundle.iterate(**kwargs):
    ...

The keyword arguments for DSSClient.get_bundle.iterate() are identical to the arguments for DSSClient.get_bundle() listed here.

Parameters:
  • uuid (<class 'str'>) – Bundle unique ID.
  • version (typing.Union[str, NoneType]) – Timestamp of bundle creation in DSS_VERSION format.
  • replica (<class 'str'>) – Replica to fetch from.
  • directurls (typing.Union[str, NoneType]) – When set to true, the response will contain API-specific URLs that are tied to the specified replica, for example gs://bucket/object or s3://bucket/object This parameter is mutually exclusive with the presigned urls parameter. The use of presigned URLs is recommended for data access. Cloud native URLs are currently provided for a limited set of use cases and may not be provided in the future. If cloud native URLs are required, please contact the data store team regarding the credentials necessary to use them.
  • presignedurls (typing.Union[str, NoneType]) – Include presigned URLs in the response. This is mutually exclusive with the directurls parameter.
  • token (typing.Union[str, NoneType]) – Token to manage retries. End users constructing queries should not set this parameter.
  • per_page (typing.Union[str, NoneType]) – Max number of results to return per page.
  • start_at (typing.Union[str, NoneType]) – An internal state pointer parameter for use with pagination. This parameter is referenced by the Link header as described in the “Pagination” section. The API client should not need to set this parameter directly; it should instead directly fetch the URL given in the Link header.

Given a bundle UUID, return the latest version of that bundle. If the version is provided, that version of the bundle is returned instead.

classmethod get_bundles_all(client, replica: str = None, prefix: Optional[str] = None, token: Optional[str] = None, per_page: Optional[str] = 100, search_after: Optional[str] = None)

List through all available bundles.

Pagination

This method supports pagination. Use DSSClient.get_bundles_all.iterate(**kwargs) to create a generator that yields all results, making multiple requests over the wire if necessary:

for result in DSSClient.get_bundles_all.iterate(**kwargs):
    ...

The keyword arguments for DSSClient.get_bundles_all.iterate() are identical to the arguments for DSSClient.get_bundles_all() listed here.

Parameters:
  • replica (<class 'str'>) – Replica to fetch from.
  • prefix (typing.Union[str, NoneType]) – Used to specify the beginning of a particular bundle UUID. Capitalized letters will be lower-cased as is done when users submit a uuid (all uuids have lower-cased letters upon ingestion into the dss). Characters other than letters, numbers, and dashes are not allowed and will error. The specified character(s) will return all available bundle uuids starting with that character(s).
  • token (typing.Union[str, NoneType]) – Token to manage retries. End users constructing queries should not set this parameter.
  • per_page (typing.Union[str, NoneType]) – Max number of results to return per page.
  • search_after (typing.Union[str, NoneType]) – Search-After-Context. An internal state pointer parameter for use with pagination. This parameter is referenced by the Link header as described in the “Pagination” section. The API client should not need to set this parameter directly; it should instead directly fetch the URL given in the Link header.

Lists all the bundles available in the data-store, responses will be returned in a paginated format, at most 500 values shall be returned at a time. Tombstoned bundles will be omitted from the list of bundles available.

classmethod get_bundles_checkout(client, replica: str = None, checkout_job_id: str = None)

Check the status of a checkout request.

Parameters:
  • replica (<class 'str'>) – Replica to fetch from.
  • checkout_job_id (<class 'str'>) – A RFC4122-compliant ID for the checkout job request.

Use this route with the checkout_job_id identifier returned by POST /bundles/{uuid}/checkout.

classmethod get_collection(client, uuid: str = None, replica: str = None, version: Optional[str] = None)

Retrieve a collection given a UUID.

Parameters:
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the collection.
  • replica (<class 'str'>) – Replica to fetch from.
  • version (typing.Union[str, NoneType]) – Timestamp of collection creation in DSS_VERSION format. If this is not provided, the latest version is returned.

Given a collection UUID, return the associated collection object.

classmethod get_collections(client, per_page: Optional[str] = 500, start_at: Optional[str] = None)

Retrieve a user’s collections.

Pagination

This method supports pagination. Use DSSClient.get_collections.iterate(**kwargs) to create a generator that yields all results, making multiple requests over the wire if necessary:

for result in DSSClient.get_collections.iterate(**kwargs):
    ...

The keyword arguments for DSSClient.get_collections.iterate() are identical to the arguments for DSSClient.get_collections() listed here.

Parameters:
  • per_page (typing.Union[str, NoneType]) – Max number of results to return per page.
  • start_at (typing.Union[str, NoneType]) – An internal state pointer parameter for use with pagination. This parameter is referenced by the Link header as described in the “Pagination” section. The API client should not need to set this parameter directly; it should instead directly fetch the URL given in the Link header.

Return a list of a user’s collections. Collections are sets of links to files, bundles, other collections, or fragments of JSON metadata files. Each entry in the input set of links is checked for referential integrity (the link target must exist in the replica referenced). Up to 1000 items can be referenced in a new collection, or added or removed using PATCH /collections. New collections are private to the authenticated user. Collection items are de-duplicated (if an identical item is given multiple times, it will only be added once). Collections are replicated across storage replicas similarly to files and bundles.

classmethod get_event(client, uuid: str = None, version: str = None, replica: str = None)

Retrieve a bundle metadata document given a UUID and version.

Parameters:
  • uuid (<class 'str'>) – Bundle unique ID.
  • version (<class 'str'>) – Timestamp of bundle creation in DSS_VERSION format.
  • replica (<class 'str'>) – Replica to fetch from.

Given a bundle UUID and version, return the bundle metadata document.

classmethod get_events(client, from_date: Optional[str] = None, to_date: Optional[str] = None, replica: str = None, per_page: Optional[str] = 1, token: Optional[str] = None)

Replay events

Pagination

This method supports pagination. Use DSSClient.get_events.iterate(**kwargs) to create a generator that yields all results, making multiple requests over the wire if necessary:

for result in DSSClient.get_events.iterate(**kwargs):
    ...

The keyword arguments for DSSClient.get_events.iterate() are identical to the arguments for DSSClient.get_events() listed here.

Parameters:
  • from_date (typing.Union[str, NoneType]) – Timestamp to begin replaying events, in DSS_VERSION format. If this is not provided, replay from the earliest event.
  • to_date (typing.Union[str, NoneType]) – Timestamp to stop replaying events, in DSS_VERSION format. If this is not provided, replay to the latest event.
  • replica (<class 'str'>) – Replica to fetch from.
  • per_page (typing.Union[str, NoneType]) – Max number of results to return per page.
  • token (typing.Union[str, NoneType]) – Token to manage retries. End users constructing queries should not set this parameter.

Return urls where event data is available, with manifest of contents.

classmethod get_file(client, uuid: str = None, replica: str = None, version: Optional[str] = None, token: Optional[str] = None, directurl: Optional[str] = None, content_disposition: Optional[str] = None)

Retrieve a file given a UUID and optionally a version.

Streaming

Use DSSClient.get_file.stream(**kwargs) to get a requests.Response object whose body has not been read yet. This allows streaming large file bodies:

fid = "7a8fbda7-d470-467a-904e-5c73413fab3e"
with DSSClient().get_file.stream(uuid=fid, replica="aws") as fh:
    while True:
        chunk = fh.raw.read(1024)
        ...
        if not chunk:
            break

The keyword arguments for DSSClient.get_file.stream() are identical to the arguments for DSSClient.get_file() listed here.

Parameters:
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the file.
  • replica (<class 'str'>) – Replica to fetch from.
  • version (typing.Union[str, NoneType]) – Timestamp of file creation in DSS_VERSION format. If this is not provided, the latest version is returned.
  • token (typing.Union[str, NoneType]) – Token to manage retries. End users constructing queries should not set this parameter.
  • directurl (typing.Union[str, NoneType]) – When set to true, the response will contain API-specific URLs that are tied to the specified replica, for example gs://bucket/object or s3://bucket/object The use of presigned URLs is recommended for data access. Cloud native URLs are currently provided for a limited set of use cases and may not be provided in the future. If cloud native URLs are required, please contact the data store team regarding the credentials necessary to use them.
  • content_disposition (typing.Union[str, NoneType]) – Optional and does not work when directurl=true (only works with the default presigned url response). If this parameter is provided, the response from fetching the returned presigned url will include the specified Content-Disposition header. This can be useful to indicate to a browser that a file should be downloaded rather than opened in a new tab, and can also supply the original filename in the response. Example: .. code:: content_disposition=”attachment; filename=data.json”

Given a file UUID, return the latest version of that file. If the version is provided, that version of the file is returned instead. Headers will contain the data store metadata for the file. This endpoint returns a HTTP redirect to another HTTP endpoint with the file contents. NOTE When using the DataBiosphere DSS CLI, this will stream the file to stdout and may need to be piped. For example, dbio dss get-file --uuid UUID --replica aws > result.txt

classmethod get_subscription(client, uuid: str = None, replica: str = None, subscription_type: Optional[str] = 'jmespath')

Retrieve an event subscription given a UUID.

Parameters:
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the subscription.
  • replica (<class 'str'>) – Replica to fetch from.
  • subscription_type (typing.Union[str, NoneType]) – type of subscriptions to fetch (elasticsearch or jmespath)

Given a subscription UUID, return the associated subscription.

classmethod get_subscriptions(client, replica: str = None, subscription_type: Optional[str] = 'jmespath')

Retrieve a user’s event subscriptions.

Parameters:
  • replica (<class 'str'>) – Replica to fetch from.
  • subscription_type (typing.Union[str, NoneType]) – Type of subscriptions to fetch (elasticsearch or jmespath).

Return a list of associated subscriptions.

classmethod head_file(client, uuid: str = None, replica: str = None, version: Optional[str] = None)

Retrieve a file’s metadata given an UUID and optionally a version.

Parameters:
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the file.
  • replica (<class 'str'>) – Replica to fetch from.
  • version (typing.Union[str, NoneType]) – Timestamp of file creation in DSS_VERSION format. If this is not provided, the latest version is returned.

Given a file UUID, return the metadata for the latest version of that file. If the version is provided, that version’s metadata is returned instead. The metadata is returned in the headers.

static load_swagger_json(swagger_json, ptr_str='$ref')

Load the Swagger JSON and resolve {“$ref”: “#/…”} internal JSON Pointer references.

login(access_token='', remote=False)

Configure and save {prog} authentication credentials.

This command may open a browser window to ask for your consent to use web service authentication credentials.

Use –remote if using the CLI in a remote environment

logout()

Clear {prog} authentication credentials previously configured with {prog} login.

classmethod patch_bundle(client, add_files: Optional[List[T]] = None, remove_files: Optional[List[T]] = None, uuid: str = None, replica: str = None, version: str = None)

Update a bundle.

Parameters:
  • add_files (typing.Union[typing.List, NoneType]) – List of new files to add to the bundle. File names must be unique.
  • remove_files (typing.Union[typing.List, NoneType]) – List of files to remove from the bundle. Files must match exactly to be removed. Files not found in the bundle are ignored.
  • uuid (<class 'str'>) – A RFC4122-compliant ID of the bundle to update.
  • replica (<class 'str'>) – Replica to update the bundle on. Updates are propagated to other replicas.
  • version (<class 'str'>) – Timestamp of the bundle to update in DSS_VERSION format format (required).

Add or remove files from a bundle. A specific version of the bundle to update must be provided, and a new version will be written. Bundle manifests exceeding 20,000 files will not be included in the Elasticsearch index document.

classmethod patch_collection(client, add_contents: Optional[List[T]] = None, description: Optional[str] = None, details: Optional[Mapping[KT, VT_co]] = None, name: Optional[str] = None, remove_contents: Optional[List[T]] = None, uuid: str = None, replica: str = None, version: str = None)

Update a collection.

Parameters:
  • add_contents (typing.Union[typing.List, NoneType]) – List of new items to add to the collection. Items are de-duplicated (if an identical item is already present in the collection or given multiple times, it will only be added once).
  • description (typing.Union[str, NoneType]) – New description for the collection.
  • details (typing.Union[typing.Mapping, NoneType]) – New details for the collection.
  • name (typing.Union[str, NoneType]) – New name for the collection.
  • remove_contents (typing.Union[typing.List, NoneType]) – List of items to remove from the collection. Items must match exactly to be removed. Items not found in the collection are ignored.
  • uuid (<class 'str'>) – A RFC4122-compliant ID of the collection to update.
  • replica (<class 'str'>) – Replica to update the collection on. Updates are propagated to other replicas.
  • version (<class 'str'>) – Timestamp of the collection to update in DSS_VERSION format format (required).

Add or remove items from a collection. A specific version of the collection to update must be provided, and a new version will be written.

classmethod post_bundles_checkout(client, destination: Optional[str] = None, email: Optional[str] = None, uuid: str = None, version: Optional[str] = None, replica: str = None)

Check out a bundle to DSS-managed or user-managed cloud object storage destination

Parameters:
  • destination (typing.Union[str, NoneType]) – User-owned destination storage bucket.
  • email (typing.Union[str, NoneType]) – An email address to send status updates to.
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the bundle.
  • version (typing.Union[str, NoneType]) – Timestamp of file creation in DSS_VERSION format. If this is not provided, the latest version is returned.
  • replica (<class 'str'>) – Replica to fetch from.

Initiate asynchronous checkout of a bundle. The response JSON contains a field, checkout_job_id, that can be used to query the status of the checkout via the GET /bundles/checkout/{checkout_job_id} API method. FIXME: document the error code returned when the bundle or specified version does not exist. TODO: After some time period, the data will be removed. TBD: This could be based on initial checkout time or last access time.

Find bundles by searching their metadata with an Elasticsearch query

Pagination

This method supports pagination. Use DSSClient.post_search.iterate(**kwargs) to create a generator that yields all results, making multiple requests over the wire if necessary:

for result in DSSClient.post_search.iterate(**kwargs):
    ...

The keyword arguments for DSSClient.post_search.iterate() are identical to the arguments for DSSClient.post_search() listed here.

Parameters:
  • es_query (typing.Mapping) – Elasticsearch query
  • output_format (typing.Union[str, NoneType]) – Specifies the output format. The default format, summary, is a list of UUIDs for bundles that match the query. Set this parameter to raw to get the verbatim JSON metadata for bundles that match the query. When using output_format raw the per_page size is limit to no more than 10 to avoid excessively large response sizes.
  • replica (<class 'str'>) – Replica to search.
  • per_page (typing.Union[str, NoneType]) – Max number of results to return per page. When using output_format raw the per_page size is limit to no more than 10 to avoid excessively large response sizes.
  • search_after (typing.Union[str, NoneType]) – Search-After-Context. An internal state pointer parameter for use with pagination. This parameter is referenced by the Link header as described in the “Pagination” section. The API client should not need to set this parameter directly; it should instead directly fetch the URL given in the Link header.

Accepts Elasticsearch JSON query and returns matching bundle identifiers Index Design: The metadata seach index is implemented as a document-oriented database using Elasticsearch. The index stores all information relevant to a bundle within each bundle document, largely eliminating the need for object-relational mapping. This design is optimized for queries that filter the data.

To illustrate this concept, say our index stored information on three entities, foo, bar, and baz. A foo can have many bars and bars can have many bazes. If we were to index bazes in a document-oriented design, the information on the foo a bar comes from and the bazes it contains are combined into a single document. A example sketch of this is shown below in JSON-schema.

{
  "definitions": {
    "bar": {
      "type": "object",
      "properties": {
        "uuid": {
          "type": "string",
          "format": "uuid"
        },
        "foo": {
          "type": "object",
          "properties": {
            "uuid": {
              "type": "string",
              "format": "uuid"
            },
            ...
          }
        },
        "bazes": {
          "type": "array",
          "items": {
            "type": "string",
            "format": "uuid"
          }
        },
        ...
      }
    }
  }
}

This closely resembles the structure of DSS bundle documents: projects have many bundles and bundles have many files. Each bundle document is a concatenation of the metadata on the project it belongs to and the files it contains. Limitations to Index Design: There are limitations to the design of DSS’s metadata search index. A few important ones are listed below.

  • Joins between bundle metadata must be conducted client-side
  • Querying is schema-specific; fields or values changed between schema version will break queries that use those fields and values
  • A new search index must be built for each schema version
  • A lot of metadata is duplicated between documents
classmethod put_bundle(client, creator_uid: int = None, files: List[T] = None, uuid: str = None, version: str = None, replica: str = None)

Create a bundle

Parameters:
  • creator_uid (<class 'int'>) – User ID who is creating this bundle.
  • files (typing.List) – This is a list of dictionaries describing each of the files. Each dictionary includes the fields: - The “uuid” of a file already previously uploaded with “PUT file/{uuid}”. - The “version” timestamp of the file. - The “name” of the file. This can be most anything, and is the name the file will have when downloaded. - The “indexed” field, which specifies whether a file should be indexed or not. Bundle manifests exceeding 20,000 files will not be included in the Elasticsearch index document. Example representing 2 files with dummy values: [{‘uuid’: ‘ce55fd51-7833-469b-be0b-5da88ebebfcd’, ‘version’: ‘2017-06-16T193604.240704Z’, ‘name’: ‘dinosaur_dna.fa’, ‘indexed’: False}, {‘uuid’: ‘ae55fd51-7833-469b-be0b-5da88ebebfca’, ‘version’: ‘0303-04-23T193604.240704Z’, ‘name’: ‘dragon_dna.fa’, ‘indexed’: False}]
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the bundle.
  • version (<class 'str'>) – Timestamp of bundle creation in DSS_VERSION format.
  • replica (<class 'str'>) – Replica to write to.

Create a new version of a bundle with a given UUID. The list of file UUID and versions to be included must be provided.

classmethod put_collection(client, contents: List[T] = None, description: str = None, details: Mapping[KT, VT_co] = None, name: str = None, replica: str = None, uuid: str = None, version: str = None)

Create a collection.

Parameters:
  • contents (typing.List) – A list of objects describing links to files, bundles, other collections, and metadata fragments that are part of the collection.
  • description (<class 'str'>) – A long description of the collection, formatted in Markdown.
  • details (typing.Mapping) – Supplementary JSON metadata for the collection.
  • name (<class 'str'>) – A short name identifying the collection.
  • replica (<class 'str'>) – Replica to write to.
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the collection.
  • version (<class 'str'>) – Timestamp of collection creation in DSS_VERSION format.

Create a new collection. Collections are sets of links to files, bundles, other collections, or fragments of JSON metadata files. Each entry in the input set of links is checked for referential integrity (the link target must exist in the replica referenced). Up to 1000 items can be referenced in a new collection, or added or removed using PATCH /collections. New collections are private to the authenticated user. Collection items are de-duplicated (if an identical item is given multiple times, it will only be added once). Collections are replicated across storage replicas similarly to files and bundles.

classmethod put_file(client, creator_uid: int = None, source_url: str = None, uuid: str = None, version: str = None)

Create a new version of a file

Parameters:
  • creator_uid (<class 'int'>) – User ID who is creating this file.
  • source_url (<class 'str'>) – Cloud bucket URL for source data. Example is “s3://bucket_name/serious_dna.fa” .
  • uuid (<class 'str'>) – A RFC4122-compliant ID for the file.
  • version (<class 'str'>) – Timestamp of file creation in DSS_VERSION format. If this is not provided, the latest version is returned.

Create a new version of a file with a given UUID. The contents of the file are provided by the client by reference using a cloud object storage URL. The file on the cloud object storage service must have metadata set listing the file checksums and content-type. The metadata fields required are:

  • dss-sha256: SHA-256 checksum of the file
  • dss-sha1: SHA-1 checksum of the file
  • dss-s3_etag: S3 ETAG checksum of the file. See https://stackoverflow.com/q/12186993 for the general algorithm for how checksum is calculated. For files smaller than 64MB, this is the MD5 checksum of the file. For files larger than 64MB but smaller than 640,000MB, we use 64MB chunks. For files larger than 640,000MB, we use a chunk size equal to the total file size divided by 10000, rounded up to the nearest MB. MB, in this section, refers to 1,048,576 bytes. Note that 640,000MB is not the same as 640GB!
  • dss-crc32c: CRC-32C checksum of the file
classmethod put_subscription(client, attachments: Optional[Mapping[KT, VT_co]] = None, callback_url: str = None, encoding: Optional[str] = 'application/json', es_query: Optional[Mapping[KT, VT_co]] = None, form_fields: Optional[Mapping[KT, VT_co]] = {}, hmac_key_id: Optional[str] = None, hmac_secret_key: Optional[str] = None, jmespath_query: Optional[str] = None, method: Optional[str] = 'POST', payload_form_field: Optional[str] = 'payload', replica: str = None)

Create an event subscription.

Parameters:
  • attachments (typing.Union[typing.Mapping, NoneType]) – The set of bundle metadata items to be included in the payload of a notification request to a subscription endpoint. Each property in this object represents an attachment to the notification payload. Each attachment will be a child property of the attachments property of the payload. The name of such a child property can be chosen freely provided it does not start with an underscore. For example, if the subscription is .. code:: { “attachments”: { “taxon”: { “type”: “jmespath”, “expression”: “files.biomaterial_json.biomaterials[].content.biomaterial_core.ncbi_taxon_id[]” } } } the corresponding notification payload will contain the following entry .. code:: “attachments”: { “taxon”: [9606, 9606] } If a general error occurs during the processing of attachments, the notification will be sent with attachments containing only the reserved _errors attachment containing a string describing the error. If an error occurs during the processing of a specific attachment, the notification will be sent with all successfully processed attachments and additionally the _errors attachment containing an object with one property for each failed attachment. For example, .. code:: “attachments”: { “taxon”: [9606, 9606] “_errors” { “biomaterial”: “Some error occurred” } } The value of the attachments property must be less than or equal to 128 KiB in size when serialized to JSON and encoded as UTF-8. If it is not, the notification will be sent with “attachments”: { “_errors”: “Attachments too large (131073 bytes)” }
  • callback_url (<class 'str'>) – The subscriber’s URL. An HTTP request is made to the specified URL for every attempt to deliver a notification to the subscriber. If the HTTP response code is 2XX, the delivery attempt is considered successful. Otherwise, more attempts will be made with an exponentially increasing delay between attempts, until an attempt is successful or the a maximum number of attempts is reached. Occasionally, duplicate notifications may be sent. It is up to the receiver of the notification to tolerate duplicate notifications.
  • encoding (typing.Union[str, NoneType]) – The MIME type describing the encoding of the request body * application/json - the HTTP request body is the notification payload as JSON * multipart/form-data - the HTTP request body is a list of form fields, each consisting of a name and a corresponding value. See https://tools.ietf.org/html/rfc7578 for details on this encoding. The actual notification payload will be placed as JSON into a field of the name specified via payload_form_field.
  • es_query (typing.Union[typing.Mapping, NoneType]) – An Elasticsearch query for restricting the set of bundles for which the subscriber is notified. The subscriber will only be notified for newly indexed bundles that match the given query. If this parameter is present the subscription will be of type elasticsearch, otherwise it will be of type jmespath.
  • form_fields (typing.Union[typing.Mapping, NoneType]) – A collection of static form fields to be supplied in the request body, alongside the actual notification payload. The value of each field must be a string. For example, if the subscriptions has this property set to {"foo" : "bar"}, the corresponding notification HTTP request body will consist of a multipart frame with two frames, .. code:: —————-2769baffc4f24cbc83ced26aa0c2f712 Content-Disposition: form-data; name=”foo” bar —————-2769baffc4f24cbc83ced26aa0c2f712 Content-Disposition: form-data; name=”payload” {“transaction_id”: “301c9079-3b20-4311-a131-bcda9b7f08ba”, “subscription_id”: … Since the type of this property is object, multi-valued fields are not supported. This property is ignored unless encoding is multipart/form-data.
  • hmac_key_id (typing.Union[str, NoneType]) – An optional key ID to use with hmac_secret_key.
  • hmac_secret_key (typing.Union[str, NoneType]) – The key for signing requests to the subscriber’s URL. The signature will be constructed according to https://tools.ietf.org/html/draft-cavage-http-signatures and transmitted in the HTTP Authorization header.
  • jmespath_query (typing.Union[str, NoneType]) – An JMESPath query for restricting the set of bundles for which the subscriber is notified. The subscriber will only be notified for new bundles that match the given query. If es_query is specified, the subscription will be of type elasticsearch. If es_query is not present, the subscription will be of type jmespath
  • method (typing.Union[str, NoneType]) – The HTTP request method to use when delivering a notification to the subscriber.
  • payload_form_field (typing.Union[str, NoneType]) – The name of the form field that will hold the notification payload when the request is made. If the default name of the payload field collides with that of a field in form_fields, this porperty can be used to rename the payload and avoid the collision. This property is ignored unless encoding is multipart/form-data.
  • replica (<class 'str'>) – Replica to write to.

Register an HTTP endpoint that is to be notified when a given event occurs. Each user is allowed 100 subscriptions, a limit that may be increased in the future. Concerns about notification service limitations should be routed to the DSS development team.

upload(src_dir, replica, staging_bucket, timeout_seconds=1200, no_progress=False, bundle_uuid=None)[source]

Upload a directory of files from the local filesystem and create a bundle containing the uploaded files.

Parameters:
  • src_dir (str) – file path to a directory of files to upload to the replica.
  • replica (str) – the replica to upload to. The supported replicas are: aws for Amazon Web Services, and gcp for Google Cloud Platform. [aws, gcp]
  • staging_bucket (str) – a client controlled AWS S3 storage bucket to upload from.
  • timeout_seconds (int) – the time to wait for a file to upload to replica.
  • no_progress (bool) – if set, will not report upload progress. Note that even if this flag is not set, progress will not be reported if the logging level is higher than INFO or if the session is not interactive.

Upload a directory of files from the local filesystem and create a bundle containing the uploaded files. This method requires the use of a client-controlled object storage bucket to stage the data for upload.

class dbio.dss.DSSFile[source]

Local representation of a file on the DSS

count()

Return number of occurrences of value.

classmethod for_bundle_manifest(manifest_bytes, bundle_uuid, version, replica)[source]

Even though the bundle manifest is not a DSS file, we need to wrap its info in a DSSFile object for consistency and logging purposes.

index()

Return first index of value.

Raises ValueError if the value is not present.

indexed

Alias for field number 5

name

Alias for field number 0

replica

Alias for field number 6

sha256

Alias for field number 3

size

Alias for field number 4

uuid

Alias for field number 1

version

Alias for field number 2

class dbio.dss.TaskRunner(threads=8)[source]

A wrapper for ThreadPoolExecutor that tracks futures for you and allows dynamic submission of tasks.

submit(info, task, *args, **kwargs)[source]

Add task to be run.

Should only be called from the main thread or from tasks submitted by this method. :param info: Something printable :param task: A callable

wait_for_futures()[source]

Wait for all submitted futures to finish.

Should only be called from the main thread.

Links: Index / Module Index / Search Page

Data Store Tutorials

This page contains tutorials for using the data store tools in this repo.

Python Open Endpoint Examples

The DataBiosphere API provides several ways for users of the data store to access and download data sets from the data store. This page covers how to access the data store using Python API bindings.

NOTE: The Data Biosphere CLI utility is compatible with Python 3.5+.

create_version

Returns a timestamp in DSS_VERSION format (e.g., 1985-04-12T232050.520000Z), necessary for versioning bundles or files.

Note

A version is a timestamp in RFC3339 format that keeps track of the most recent iteration of a bundle or file. A bundle is a collection of many different data files, and both bundles and files have version numbers.

Example call to create_version():

from dbio.dss import DSSClient

dss = DSSClient()

dss.create_version()
download

Downloads a bundle to the local filesystem as a directory. By default, both data and metadata files are downloaded. The no_data or no_metadata flags can be set to True to download only the metadata or data, respectively (see example below).

Implementation detail: All files are downloaded to a local cache directory called .dbio that is created in the directory where the download is initiated. The user should never need to interact directly with the .dbio directory.

See note above regarding version numbering.

Example call to download():

from dbio.dss import DSSClient

dss = DSSClient()

dss.download(
    bundle_uuid="ffffaf55-f19c-40e3-aa81-a6c69d357265",
    version="2019-08-01T200147.836832Z",
    replica="aws",
    download_dir="download_test",
)

Example response:

{
    "bundle": {
        "creator_uid": 8008,
        "files": [
          {
            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
            "crc32c": "5c084696",
            "indexed": true,
            "name": "cell_suspension_0.json",
            "s3_etag": "bd60da05055d1cd544855dd35cb12470",
            "sha1": "fdeb52d3caf0becce0575528c81bf0a06cb4a023",
            "sha256": "e0ff1c402a4d6c659937f90d00d9820a2ebf0ebc920260a2a2bddf0961c30de5",
            "size": 847,
            "uuid": "134c0f04-76ae-405d-aea4-b72c08a53dd9",
            "version": "2019-07-09T230754.589000Z"
          },
          {
            "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
            "crc32c": "39e6f9e1",
            "indexed": true,
            "name": "specimen_from_organism_0.json",
            "s3_etag": "f30917f841530d78e16223354049c8dc",
            "sha1": "98171c05647a3b771afb3bd61e65d0a25b0afe7f",
            "sha256": "35406f0b8fa1ece3e3589151978aefef28f358afa163874b286eab837fcabfca",
            "size": 864,
            "uuid": "577a91d8-e579-41b6-9353-7e4e774c161a",
            "version": "2019-07-09T222811.151000Z"
          },

          ...

          {
            "content-type": "application/gzip; dcp-type=data",
            "crc32c": "38f31e58",
            "indexed": false,
            "name": "SRR6579532_2.fastq.gz",
            "s3_etag": "ac67e10df687471f5808be96499836c6",
            "sha1": "8743feb4d1ce82328127d10e2b1dfa35e5ae4b5a",
            "sha256": "3d788e06b5ca4c8fc679b47c790b1e266f73d48818a1749743ec85f096d657ea",
            "size": 43810957,
            "uuid": "1330ef1a-7a21-40c6-84c5-5cec18204028",
            "version": "2019-08-03T150636.729022Z"
          }
        ],
        "uuid": "ffffaf55-f19c-40e3-aa81-a6c69d357265",
        "version": "2019-08-01T200147.836832Z"
    }
}

Example call to download(), specifying the flags needed to download the data or the metadata only:

from dbio.dss import DSSClient

dss = DSSClient()

UUID = "ffffaf55-f19c-40e3-aa81-a6c69d357265"
VERSION = "ffffaf55-f19c-40e3-aa81-a6c69d357265"

# Download the metadata only
dss.download(
    bundle_uuid=UUID,
    version=VERSION,
    replica="aws",
    download_dir=".dbio_metadata_only"
)

# Download the data only
dss.download(
    bundle_uuid=UUID,
    version=VERSION,
    replica="aws",
    download_dir=".dbio_data_only"
)
download_manifest

Downloads a list of files specified in a user-provided manifest file.

The manifest file should be in TSV (tab-separated variable) format, with one line in the manifest per file to download. The manifest should contain information about files (one file per line). The information that must be provided for a given bundle is available from the get_bundle() method.

The header row must define the columns:

  • bundle_uuid - UUID of the requested bundle
  • bundle_version - the version of the requested bundle
  • file_name - the name of the file as specified in the bundle
  • file_uuid - the UUID of the file in the DSS
  • file_sha256 - the SHA-256 hash of the file
  • file_size - the size of the file

Example call to download_manifest():

from dbio.dss import DSSClient
import os
from dbio.util import tsv
import json
import pprint
from get_bundle_api import fetch_bundle, save_bundle, BUNDLE_JSON

dss = DSSClient()

if not os.path.isfile(BUNDLE_JSON):
    bundle = fetch_bundle()
    save_bundle(bundle)

with open("manifest.tsv", "w", newline='') as manifest:
    writer = tsv.DictWriter(
        manifest,
        fieldnames=(
            "bundle_uuid",
            "bundle_version",
            "file_name",
            "file_uuid",
            "file_version",
            "file_sha256",
            "file_size",
        )
    )
    writer.writeheader()

    with open(BUNDLE_JSON, "w") as jsonfile:
        try:
            data = json.load(jsonfile)
            bundle_uuid, bundle_version = (
                data["bundle"]["uuid"],
                data["bundle"]["version"],
            )
            pprint.pprint(data)
            for content in data["bundle"]["files"]:
                if content["name"].endswith(".json"):
                    writer.writerow(
                        dict(
                            bundle_uuid=bundle_uuid,
                            bundle_version=bundle_version,
                            file_name=content["name"],
                            file_uuid=content["uuid"],
                            file_version=content["version"],
                            file_sha256=content["sha256"],
                            file_size=content["size"],
                        )
                    )
        except ValueError as e:
            print("Not a JSON file: %s" % e)

dss.download_manifest(replica="aws", manifest="manifest.tsv")

Example manifest TSV file:

bundle_uuid                             bundle_version              file_name               file_uuid                               file_version                file_sha256                                                         file_size   file_path
002aeac5-4d74-462d-baea-88f5c620cb50    2019-08-01T200147.836900Z   cell_suspension_0.json  c14b99ea-d8e2-4c84-9dc2-ce2245d8a743    2019-07-09T231935.003000Z   b43cebcca9cd5213699acce7356d226de07edef5c5604510a697159af1a12149    847         .dbio/v2/files_2_4/b4/3ceb/b43cebcca9cd5213699acce7356d226de07edef5c5604510a697159af1a12149
file_head

Returns the metadata for the latest version of a file with a given UUID. If the version is provided, the metadata for that specific version is returned instead. The metadata is returned in the headers.

Example call to file_head():

from dbio.dss import DSSClient

dss = DSSClient()

print("Calling dss.head_file() with a file UUID:")
response = dss.head_file(
    uuid="6887bd52-8bea-47d9-bbd9-ff71e05faeee",
    replica="aws",
)
if response.status_code==200:
    print("Success!")
    print("Headers: %s"%(response.headers))

print()

# Optionally, add a version
print("Calling dss.head_file() with a file UUID and version:")
response = dss.head_file(
    uuid="6887bd52-8bea-47d9-bbd9-ff71e05faeee",
    replica="aws",
    version="2019-01-30T165057.189000Z",
)
if response.status_code==200:
    print("Success!")
    print("Headers: %s"%(response.headers))

Example JSON header returned by API:

{
  "Date": "Tue, 22 Oct 2019 19:16:50 GMT",
  "Content-Type": "text/html; charset=utf-8",
  "Content-Length": "0",
  "Connection": "keep-alive",
  "x-amzn-RequestId": "bea3fd18-f373-4cb9-b0d2-0642c955eb5b",
  "X-DSS-SHA1": "ccac0f3fb16d1209ac88de8f293e61a115cfee38",
  "Access-Control-Allow-Origin": "*",
  "X-DSS-S3-ETAG": "d1634210a190ae78f6dd7a21f3c6ef1d",
  "X-DSS-SHA256": "24265fd0ebcdfe84eb1a09227c58c117ed03006b1de3f1e0694e50ed63b2f9e7",
  "Strict-Transport-Security": "max-age=31536000; includeSubDomains; preload",
  "Access-Control-Allow-Headers": "Authorization,Content-Type,X-Amz-Date,X-Amz-Security-Token,X-Api-Key",
  "X-DSS-CONTENT-TYPE": 'application/json; dcp-type="metadata/biomaterial"',
  "X-DSS-CRC32C": "ec41da6a",
  "X-DSS-CREATOR-UID": "8008",
  "x-amz-apigw-id": "B-pROGlIoAMFUwg=",
  "X-DSS-VERSION": "2019-01-30T165057.189000Z",
  "X-Amzn-Trace-Id": "Root=1-5daf55a1-132caa16297ffc40a4046739;Sampled=0",
  "X-AWS-REQUEST-ID": "eeeb46a0-61a2-4fb5-aae9-21fe6a01f277",
  "X-DSS-SIZE": "856",
}
get_bundle

For a given bundle UUID and optionally a bundle version, returns information about the latest version of that bundle. Information returned includes the bundle creator, UUID, and version, as well as information about each file in the bundle, such as the file name, UUID, version, etc.

Example call to get_bundle():

import os
import json
import subprocess
from dbio.dss import DSSClient

BUNDLE_JSON = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'data', 'get_bundle.json')

def main():
    bundle = fetch_bundle()
    print_bundle(bundle)
    save_bundle(bundle)

def fetch_bundle():
    dss = DSSClient()
    return dss.get_bundle(
        replica="aws", uuid="002aeac5-4d74-462d-baea-88f5c620cb50", version="2019-08-01T200147.836900Z"
    )

def print_bundle(bundle):
    """Print a bundle and its contents to the console"""
    print("Bundle Contents:")
    for file in bundle["bundle"]["files"]:
        print(f"File: {json.dumps(file, indent=4)}")
    
    print(f'Bundle Creator: {bundle["bundle"]["creator_uid"]}')
    print(f'Bundle UUID   : {bundle["bundle"]["uuid"]}')
    print(f'Bundle Version: {bundle["bundle"]["version"]}')

def save_bundle(bundle):
    """Save bundle information to a JSON file. Useful for download_manifest_api.py script."""
    if not os.path.exists("data"):
        subprocess.call(["mkdir", "data"])
    with open(BUNDLE_JSON, 'w') as f:
        f.write(json.dumps(bundle))

if __name__=="__main__":
    main()

Example of the JSON returned by get_bundle():

{
  "bundle": {
    "creator_uid": 8008,
    "files": [
      {
        "name": "cell_suspension_0.json",
        "uuid": "c14b99ea-d8e2-4c84-9dc2-ce2245d8a743",
        "version": "2019-07-09T231935.003000Z"
        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
        "crc32c": "892ad18b",
        "indexed": true,
        "s3_etag": "57814b3405165d975a6688dc8110dea0",
        "sha1": "849ebad4cff8f4fdf10ad25ad801ebb8aacc58b7",
        "sha256": "b43cebcca9cd5213699acce7356d226de07edef5c5604510a697159af1a12149",
        "size": 847,
      },
      {
        "name": "specimen_from_organism_0.json",
        "uuid": "05998af7-fa6f-44fe-bd16-ac8eafb42f28",
        "version": "2019-07-09T222953.739000Z"
        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
        "crc32c": "8686eb38",
        "indexed": true,
        "s3_etag": "c3079914aa72f4aafa926594c756c978",
        "sha1": "885f0d6c524796116394fc4e60f0d9f65988765f",
        "sha256": "d0c8cc0d13e30b73241405035d98265eab891ea94fbccc3da4bb0ca10c3d0f24",
        "size": 872,
      },
      ...
    ],
    "uuid": "002aeac5-4d74-462d-baea-88f5c620cb50",
    "version": "2019-08-01T200147.836900Z"
  }
}
get_bundles_checkout

Check the status and location of a checkout request.

Example call to get_bundles_checkout():

from dbio.dss import DSSClient

dss = DSSClient()

bundle_checkout_status = dss.get_bundles_checkout(
    replica="aws", checkout_job_id="4de1c603-fa8b-4c07-af37-06159e6951e0"
)

print(f'Bundle checkout status: {bundle_checkout_status["status"]}!')
if bundle_checkout_status["status"] == "SUCCEEDED":
    print(f'File is located at: {bundle_checkout_status["location"]}')

Example of the JSON returned by get_bundles_checkout():

{
  "location": "s3://ucsc-cgp-dss-checkout-prod/bundles/fff54b87-26fe-42a9-be54-3f5a7ef8176e.2019-03-26T131455.775610Z",
  "status": "SUCCEEDED"
}
get_file

Retrieves file metadata given a UUID, optionally a version. (To download a file, use the dbio download command.)

Example call to get_file():

from dbio.dss import DSSClient
import json

dss = DSSClient()

json_response = dss.get_file(replica="aws", uuid="666ff3f0-67a1-4ead-82e9-3f96a8c0a9b1")

for content in json_response:
    print(f"{content}: {json.dumps(json_response[content], indent=4)}")

Example of the JSON returned by get_file():

{
  "describedBy": "https://schema.humancellatlas.org/type/file/7.0.2/sequence_file",
  "schema_type": "file",
  "file_core": {
    "file_name": "SRR6546754_2.fastq.gz",
    "file_format": "fastq.gz"
  },
  "read_index": "read2",
  "insdc_run": [
    "SRR6546754"
  ],
  "technical_replicate_group": "Rep_id_7031",
  "provenance": {
    "document_id": "39a93f75-0db3-4ee2-ab22-3eaa9932cf67",
    "submission_date": "2019-01-30T11:15:21.403Z",
    "update_date": "2019-02-19T17:17:10.540Z"
  }
}
login

Configures and saves authentication credentials.

Example call to login():

from dbio.dss import DSSClient

dss = DSSClient()

access_token = "test_access_token"
dss.login(access_token=access_token)
logout

Clears authentication credentials previously configured with login.

Example call to logout():

from dbio.dss import DSSClient

dss = DSSClient()

dss.logout()
post_bundles_checkout

Returns a checkout-job-id (e.g., 4de1c603-fa8b-4c07-af37-06159e6951e0). This checkout-job-id can then be used with the get_bundles_checkout() method.

Example call to post_bundles_checkout():

from dbio.dss import DSSClient

dss = DSSClient()

checkout_id = dss.post_bundles_checkout(uuid="fff746b3-e3eb-496a-88a3-5fa1fa358392", replica="aws")
print(checkout_id)
post_search

Find bundles by their bundle_fqid, which is the bundle’s UUID and version separated by a dot (.).

For example, the bundle FQID fff807ba-bc98-4247-a560-49fb90c9675c.2019-08-01T200147.111027Z is a bundle with the UUID fff807ba-bc98-4247-a560-49fb90c9675c and the version number 2019-08-01T200147.111027Z.

This method returns an FQID and URL for each matching bundle.

Example call to post_search():

from dbio.dss import DSSClient

dss = DSSClient()

# Note:
# Passing es_query={} runs an empty search, which will match all bundles.

# Iterable post_search
for results in dss.post_search.iterate(replica="aws", es_query={}):
    print(results)
    break

# Non-iterable (first page only) post_search
print(dss.post_search(replica='aws', es_query={}))

Example output:

{
    ...
},
{
    "bundle_fqid": "fff807ba-bc98-4247-a560-49fb90c9675c.2019-08-01T200147.111027Z",
    "bundle_url": "https://dss.dev.ucsc-cgp-redwood.org/v1/bundles/fff807ba-bc98-4247-a560-49fb90c9675c?version=2019-08-01T200147.111027Z&replica=aws",
    "search_score": null
},
{
    ...
}
put_subscription, delete_subscription, get_subscription, get_subscriptions
  • get_subscriptions(): Gets a list of user subscriptions.
  • put_subscription(): Create a collection for the user given a replica and a call-back url.
  • get_subscription(): Given the UUID of the subscription, show a subscription that the user created.
  • delete_subscription(): Given a UUID and replica or the subscription, delete the subscription the user created.

Example API calls:

from dbio import DataBiosphereConfig
from dbio.dss import DSSClient

dbio_config = DataBiosphereConfig()
dbio_config["DSSClient"].swagger_url = f"https://dss.dev.data.humancellatlas.org/v1/swagger.json"
dss = DSSClient(config=dbio_config)

# Creates a sub based given a replica and a url
subscription = dss.put_subscription(
    replica="aws",
    callback_url=" https://dcp-cli-tutorials-put-delete-get-sub-api.humancellatlas.org`"
)

callback, owner, replica, uuid = (
    subscription["callback_url"],
    subscription["owner"],
    subscription["replica"],
    subscription["uuid"],
)

# Lists all subs created
print(dss.get_subscriptions(replica="aws"))

# Lists a sub
print(dss.get_subscription(replica="aws", uuid=uuid))

# Deletes a sub based on a UUID
print(dss.delete_subscription(replica="aws", uuid=uuid))
refresh_swagger

Manually refresh the swagger document.

Links: Index / Module Index / Search Page

CLI Open Endpoint Examples

The DataBiosphere CLI provides several ways for users of the data store to access and download data sets from the data store. This page covers how to access the data store using the dbio command line utility.

NOTE: The Data Biosphere CLI utility is compatible with Python 3.5+.

dbio create-version

Returns a timestamp in DSS_VERSION format (e.g., 1985-04-12T232050.520000Z), necessary for versioning bundles or files.

Note

A version is a timestamp in RFC3339 format that keeps track of the most recent iteration of a bundle or file. A bundle is a collection of many different data files, and both bundles and files have version numbers.

Example call to dbio create-version:

#!/usr/bin/env bash

dbio dss create-version
dbio download

Downloads a bundle to the local filesystem as a directory. By default, both data and metadata files are downloaded (flags can be added to download only the data or the metadata).

Implementation detail: All files are downloaded to a local cache directory called .dbio that is created in the directory where the download is initiated. The user should never need to interact directly with the .dbio directory.

See note above regarding version numbering.

Example call to dbio get-bundle:

#!/usr/bin/env bash

dbio dss download --replica aws --bundle-uuid ffffaf55-f19c-40e3-aa81-a6c69d357265 --version 2019-08-01T200147.836832Z --download-dir download_test

Example response:

{
  "bundle": {
    "creator_uid": 8008,
    "files": [
      {
        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
        "crc32c": "5c084696",
        "indexed": true,
        "name": "cell_suspension_0.json",
        "s3_etag": "bd60da05055d1cd544855dd35cb12470",
        "sha1": "fdeb52d3caf0becce0575528c81bf0a06cb4a023",
        "sha256": "e0ff1c402a4d6c659937f90d00d9820a2ebf0ebc920260a2a2bddf0961c30de5",
        "size": 847,
        "uuid": "134c0f04-76ae-405d-aea4-b72c08a53dd9",
        "version": "2019-07-09T230754.589000Z"
      },
      {
        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
        "crc32c": "39e6f9e1",
        "indexed": true,
        "name": "specimen_from_organism_0.json",
        "s3_etag": "f30917f841530d78e16223354049c8dc",
        "sha1": "98171c05647a3b771afb3bd61e65d0a25b0afe7f",
        "sha256": "35406f0b8fa1ece3e3589151978aefef28f358afa163874b286eab837fcabfca",
        "size": 864,
        "uuid": "577a91d8-e579-41b6-9353-7e4e774c161a",
        "version": "2019-07-09T222811.151000Z"
      },

      ...

      {
        "content-type": "application/gzip; dcp-type=data",
        "crc32c": "38f31e58",
        "indexed": false,
        "name": "SRR6579532_2.fastq.gz",
        "s3_etag": "ac67e10df687471f5808be96499836c6",
        "sha1": "8743feb4d1ce82328127d10e2b1dfa35e5ae4b5a",
        "sha256": "3d788e06b5ca4c8fc679b47c790b1e266f73d48818a1749743ec85f096d657ea",
        "size": 43810957,
        "uuid": "1330ef1a-7a21-40c6-84c5-5cec18204028",
        "version": "2019-08-03T150636.729022Z"
      }
    ],
    "uuid": "ffffaf55-f19c-40e3-aa81-a6c69d357265",
    "version": "2019-08-01T200147.836832Z"
  }
}
dbio download-manifest

Downloads a list of files specified in a user-provided manifest file.

The manifest file should be in TSV (tab-separated variable) format, with one line in the manifest per file to download. The manifest should contain information about files (one file per line). The information that must be provided for a given bundle is available from the get_bundle() method.

The header row must define the columns:

  • bundle_uuid - UUID of the requested bundle
  • bundle_version - the version of the requested bundle
  • file_name - the name of the file as specified in the bundle
  • file_uuid - the UUID of the file in the DSS
  • file_sha256 - the SHA-256 hash of the file
  • file_size - the size of the file

Example call to dbio download-manifest:

#!/usr/bin/env bash

MANIFEST="manifest.tsv"

# Make the manifest file
cat /dev/null > ${MANIFEST}
echo -e "bundle_uuid\tbundle_version\tfile_name\tfile_uuid\tfile_version\tfile_sha256\tfile_size\tfile_path\n" >> ${MANIFEST}
echo -e "ffffaf55-f19c-40e3-aa81-a6c69d357265\t2019-08-01T200147.836832Z\tlinks.json\tdbf7bd27-b58e-431d-ba05-6a48f29e7cef\t2019-08-03T150636.118831Z\tda4df14eb39cacdff01a08f27685534822c2d40adf534ea7b3e4adf261b9079a\t2081\t.dbio/v2/files_2_4/da/4df1/da4df14eb39cacdff01a08f27685534822c2d40adf534ea7b3e4adf261b9079a\n" >> ${MANIFEST}

echo "manifest.json file: ${MANIFEST}"

# Download files in the manifest
dbio dss download-manifest --replica aws --manifest ${MANIFEST}

Example manifest TSV file:

bundle_uuid                             bundle_version              file_name               file_uuid                               file_version                file_sha256                                                         file_size   file_path
002aeac5-4d74-462d-baea-88f5c620cb50    2019-08-01T200147.836900Z   cell_suspension_0.json  c14b99ea-d8e2-4c84-9dc2-ce2245d8a743    2019-07-09T231935.003000Z   b43cebcca9cd5213699acce7356d226de07edef5c5604510a697159af1a12149    847         .dbio/v2/files_2_4/b4/3ceb/b43cebcca9cd5213699acce7356d226de07edef5c5604510a697159af1a12149
dbio file-head

Returns the metadata for the latest version of a file with a given UUID. If the version is provided, the metadata for that specific version is returned instead. The metadata is returned in the headers.

Example call to dbio file-head:

#!/usr/bin/env bash

# Get the latest version
dbio dss head-file --replica aws --uuid 666ff3f0-67a1-4ead-82e9-3f96a8c0a9b1

# Get the specified version
dbio dss head-file --replica aws --uuid 6887bd52-8bea-47d9-bbd9-ff71e05faeee --version 2019-01-30T165057.189000Z

Example JSON header returned by API:

{
    "Date": "Tue, 22 Oct 2019 19:16:50 GMT",
    "Content-Type": "text/html; charset=utf-8",
    "Content-Length": "0",
    "Connection": "keep-alive",
    "x-amzn-RequestId": "bea3fd18-f373-4cb9-b0d2-0642c955eb5b",
    "X-DSS-SHA1": "ccac0f3fb16d1209ac88de8f293e61a115cfee38",
    "Access-Control-Allow-Origin": "*",
    "X-DSS-S3-ETAG": "d1634210a190ae78f6dd7a21f3c6ef1d",
    "X-DSS-SHA256": "24265fd0ebcdfe84eb1a09227c58c117ed03006b1de3f1e0694e50ed63b2f9e7",
    "Strict-Transport-Security": "max-age=31536000; includeSubDomains; preload",
    "Access-Control-Allow-Headers": "Authorization,Content-Type,X-Amz-Date,X-Amz-Security-Token,X-Api-Key",
    "X-DSS-CONTENT-TYPE": 'application/json; dcp-type="metadata/biomaterial"',
    "X-DSS-CRC32C": "ec41da6a",
    "X-DSS-CREATOR-UID": "8008",
    "x-amz-apigw-id": "B-pROGlIoAMFUwg=",
    "X-DSS-VERSION": "2019-01-30T165057.189000Z",
    "X-Amzn-Trace-Id": "Root=1-5daf55a1-132caa16297ffc40a4046739;Sampled=0",
    "X-AWS-REQUEST-ID": "eeeb46a0-61a2-4fb5-aae9-21fe6a01f277",
    "X-DSS-SIZE": "856",
}
dbio get-bundle

For a given bundle UUID and optionally a bundle version, returns information about the latest version of that bundle. Information returned includes the bundle creator, UUID, and version, as well as information about each file in the bundle, such as the file name, UUID, version, etc.

Example call to dbio get-bundle:

#!/usr/bin/env bash

dbio dss get-bundle --replica aws --uuid fff746b3-e3eb-496a-88a3-5fa1fa358392 --version 2019-08-01T200147.130156Z

Example JSON returned by dbio get-bundle:

{
  "bundle": {
    "creator_uid": 8008,
    "files": [
      {
        "name": "cell_suspension_0.json",
        "uuid": "c14b99ea-d8e2-4c84-9dc2-ce2245d8a743",
        "version": "2019-07-09T231935.003000Z"
        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
        "crc32c": "892ad18b",
        "indexed": true,
        "s3_etag": "57814b3405165d975a6688dc8110dea0",
        "sha1": "849ebad4cff8f4fdf10ad25ad801ebb8aacc58b7",
        "sha256": "b43cebcca9cd5213699acce7356d226de07edef5c5604510a697159af1a12149",
        "size": 847,
      },
      {
        "name": "specimen_from_organism_0.json",
        "uuid": "05998af7-fa6f-44fe-bd16-ac8eafb42f28",
        "version": "2019-07-09T222953.739000Z"
        "content-type": "application/json; dcp-type=\"metadata/biomaterial\"",
        "crc32c": "8686eb38",
        "indexed": true,
        "s3_etag": "c3079914aa72f4aafa926594c756c978",
        "sha1": "885f0d6c524796116394fc4e60f0d9f65988765f",
        "sha256": "d0c8cc0d13e30b73241405035d98265eab891ea94fbccc3da4bb0ca10c3d0f24",
        "size": 872,
      },
      ...
    ],
    "uuid": "002aeac5-4d74-462d-baea-88f5c620cb50",
    "version": "2019-08-01T200147.836900Z"
  }
}
dbio get-bundles-checkout

Check the status and location of a checkout request.

Example call to dbio get-bundles-checkout:

#!/usr/bin/env bash

dbio dss get-bundles-checkout --replica aws --checkout-job-id 4de1c603-fa8b-4c07-af37-06159e6951e0

Example JSON returned by dbio get-bundles-checkout:

{
  "location": "s3://ucsc-cgp-dss-checkout-prod/bundles/fff54b87-26fe-42a9-be54-3f5a7ef8176e.2019-03-26T131455.775610Z",
  "status": "SUCCEEDED"
}
dbio get-file

Retrieves a file given a UUID, optionally a version, and displays the details of the file.

Example call to dbio get-file:

#!/usr/bin/env bash

dbio dss get-file --replica aws --uuid 666ff3f0-67a1-4ead-82e9-3f96a8c0a9b1

Example JSON returned by dbio get-file:

{
  "describedBy": "https://schema.humancellatlas.org/type/file/7.0.2/sequence_file",
  "schema_type": "file",
  "file_core": {
    "file_name": "SRR6546754_2.fastq.gz",
    "file_format": "fastq.gz"
  },
  "read_index": "read2",
  "insdc_run": [
    "SRR6546754"
  ],
  "technical_replicate_group": "Rep_id_7031",
  "provenance": {
    "document_id": "39a93f75-0db3-4ee2-ab22-3eaa9932cf67",
    "submission_date": "2019-01-30T11:15:21.403Z",
    "update_date": "2019-02-19T17:17:10.540Z"
  }
}
dbio login

Configures and saves authentication credentials.

Example call to dbio login:

#!/usr/bin/env bash

dbio dss login --access-token test
dbio logout

Clears authentication credentials previously configured with login.

Example call to dbio logout:

#!/usr/bin/env bash

dbio dss logout
dbio post-bundles-checkout

Returns a checkout-job-id (e.g., 4de1c603-fa8b-4c07-af37-06159e6951e0). This checkout-job-id can then be used with the get_bundles_checkout() method.

Example call to dbio post-bundles-checkout:

#!/usr/bin/env bash

dbio dss post-bundles-checkout --replica aws --uuid fff746b3-e3eb-496a-88a3-5fa1fa358392
dbio post-search

Find bundles by their bundle_fqid, which is the bundle’s UUID and version separated by a dot (.).

For example, the bundle FQID fff807ba-bc98-4247-a560-49fb90c9675c.2019-08-01T200147.111027Z is a bundle with the UUID fff807ba-bc98-4247-a560-49fb90c9675c and the version number 2019-08-01T200147.111027Z.

This method returns an FQID and URL for each matching bundle.

Example call to dbio post-search:

#!/usr/bin/env bash

dbio dss post-search --replica aws --es-query {} --no-paginate

Example output:

{
  ...
},
{
  "bundle_fqid": "fff807ba-bc98-4247-a560-49fb90c9675c.2019-08-01T200147.111027Z",
  "bundle_url": "https://dss.dev.ucsc-cgp-redwood.org/v1/bundles/fff807ba-bc98-4247-a560-49fb90c9675c?version=2019-08-01T200147.111027Z&replica=aws",
  "search_score": null
},
{
  ...
}
dbio get-subscription(s), dbio put-subscription, dbio delete-subscription
  • get_subscriptions(): Gets a list of users subscription.
  • put_subscription(): Create a collection for the user given a replica and a call-back url.
  • get_subscription(): Given the UUID of the subscription, show a subscription that the user created.
  • delete_subscription(): Given a UUID and rpelica or the subscription, delete the subscription the user created.

Example CLI calls:

#!/usr/bin/env bash

# Creates a sub based given a replica and a url
instance_info=$(dbio dss put-subscription --callback-url https://dcp-cli-tutorials-put-get-delete-sub.data.ucsc-cgp-redwood.org --replica aws) 

ID=`echo ${instance_info} | jq -r '.uuid'`

echo $ID

# Lists all of subs created
dbio dss get-subscriptions --replica aws

# List a sub
dbio dss get-subscription --replica aws --uuid $ID

# Deletes a sub based on a UUID
dbio dss delete-subscription --replica aws --uuid $ID
dbio refresh-swagger

Manually refresh the swagger document.

#!/usr/bin/env bash

dbio dss refresh-swagger

Links: Index / Module Index / Search Page

Python Restricted Endpoint Examples

The DataBiosphere API provides several ways for users of the data store to access and download data sets from the data store. This page covers how to access the data store using Python API bindings.

The API calls listed here are restricted to those with upload or ingest permissions.

In the document that follows, privileged user refers to a user with proper credentials and permission to upload/ingest data into the DSS.

NOTE: The Data Biosphere CLI utility is compatible with Python 3.5+.

delete_bundle

Deletes an existing bundle given a UUID, version, and replica.

Inputs:

  • uuid - a unique, user-created UUID.
  • creator-uid - a unique user ID (uid) for the bundle creator uid. This accepts integer values.
  • version - a unique, user-created version number. Use the create_verson() API function to generate a DSS_VERSION.
  • replica - which replica to use (corresponds to cloud providers; choices: aws or gcp)
  • files - a valid list of file objects, separated by commas (e.g., [{<first_file>}, {<second_file>}, ...  ]). Each file object must include the following details:
    • Valid UUID of the file
    • Valid version number of the file
    • Name of the file
    • Boolean value - is this file indexed

Example call to delete_bundle():

from dbio import DataBiosphereConfig
from dbio.dss import DSSClient

dbio_config = DataBiosphereConfig()
dbio_config["DSSClient"].swagger_url = f"https://dss.dev.data.humancellatlas.org/v1/swagger.json"
dss = DSSClient(config=dbio_config)

print(dss.delete_bundle(reason='test', uuid='98f6c379-cb78-4a61-9310-f8cc0341c0ea', version='2019-08-02T202456.025543Z', replica='aws'))
put_bundle

Creates a bundle. A bundle can contain multiple files of arbitrary type.

Inputs:

  • uuid - a unique, user-created UUID.
  • creator-uid - a unique user ID (uid) for the bundle creator uid. This accepts integer values.
  • version - a unique, user-created version number. Use the create_verson() API function to generate a DSS_VERSION.
  • replica - which replica to use (corresponds to cloud providers; choices: aws or gcp)
  • files - a valid list of file objects, separated by commas (e.g., [{<first_file>}, {<second_file>}, ...  ]). Each file object must include the following details:
    • Valid UUID of the file
    • Valid version number of the file
    • Name of the file
    • Boolean value - is this file indexed

Example call to put_bundle():

from dbio import DataBiosphereConfig
from dbio.dss import DSSClient
import os

dbio_config = DataBiosphereConfig()

dbio_config["DSSClient"].swagger_url = f"https://dss.dev.data.humancellatlas.org/v1/swagger.json"
dss = DSSClient(config=dbio_config)

dss.put_bundle(
    creator_uid=0,
    uuid="98f6c379-cb78-4a61-9310-f8cc0341c0ea",
    version="2019-08-02T202456.025543Z",
    replica="aws",
    files=[
        {
            "uuid": "2196a626-38da-4489-8b2f-645d342f6aab",
            "version": "2019-07-10T001103.121000Z",
            "name": "process_1.json1",
            "indexed": False,
        }
    ],
)
patch_bundle

Allows a user to modify an existing bundle. User passes in an optional list of files to add or remove from an existing bundle.

add_files/remove_files follow this format:

[
  {
    "path": "string",
    "type": "string",
    "uuid": "string",
    "version": "string"
  }
]

Example call to patch_bundle():

from dbio import DataBiosphereConfig
from dbio.dss import DSSClient

dbio_config = DataBiosphereConfig()
dbio_config["DSSClient"].swagger_url = f"https://dss.dev.data.humancellatlas.org/v1/swagger.json"
dss = DSSClient(config=dbio_config)

print(dss.patch_bundle(uuid='98f6c379-cb78-4a61-9310-f8cc0341c0ea', version='2019-08-02T202456.025543Z', replica='aws'))
put_file

Creates a new version of a file, given an existing UUID, version, creator uid, and source URL.

Example call to put_file():

from dbio import DataBiosphereConfig
from dbio.dss import DSSClient

dbio_config = DataBiosphereConfig()

dbio_config["DSSClient"].swagger_url = f"https://dss.dev.data.humancellatlas.org/v1/swagger.json"
dss = DSSClient(config=dbio_config)

print(
    dss.put_file(
        uuid="ead6434d-efb5-4554-98bc-027e160547c5",
        version="2019-07-30T174916.268875Z",
        creator_uid=0,
        source_url="s3://jeffwu-test/ead6434d-efb5-4554-98bc-027e160547c5/get_bundle.json",
    )
)
put_collection, delete_collection, patch_collection, get_collection(s)
  • get_collection() - Given a collection UUID, get the collection.
  • get_collections() - Get a list of collections for a given user.
  • delete_collection() - Given a collection UUID and replica, delete the collection from the replica.
  • put_collection() - Create a collection.
  • patch_collection() - Add or remove a given list of files from an existing collection.

To add or remove files with the API endpoints above, specify each file in the following format:

[
  {
    "path": "string",
    "type": "string",
    "uuid": "string",
    "version": "string"
  }
]

Example API calls:

from dbio import DataBiosphereConfig
from dbio.dss import DSSClient
import uuid
import os

dbio_config = DataBiosphereConfig()
dbio_config["DSSClient"].swagger_url = f"https://dss.dev.data.humancellatlas.org/v1/swagger.json"
dss = DSSClient(config=dbio_config)

# Creates a new collection
collection = dss.put_collection(
    uuid=str(uuid.uuid4()),
    version="2018-09-17T161441.564206Z",  # arbitrary
    description="foo",
    details={},
    replica="aws",
    name="bar",
    contents=[
        {
            "type": "bundle",
            "uuid": "ff818282-9735-45fa-a094-e9f2d3d0a954",  # overwrite if necessary
            "version": "2019-08-06T170839.843085Z",  # arbitrary
            "path": "https://dss.dev.data.humancellatlas.org/v1/bundles/ff818282-9735-45fa-a094-e9f2d3d0a954?version=2019-08-06T170839.843085Z&replica=aws",
        }
    ],
)

uuid, version = collection["uuid"], collection["version"]

# Gets a list of collections
print(dss.get_collections(replica="aws"))

# Can add/remove files from a collection
print(dss.patch_collection(replica="aws", uuid=uuid, version=version))

# Gets a collection based on replcia and uuid
print(dss.get_collection(replica="aws", uuid=uuid))

# Deletes a colelction based on replica and uuid
print(dss.delete_collection(replica="aws", uuid=uuid))
upload

Uploads a directory of files from the local filesystem and creates a bundle containing the uploaded files.

Example call to upload():

from dbio import DataBiosphereConfig
from dbio.dss import DSSClient
import boto3    

s3 = boto3.resource('s3')
bucket = s3.Bucket('upload-test-unittest') 

dbio_config = DataBiosphereConfig()
dbio_config["DSSClient"].swagger_url = f"https://dss.dev.ucsc-cgp-redwood.org/v1/swagger.json"
dss = DSSClient(config=dbio_config)

print(dss.upload(src_dir="data/", replica="aws", staging_bucket="upload-test-unittest"))
 
bucket.objects.all().delete()

print("Upload successful")

Links: Index / Module Index / Search Page

CLI Restricted Endpoint Examples

The DataBiosphere CLI provides several ways for users of the data store to access and download data sets from the data store. This page covers how to access the data store using the dbio command line utility.

The CLI calls listed here are restricted to those with upload or ingest permissions.

In the document that follows, privileged user refers to a user with proper credentials and permission to upload/ingest data into the DSS.

NOTE: The Data Biosphere CLI utility is compatible with Python 3.5+.

dbio delete-bundle

Deletes an existing bundle given a UUID, version, and replica.

Example call to dbio delete-bundle:

#!/usr/bin/env bash

dbio dss delete-bundle --reason test --replica gcp --uuid 98f6c379-cb78-4a61-9310-f8cc0341c0ea --version 2019-08-02T202456.025543Z
dbio put-bundle

Creates a bundle. A bundle can contain multiple files of arbitrary type.

Inputs:

  • uuid - a unique, user-created UUID.
  • creator-uid - a unique user ID (uid) for the bundle creator uid. This accepts integer values.
  • version - a unique, user-created version number. Use the create_verson() API function to generate a DSS_VERSION.
  • replica - which replica to use (corresponds to cloud providers; choices: aws or gcp)
  • files - a valid list of file objects, separated by commas (e.g., [{<first_file>}, {<second_file>}, ...  ]). Each file object must include the following details:
    • Valid UUID of the file
    • Valid version number of the file
    • Name of the file
    • Boolean value - is this file indexed

Example call to dbio put-bundle:

#!/usr/bin/env bash

dbio dss put-bundle --creator-uid 0 --replica aws --uuid 98f6c379-cb78-4a61-9310-f8cc0341c0ea --version 2019-08-02T202456.025543Z --files '{"uuid": "2196a626-38da-4489-8b2f-645d342f6aab", "version": "2019-07-10T001103.121000Z" , "name": "process_1.json", "indexed":false}'
dbio patch-bundle

Allows user to pass in an optional list of files to add or remove from an exisiting bundle.

add_files/remove_files follow this format:

[
  {
    "path": "string",
    "type": "string",
    "uuid": "string",
    "version": "string"
  }
]

Example call to dbio patch-bundle:

 #!/usr/bin/env bash

dbio dss patch-bundle --replica aws --uuid 98f6c379-cb78-4a61-9310-f8cc0341c0ea --version 2019-08-02T202456.025543Z
dbio put-file

Creates a new version of a file, given an existing UUID, version, creator uid, and source URL.

Example call to dbio put-file:

#!/usr/bin/env bash

dbio dss put-file --uuid 38f6c379-cb78-4a61-9310-f8cc0341c0eb --version 2019-07-30T164352.961501Z --creator-uid 0 --source-url s3://ucsc-cgp-dss-cli-test/930a927d-0138-4a79-8c87-e45936fe4fc3/get_bundle.json
dbio get-collection(s), dbio put-collection, dbio patch-collection, dbio delete-collection
  • dbio get-collection - Given a collection UUID, get the collection.
  • dbio get-collections - Get a list of collections for a given user.
  • dbio delete-collection - Given a collection UUID and replica, delete the collection from the replica.
  • dbio put-collection - Create a collection.
  • dbio patch-collection - Add or remove a given list of files from an existing collection.

To add or remove files with the CLI actions above, specify each file in the following format:

[
  {
    "path": "string",
    "type": "string",
    "uuid": "string",
    "version": "string"
  }
]

Example CLI calls:

#!/usr/bin/env bash

info_instance=$(dbio dss put-collection --uuid fff01947-bf94-43e9-86ca-f6ff6ae45d2c --description foo --details {} --version 2018-09-17T161441.564206Z --replica aws --name bar --contents '{"path": "https://dss.dev.ucsc-cgp-redwood.org/v1/bundles/ff818282-9735-45fa-a094-e9f2d3d0a954?version=2019-08-06T170839.843085Z&replica=aws", "version": "2019-08-06T170839.843085Z", "type": "bundle", "uuid": "ff818282-9735-45fa-a094-e9f2d3d0a954"}')

ID=`echo ${info_instance} | jq -r '.uuid'`
VERSION=`echo ${info_instance} | jq -r '.version'`

dbio dss get-collections

dbio dss patch-collection --replica aws --uuid $ID --verison $VERSION

dbio dss get-collection --replica aws --uuid $ID

dbio dss delete-collection --replica aws --uuid $ID
dbio upload

Uploads a directory of files from the local filesystem and creates a bundle containing the uploaded files.

Example call to dbio upload:

#!/usr/bin/env bash

dbio dss upload --src-dir data/ --replica aws --staging-bucket upload-test-unittest

aws s3 rm s3://upload-test-unittest --recursive

Links: Index / Module Index / Search Page

Links: Index / Module Index / Search Page

Links: Index / Module Index / Search Page