Package: hca
DEPRECATEDThis repository has been deprecated. For information about accessing Human Cell Atlas data please refer to theData Browser quick start guide.HCA CLIThis repository is a pip installable Command Line Interface (CLI) and Python library (API) for interacting with the
Data Coordination Platform (DCP) of the Human Cell Atlas (HCA).Currently thehcapackage supports interaction with theUpload ServiceandData Storage Service (DSS)for services such as uploading, downloading,
and querying data.The HCA CLI is compatible with Python versions 3.5+ (we are no longer compatible with Python 2.7, and our last compatible Python 2.7 version washca==6.4.0).Installationpip install hca.UsageDocumentation on readthedocs.io:CLI documentationPython API documentationExample CLI/API usage:CLI examples (open endpoints)CLI examples (restricted endpoints)Python API examples (open endpoints)Python API examples (restricted endpoints)To see the list of commands you can use, typehca --help.Configuration managementThe HCA 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/hca/config.jsonUser configuration source,~/.config/hca/config.jsonAny sources listed in the colon-delimited variableHCA_CONFIG_FILECommand line optionsArray merge operators: When loading a chain of configuration sources, the HCA 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. Seehttps://github.com/kislyuk/tweak#array-merge-operatorsfor a list of these operators.Service to Service AuthorizationGoogle service credentials must be whitelisted before they will authenticate with the HCA CLI.Set the environment variableGOOGLE_APPLICATION_CREDENTIALSto the path of your Google service credentials file to
authenticate.One can also use:hca dss login.SeeGoogle service credentialsfor more information about service accounts. Use theGoogle Cloud IAM web consoleto manage service accounts.DevelopmentTo develop on the CLI, first runpip install-rrequirements-dev.txt. You can install your locally modified copy of
the hca package by runningmake installin the repository root directory.To use the command line interface with a local or test DSS, first runhca(orscripts/hcaif you want to use the
package in-place from the repository root directory). This will create the file~/.config/hca/config.json, which you
can modify to update the value ofDSSClient.swagger_urlto 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 indcp-cli/hca/util/__init__.pyin theSwaggerClientobject:scheme = "http"To use the Python interface with a local or test DSS, pass the URL of the Swagger definition to theDSSClientconstructor via theswagger_urlparameter:client = DSSClient(swagger_url="https://dss.example.com/v1/swagger.json")You can also layer a minimal config file on top of the defaultconfig.jsonusing theHCA_CONFIG_FILEenvironment
variable, for example:export SWAGGER_URL="https://dss.staging.data.humancellatlas.org/v1/swagger.json"
jq -n .DSSClient.swagger_url=env.SWAGGER_URL > ~/.config/hca/config.staging.json
export HCA_CONFIG_FILE=~/.config/hca/config.staging.jsonTestingBefore you run tests, first runhca 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 (inDSS_SUBSCRIPTION_AUTHORIZED_DOMAINS_ARRAYfromhere).Thenmake test.Primary CI testing is through Travis CI; there is also additional testing with theGitlab Allspark instancethat runs tests for Windows.
(Note that Allspark is not open to the public, members of the Human Cell Atlas project can access the Allspark cluster using the Github account
associated with the Human Cell Atlas organization on Github.) If submitting PRs that have the potential of being platform-dependent, please ensure
the status of “Windows Testing” is verified before merging.BugsPlease report bugs, issues, feature requests, etc. in theHumanCellAtlas/dcp-cli repository on GitHub.Security PolicySee ourSecurity Policy.LicenseLicensed under the terms of theMIT License.