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@@ -31,14 +31,20 @@ This version should match the latest version on the [PyPi page](https://pypi.org | |
pip install -U gen3_util | ||
``` | ||
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### Configuration | ||
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gen3_util uses the [gen3-client](https://gen3.org/resources/user/gen3-client/#2-configure-a-profile-with-credentials) configuration flow. | ||
After configuration, you can either specify the `--profile` option or set the `GEN3_UTIL_PROFILE=profile-name` environmental variable. | ||
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### Testing the configuration | ||
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The command `gen3_util ping` will confirm that the access key and gen3-client have been configured correctly | ||
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```sh | ||
gen3_util ping | ||
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# msg: Configuration OK, access key found, gen3-client found, gen3-client profile found 'aced' | ||
msg: 'Configuration OK: Connected using profile:production' | ||
# endpoint: https://aced-idp.org | ||
# username: [email protected] | ||
``` | ||
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@@ -57,7 +63,7 @@ The following options and environmental variables are synonymous, you may set th | |
| --patient_id | PATIENT_ID | meta data | | | ||
| --specimen_id | SPECIMEN_ID | meta data | | | ||
| --task_id | TASK_ID | meta data | | | ||
| --profile | GEN3_PROFILE | gen3-client profile | | | ||
| --profile | GEN3_UTIL_PROFILE | gen3-client profile | | | ||
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Alternatively, you can set the environmental variables using the `EXPORT` function: | ||
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| GEN3_UTIL_CONFIG | Path to config file. | None | | ||
| GEN3_UTIL_FORMAT | Output format. | yaml | | ||
| GEN3_UTIL_STATE_DIR | Path for logs and state information. | ~/.gen3/gen3_util | | ||
| GEN3_API_KEY | location of credentials.json file. | ~/.gen3/credentials.json | | ||
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## Next steps | ||
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