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Merge pull request #62 from gf-dcc/patch/supp-details
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Emphasize and clarify dependencies for onboarding and data upload
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cconrad8 authored Oct 23, 2023
2 parents 8a4368f + 4254935 commit 6ffe2ca
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13 changes: 9 additions & 4 deletions pages/onboarding/account-setup.mdx
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## Account Setup

1. Please familiarize yourself with the different [account types available](https://help.synapse.org/docs/Synapse-User-Account-Types.2007072795.html).
2. In most cases, it is necessary to become a **Certified User** before proceeding. Make sure you complete this step.
3. After creating your account, please inform the DCC so that a team-specific invitation can be sent to you.
4. To join a team, you must accept the invitation by clicking on the link provided in the email and following the instructions on the Synapse team page.
1. First, it is helpful to understand the different [account types available](https://help.synapse.org/docs/Synapse-User-Account-Types.2007072795.html).
2. For nearly everyone, you'll need to become a **Certified User**. Access your account via the icon at the bottom left, so: **Account profile > Account Settings > Certification panel**.
Click on link to start the quiz. You should pass the quiz and receive a green certified badge. This is needed for data download/upload.

3. After the above steps, please inform the DCC so that a team-specific invitation can be sent to you.
4. To join a team, you must accept the invitation by clicking on the link provided in the email and following the instructions on the Synapse team page.

5. (For designated data uploaders with high-throughput data) You should also generate a *Personal Access Token* if you are designated to upload large amounts of data via the Synapse API (e.g. raw sequencing data).
Do so via **Account profile > Account Settings > Personal Access Tokens > Create new token**.
6 changes: 4 additions & 2 deletions pages/onboarding/data-sharing.mdx
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Expand Up @@ -39,7 +39,7 @@ If you need help, please contact the DCC.
**For the most typical and robust workflow, here are the steps with the Python command-line client:**

1. **Install Python package** from PyPI: https://pypi.org/project/synapseclient/. This will also automatically install the command line utility. Test out that the command line utility is working by typing `synapse help` and feel free to review [docs](https://python-docs.synapse.org/build/html/articles/cli.html) for the Python CLI client.
2. For large uploads, it is best to **create an access token**. Go to your **Account profile > Account Settings > Personal Access Tokens > Create new token**.
2. For large uploads, it is best to **create an access token**, if you haven't already through the earlier [Account Setup](/onboarding/account-setup) guidance. Go to your **Account profile > Account Settings > Personal Access Tokens > Create new token**.
3. For convenience, copy and paste the token into a `.synapseConfig` text file. This text file simply looks like:
```
[authentication]
Expand All @@ -50,7 +50,9 @@ authtoken = sometokenstringxxxxxxxxxxxxxxxxxx

`synapse manifest --parent-id syn12345678 --manifest-file manifest.txt PATH_TO_DIR_WITH_FILES`

5. This should create a manifest file `manifest.txt` for the tool to reference. Now check that `.synapseConfig` is present locally to provide authentication. You can now do:
At this step, if you are *not* a Certified User, the tool will output a message for this issue. Review and complete the Certified User portion of [Account Setup](/onboarding/account-setup) before proceeding.

5. Successful execution should create a manifest file `manifest.txt` for the tool to use. Now make sure that `.synapseConfig` is present locally to provide authentication. You can now do:

`synapse sync manifest.txt`

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6 changes: 3 additions & 3 deletions pages/onboarding/onboarding-checklist.mdx
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### New Teams Onboarding Checklist

#### For Principal Investigators:
#### For Principal Investigators
- [ ] Designate at least one data lead contact for team. (_There may be multiple data lead(s) because there are multiple individuals responsible for different data types._)
- [ ] Create a certified account on the Synapse platform. See [Account Setup](/onboarding/account-setup).
- [ ] Complete a data sharing plan.
Expand All @@ -23,10 +23,10 @@
- [ ] Finalize governance/data sharing policy plans
- [ ] (Optional) Join the Gray Foundation Slack workspace.

#### For data leads and contributors:
#### For data leads and contributors
- [ ] Confirm review of documentation and forward any questions or concerns to be addressed early on.
- [ ] Decide a preferred touchbase baseline schedule and medium (e.g. quarterly over videochat or monthly over email).
- [ ] Create certified accounts on the Synapse platform.
- [ ] Create certified accounts on the Synapse platform. See [Account Setup](/onboarding/account-setup).
- [ ] Confirm that they have been added with appropriate team access permissions on the platform.
- [ ] (Optional) Get more interactive training on Synapse platform. This is recommended if data lead(s) have never used Synapse or a similar platform and are not comfortable with usage based solely upon the documentation.
- [ ] (Optional, upon request) Get more interactive training of the clinical data and metadata intake process. This is recommended if data lead(s) are not comfortable with usage based solely upon the documentation.
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