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Incorrect invocation of add_data_to_graph.sh for Stardog setup #93

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alyssadai opened this issue Sep 23, 2023 · 0 comments · Fixed by #92
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Incorrect invocation of add_data_to_graph.sh for Stardog setup #93

alyssadai opened this issue Sep 23, 2023 · 0 comments · Fixed by #92
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@surchs

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@alyssadai
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In this section of the graph setup page https://neurobagel.org/infrastructure/#uploading-example-neurobagel-data,

the invocation of add_data_to_graph.sh uses values for the graph URL and database arguments that is for GraphDB syntax instead of Stardog.

Instead of:

./add_data_to_graph.sh PATH/TO/neurobagel_examples/data-upload/pheno-bids-output \ 
  localhost:7200 repositories/my_db/statements NewUser NewUserPassword \
  --clear-data

it should be

./add_data_to_graph.sh PATH/TO/neurobagel_examples/data-upload/pheno-bids-output \ 
  localhost:5820 my_db NewUser NewUserPassword \
  --clear-data
@alyssadai alyssadai mentioned this issue Sep 23, 2023
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@alyssadai alyssadai added the flag:schedule Flag issue that should go on the roadmap or backlog. label Sep 23, 2023
@alyssadai alyssadai moved this to Backlog in Neurobagel Sep 25, 2023
@alyssadai alyssadai added bug:docs and removed flag:schedule Flag issue that should go on the roadmap or backlog. labels Sep 25, 2023
surchs added a commit that referenced this issue Sep 25, 2023
@surchs
Split upload instructions for graph backend
8c6908f 
Fixes #93
@surchs surchs moved this from Backlog to Implement - Active in Neurobagel Sep 25, 2023
@surchs surchs mentioned this issue Sep 25, 2023
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@surchs surchs moved this from Implement - Active to Implement - Done in Neurobagel Sep 25, 2023
@rmanaem rmanaem moved this from Implement - Done to Review - Active in Neurobagel Sep 25, 2023
@surchs surchs self-assigned this Sep 25, 2023
surchs added a commit that referenced this issue Sep 26, 2023
@surchs
[REF] Combine Stardog and graphDB setup instructions (#92)
f14d94d 
* Explain the difference between backend and graph

* Explain license differences

* Explain changes to env variables

* Describe initial security setup

* Adding DB user

* Split upload instructions for graph backend

Fixes #93

* Use consistent user name templates across both backends

Fixes neurobagel/api#119

* Also talk about query tool

and show it with a nicer figure
@github-project-automation github-project-automation bot moved this from Review - Active to Review - Done in Neurobagel Sep 26, 2023
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[REF] Combine Stardog and graphDB setup instructions neurobagel/documentation
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@surchs @alyssadai