From 6b0d753c4c885753aecec39972964af852546c99 Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Mon, 9 Sep 2024 20:14:56 -0400 Subject: [PATCH 1/6] restructure getting help page & add Discord link --- docs/getting_help.md | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/docs/getting_help.md b/docs/getting_help.md index 665e352f..b3f705e6 100644 --- a/docs/getting_help.md +++ b/docs/getting_help.md @@ -1,13 +1,25 @@ # Getting Help +There are several ways to interact with the Neurobagel team, including: + +- Issues in our [GitHub repositories](https://github.com/neurobagel) +- Our [Neurostars forum](https://neurostars.org/tag/neurobagel) +- Our [Discord server](https://discord.gg/BEXXgt3hXk) + +## Usage or general questions +If you have a _usage question_ about Neurobagel (e.g., troubleshooting setup, feedback on a specific use case), +or want to _discuss the Neurobagel project in general_ with the development team or other users, +please either: + +- open an issue on Neurostars with the `neurobagel` tag: [https://neurostars.org/tag/neurobagel](https://neurostars.org/tag/neurobagel) or +- send us a message in the [Neurobagel Discord server](https://discord.gg/BEXXgt3hXk) + ## Report a bug or request a feature -For a bug or feature request, feel free to open an issue in the repository for the relevant tool in the [Neurobagel GitHub organization](https://github.com/neurobagel). +For _bug reports_ or _feature requests_, we prefer if you open an issue in the repository for the relevant tool in the [Neurobagel GitHub organization](https://github.com/neurobagel). -If you are using one of our web tools ([https://annotate.neurobagel.org](https://annotate.neurobagel.org) or [https://query.neurobagel.org](https://query.neurobagel.org), you can also submit suggestions and bugs using the feedback widget directly on the site. +If you are using one of our web tools ([https://annotate.neurobagel.org](https://annotate.neurobagel.org) or [https://query.neurobagel.org](https://query.neurobagel.org)), +you may also submit bug reports and feature requests using the feedback widget directly on the site. ## Documentation feedback We are always looking to improve our user documentation. To request a change or addition to existing documentation, please [open an issue in the `neurobagel/documentation` repo](https://github.com/neurobagel/documentation/issues). - -## General questions -For general questions about Neurobagel, please open an issue on Neurostars with the `neurobagel` tag: [https://neurostars.org/tag/neurobagel](https://neurostars.org/tag/neurobagel). From 57110b49509c8e7bd55703c1c16f25d3f64f9c5e Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Mon, 9 Sep 2024 20:43:53 -0400 Subject: [PATCH 2/6] explain how to find semver for a 'latest' image --- docs/maintaining.md | 27 +++++++++++++++++++++++++-- 1 file changed, 25 insertions(+), 2 deletions(-) diff --git a/docs/maintaining.md b/docs/maintaining.md index 5c0386fb..ee5dacb7 100644 --- a/docs/maintaining.md +++ b/docs/maintaining.md @@ -7,9 +7,9 @@ there are some recurring tasks you may have to do to keep it operating correctly We are continuously improving Neurobagel tools and services, so you may want to update your Neurobagel node to the latest version to benefit from new features and bug fixes. -We always publish our tools as [Docker images on Dockerhub](https://hub.docker.com/repositories/neurobagel). +We always publish our tools as [Docker images on DockerHub](https://hub.docker.com/repositories/neurobagel). -Each Docker image has a version tag, and also two rolling tags: +Each Docker image has a semantic version tag (vX.Y.Z), and also two rolling tags: - `latest` (the latest stable release). This is the default tag used in the Neurobagel `docker-compose.yml` file. - `nightly` (the latest build from the main branch). This tag is only used for compatibility testing and should not be used in production. @@ -20,6 +20,29 @@ You can pull the most recent docker images for Neurobagel tools by running: docker compose --profile full_stack pull ``` +??? tip "Not sure what version you have?" + + Since `latest` is a rolling tag, each `latest` Docker image for a Neurobagel tool includes its corresponding semver number (vX.Y.X) as part of its Docker image labels. + + You can find the labels for an image you have pulled in the image metadata, e.g.: + ```bash + docker image inspect neurobagel/api:latest + ``` + or, to view only the labels: + ```bash + docker image inspect --format='{{json .Config.Labels}}' neurobagel/api:latest + ``` + In either case, you should see something like this in the output: + + ```bash + "Labels": { + "org.opencontainers.image.created": "https://github.com/neurobagel/api", + "org.opencontainers.image.revision": "01530f467e163f3dff595d3327bc60ba453de47d", + "org.opencontainers.image.version": "v0.3.1" + } + ``` + where `"org.opencontainers.image.version"` refers to the version number. + !!! warning "`docker compose` will only pull the images that are used by the current deployment profile." If you don't specify a deployment profile, the default profile (`local_node`) will be used, From 511bd5b9ce87b689c39f7ff21c74bb8d360b2c3a Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Mon, 9 Sep 2024 21:22:10 -0400 Subject: [PATCH 3/6] remove outdated warning about updating graph data --- docs/maintaining.md | 15 --------------- 1 file changed, 15 deletions(-) diff --git a/docs/maintaining.md b/docs/maintaining.md index ee5dacb7..ce5788e3 100644 --- a/docs/maintaining.md +++ b/docs/maintaining.md @@ -56,21 +56,6 @@ docker compose --profile full_stack pull Whether you have updated the Docker images, the [configuration](config.md), or the [data](#updating-the-data-in-your-graph) of your Neurobagel node, you will need to restart the services to apply the changes. -!!! warning "Restarting the graph backend after an update can introduce problems" - - If you have updated the data model or the data in your graph, - you should **not** restart the graph backend services without first updating the data in the graph. - - This is a current limitation of the deployment profile and we are working to resolve it. - - In the meantime, here is how you can restart and update the services in your Neurobagel node - without affecting the graph backend: - - ```bash - docker compose down api query_federation federation - docker compose pull && docker compose up -d - ``` - To shut down a running Neurobagel node, navigate to the path on your file system where you have stored the `docker-compose.yml` file from the [initial setup](getting_started.md) and run: From e78b5428d5786672bb847d26300b89bf8170121a Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Wed, 11 Sep 2024 13:20:14 -0400 Subject: [PATCH 4/6] Update phrasing Co-authored-by: Sebastian Urchs --- docs/getting_help.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/docs/getting_help.md b/docs/getting_help.md index b3f705e6..776534aa 100644 --- a/docs/getting_help.md +++ b/docs/getting_help.md @@ -2,23 +2,23 @@ There are several ways to interact with the Neurobagel team, including: -- Issues in our [GitHub repositories](https://github.com/neurobagel) -- Our [Neurostars forum](https://neurostars.org/tag/neurobagel) -- Our [Discord server](https://discord.gg/BEXXgt3hXk) +- Create an issue in our [GitHub repositories](https://github.com/neurobagel) +- Our tag on the [Neurostars forum](https://neurostars.org/tag/neurobagel) +- Join our [Discord server](https://discord.gg/BEXXgt3hXk) to chat with us ## Usage or general questions If you have a _usage question_ about Neurobagel (e.g., troubleshooting setup, feedback on a specific use case), or want to _discuss the Neurobagel project in general_ with the development team or other users, please either: -- open an issue on Neurostars with the `neurobagel` tag: [https://neurostars.org/tag/neurobagel](https://neurostars.org/tag/neurobagel) or +- search for or start a new thread on Neurostars with the `neurobagel` tag: [https://neurostars.org/tag/neurobagel](https://neurostars.org/tag/neurobagel) or - send us a message in the [Neurobagel Discord server](https://discord.gg/BEXXgt3hXk) ## Report a bug or request a feature For _bug reports_ or _feature requests_, we prefer if you open an issue in the repository for the relevant tool in the [Neurobagel GitHub organization](https://github.com/neurobagel). If you are using one of our web tools ([https://annotate.neurobagel.org](https://annotate.neurobagel.org) or [https://query.neurobagel.org](https://query.neurobagel.org)), -you may also submit bug reports and feature requests using the feedback widget directly on the site. +you may also submit bug reports and feature requests using the feedback widget directly on the app. ## Documentation feedback We are always looking to improve our user documentation. From fc2178d213648e5ae6531e4c9aa2d951854bfb46 Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Wed, 11 Sep 2024 13:32:41 -0400 Subject: [PATCH 5/6] Rephrasing and add link to semver website --- docs/getting_help.md | 2 +- docs/maintaining.md | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/getting_help.md b/docs/getting_help.md index 776534aa..3ed47af3 100644 --- a/docs/getting_help.md +++ b/docs/getting_help.md @@ -1,6 +1,6 @@ # Getting Help -There are several ways to interact with the Neurobagel team, including: +There are several ways you can interact with the Neurobagel team: - Create an issue in our [GitHub repositories](https://github.com/neurobagel) - Our tag on the [Neurostars forum](https://neurostars.org/tag/neurobagel) diff --git a/docs/maintaining.md b/docs/maintaining.md index ce5788e3..4630fd2f 100644 --- a/docs/maintaining.md +++ b/docs/maintaining.md @@ -9,7 +9,7 @@ We are continuously improving Neurobagel tools and services, so you may want to update your Neurobagel node to the latest version to benefit from new features and bug fixes. We always publish our tools as [Docker images on DockerHub](https://hub.docker.com/repositories/neurobagel). -Each Docker image has a semantic version tag (vX.Y.Z), and also two rolling tags: +Each Docker image has a [semantic version](https://semver.org/) tag (vX.Y.Z), and also two rolling tags: - `latest` (the latest stable release). This is the default tag used in the Neurobagel `docker-compose.yml` file. - `nightly` (the latest build from the main branch). This tag is only used for compatibility testing and should not be used in production. From f63a3b4993e79ef62e70ce5d0b88506cf05b43e6 Mon Sep 17 00:00:00 2001 From: Alyssa Dai Date: Wed, 11 Sep 2024 15:43:12 -0400 Subject: [PATCH 6/6] ignore old nipoppy repo links and fix regex patterns in mlc config --- md_link_check_config.json | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/md_link_check_config.json b/md_link_check_config.json index ce784d27..a20b86bd 100644 --- a/md_link_check_config.json +++ b/md_link_check_config.json @@ -1,12 +1,13 @@ { "ignorePatterns": [ - {"pattern": "http://neurobagel.org/vocab/*"}, + {"pattern": "http://neurobagel.org/vocab/.*"}, {"pattern": "http://neurobagel.org/graph/"}, {"pattern": "https://www.cognitiveatlas.org/task/id/"}, - {"pattern": "^../"}, - {"pattern": "localhost*"}, - {"pattern": "https://api.neurobagel.org/*"}, - {"pattern": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"} + {"pattern": "^../.*"}, + {"pattern": ".*localhost.*"}, + {"pattern": "https://api.neurobagel.org/.*"}, + {"pattern": "http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#"}, + {"pattern": "https://github.com/neurodatascience/nipoppy/.*"} ], "timeout": "60s" } \ No newline at end of file