From 4d655220a22477db2980620466386341dd790bc6 Mon Sep 17 00:00:00 2001 From: Mitchell Rysavy Date: Wed, 18 Oct 2023 22:23:51 -0400 Subject: [PATCH 1/4] Initial commit for blis-cloud-cli docs --- docs/user_guide/99_experimental_blis_cli.md | 51 +++++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 docs/user_guide/99_experimental_blis_cli.md diff --git a/docs/user_guide/99_experimental_blis_cli.md b/docs/user_guide/99_experimental_blis_cli.md new file mode 100644 index 000000000..2c35d5dc6 --- /dev/null +++ b/docs/user_guide/99_experimental_blis_cli.md @@ -0,0 +1,51 @@ +# Experimental: BLIS Cloud Command-Line Interface + +The BLIS Cloud CLI is an experimental way to install and manage BLIS on cloud-based virtual machines. + +!!! warning "This tool is in preview!" + + Unless you are comfortable debugging issues, you should instead use the [article on Running BLIS on a Cloud Provider.](../11_blis_cloud/) + +## Installation + +The tool is intended to be used on **Ubuntu** installations only. In order to install the tool, you must first install the prerequisites: + +```bash +sudo apt-get install -y python3-pip +echo "export PATH=\"\$HOME/.local/bin:\$PATH\"" | tee -a ~/.bashrc +``` + +Then you can install the tool with: + +```bash +pip3 install git+https://github.com/mrysav/blis-cloud-cli.git +``` + +## Usage + +### Docker status + +You can check the status of Docker with: + +```bash +blis docker status +``` + +If Docker is not installed, then you should run: + +```bash +blis docker install +# You might need to run this with "sudo" +``` + +### BLIS Installation + +```bash +blis install +``` + +### BLIS Update + +```bash +blis update +``` From 6ca45482d17113612c5fc2890ddba1b3532fd0b4 Mon Sep 17 00:00:00 2001 From: Mitchell Rysavy Date: Sat, 28 Oct 2023 09:56:25 -0400 Subject: [PATCH 2/4] Update some commands --- docs/user_guide/99_experimental_blis_cli.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/user_guide/99_experimental_blis_cli.md b/docs/user_guide/99_experimental_blis_cli.md index 2c35d5dc6..f984fd791 100644 --- a/docs/user_guide/99_experimental_blis_cli.md +++ b/docs/user_guide/99_experimental_blis_cli.md @@ -11,14 +11,16 @@ The BLIS Cloud CLI is an experimental way to install and manage BLIS on cloud-ba The tool is intended to be used on **Ubuntu** installations only. In order to install the tool, you must first install the prerequisites: ```bash +sudo apt-get update sudo apt-get install -y python3-pip echo "export PATH=\"\$HOME/.local/bin:\$PATH\"" | tee -a ~/.bashrc +source ~/.bashrc ``` Then you can install the tool with: ```bash -pip3 install git+https://github.com/mrysav/blis-cloud-cli.git +pip3 install -U git+https://github.com/mrysav/blis-cloud-cli.git ``` ## Usage From e4657836f904d6da17607d3e1605326cb5945d15 Mon Sep 17 00:00:00 2001 From: Mitchell Rysavy Date: Sat, 28 Oct 2023 21:06:07 -0400 Subject: [PATCH 3/4] Update deprecated features --- docs/index.md | 4 ++-- docs/user_guide/10_getting_started.md | 4 ++-- docs/user_guide/40_technician_overview.md | 2 +- mkdocs.yml | 4 ++-- 4 files changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/index.md b/docs/index.md index 7ff238575..4f9c4d4a6 100644 --- a/docs/index.md +++ b/docs/index.md @@ -3,8 +3,8 @@ C4G Basic Laboratory Information System is a collaboration between Computing-for-Good (C4G) at Georgia Tech, the Center for Disease Control (CDC), and participating PEPFAR countries. * [BLIS Home Page](http://blis.cc.gatech.edu) -* [BLIS User Guide](user_guide/00_introduction/) -* [BLIS Developer Guide](developer_documentation/) +* [BLIS User Guide](user_guide/00_introduction.md) +* [BLIS Developer Guide](developer_documentation/index.md) * [BLIS GitHub Repo](https://github.com/C4G/BLIS) You may download a copy of this documentation at this link: [C4G BLIS Documentation](pdf/document.pdf) diff --git a/docs/user_guide/10_getting_started.md b/docs/user_guide/10_getting_started.md index 18a1805b6..8db2e56bd 100644 --- a/docs/user_guide/10_getting_started.md +++ b/docs/user_guide/10_getting_started.md @@ -8,14 +8,14 @@ Secondly, **BLIS on the Cloud** is a newly deployed version of BLIS that is capa !!! info "Installation Instructions for **BLIS on the Cloud**" - For instructions on installing **BLIS on the Cloud**, please see the [article on Running BLIS on a Cloud Provider.](../11_blis_cloud/) + For instructions on installing **BLIS on the Cloud**, please see the [article on Running BLIS on a Cloud Provider.](11_blis_cloud.md) Thirdly, **BLIS in a Devcontainer** is an instantiation of BLIS that allows for developers to specify the development environment, and is intended to be used by developers only. !!! info "Installation Instructions for **BLIS in a Devcontainer**" - For instructions on installing **BLIS in a Devcontainer**, please see the [Developer Documentation](../../developer_documentation/). + For instructions on installing **BLIS in a Devcontainer**, please see the [Developer Documentation](../developer_documentation/index.md). ### BLIS For Windows diff --git a/docs/user_guide/40_technician_overview.md b/docs/user_guide/40_technician_overview.md index 7d3cc448b..736159631 100644 --- a/docs/user_guide/40_technician_overview.md +++ b/docs/user_guide/40_technician_overview.md @@ -144,4 +144,4 @@ Clicking **Generate Barcodes** allows the Technician to generate a unique barcod The Backup Page is similarly designed to the Backup Data feature available for Lab Managers. !!! tip "See Also" - The Backup Data functionality can be found in the [Lab Manager section on Backup Data.](../30_manager_overview/#backup-data) + The Backup Data functionality can be found in the [Lab Manager section on Backup Data.](30_manager_overview.md#backup-data) diff --git a/mkdocs.yml b/mkdocs.yml index ba6f375c1..fc5815a0b 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -14,8 +14,8 @@ markdown_extensions: - pymdownx.details - attr_list - pymdownx.emoji: - emoji_index: !!python/name:materialx.emoji.twemoji - emoji_generator: !!python/name:materialx.emoji.to_svg + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg plugins: From 8ccf7c2c7feb7789b66a4009bf57fbc12af18771 Mon Sep 17 00:00:00 2001 From: Mitchell Rysavy Date: Mon, 30 Oct 2023 22:47:51 -0400 Subject: [PATCH 4/4] Add rest of commands --- docs/user_guide/99_experimental_blis_cli.md | 51 +++++++++++++++++++-- 1 file changed, 48 insertions(+), 3 deletions(-) diff --git a/docs/user_guide/99_experimental_blis_cli.md b/docs/user_guide/99_experimental_blis_cli.md index f984fd791..be88c9265 100644 --- a/docs/user_guide/99_experimental_blis_cli.md +++ b/docs/user_guide/99_experimental_blis_cli.md @@ -4,7 +4,7 @@ The BLIS Cloud CLI is an experimental way to install and manage BLIS on cloud-ba !!! warning "This tool is in preview!" - Unless you are comfortable debugging issues, you should instead use the [article on Running BLIS on a Cloud Provider.](../11_blis_cloud/) + Unless you are comfortable debugging issues, you should instead use the [article on Running BLIS on a Cloud Provider.](11_blis_cloud.md) ## Installation @@ -25,7 +25,7 @@ pip3 install -U git+https://github.com/mrysav/blis-cloud-cli.git ## Usage -### Docker status +### Installing Docker You can check the status of Docker with: @@ -33,21 +33,66 @@ You can check the status of Docker with: blis docker status ``` +The tool will check to see if Docker is installed and configured correctly. If Docker is not installed, then you should run: ```bash blis docker install -# You might need to run this with "sudo" ``` +### Checking the status of BLIS + +```bash +blis status +``` + +This command will check the status of BLIS: whether or not it is running, and if the system is supported. + ### BLIS Installation ```bash blis install ``` +This command will install the BLIS configuration file to `~/.blis/` and provision the database as a Docker container. + +### Starting BLIS + +```bash +blis start +``` + +This command will start BLIS. + + ### BLIS Update ```bash blis update ``` + +This command will update the container used by BLIS. If BLIS is running, it will stop and start BLIS as needed. + +### Stopping BLIS + +```bash +blis stop +``` + +This command will stop BLIS. + +### Accessing log files + +```bash +blis logs application +blis logs database +``` + +These two log files are generated by the BLIS application. The `application` log is most useful for debugging issues. + +```bash +blis logs apache2/error +blis logs apache2/access +``` + +These two log files are generated by the Apache2 webserver. The `apache2/error` log contains PHP errors useful for debugging issues.