Merge pull request #30 from brain-bican/sprint_1

Sprint 1 completed

Dockerfile

@@ -21,7 +21,8 @@ RUN apt-get update &&  \
     libcurl4-openssl-dev  \
     openssl \
     r-base  \
-    leiningen
+    leiningen \
+    gpg
 
 # to speedup R package installations (try apt-cache search r-cran-remotes) https://datawookie.dev/blog/2019/01/docker-images-for-r-r-base-versus-r-apt/
 #RUN apt-get update && \
@@ -71,10 +72,19 @@ RUN mkdir $WORKSPACE/nanobot/src/resources
 ADD nanobot/src/resources/cross_taxonomy.html $WORKSPACE/nanobot/src/resources
 ADD nanobot/src/resources/ols_form.html $WORKSPACE/nanobot/src/resources
 ADD nanobot/src/resources/taxonomy_view.html $WORKSPACE/nanobot/src/resources
+ADD nanobot/src/resources/table.html $WORKSPACE/nanobot/src/resources
 
-RUN apt-get install -y aha \
+# GH cli on linux is old (2.4.0), get the latest
+RUN curl -fsSL https://cli.github.com/packages/githubcli-archive-keyring.gpg | dd of=/usr/share/keyrings/githubcli-archive-keyring.gpg
+RUN chmod go+r /usr/share/keyrings/githubcli-archive-keyring.gpg
+RUN echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/githubcli-archive-keyring.gpg] https://cli.github.com/packages stable main" | tee /etc/apt/sources.list.d/github-cli.list > /dev/null
+
+
+RUN apt-get update &&  \
+    apt-get install -y aha \
     sqlite3 \
-    python3-psycopg2
+    python3-psycopg2 \
+    gh
 
 # restore WORKDIR
 WORKDIR /tools

docs/Build.md

@@ -6,10 +6,62 @@ You can download TDT Docker image through following the steps defined in project
 docker pull ghcr.io/brain-bican/taxonomy-development-tools:latest
 ```
 
-## Build Taxonomy Development Tools
+# Install requirements
 
-Alternatively, you can build TDT docker image in your local. Checkout the project and run given command in the project root folder:
+## Docker
+
+- Install [Docker](https://www.docker.com/get-docker) and make sure its runnning properly, for example by typing `docker ps` in your terminal or command line (CMD). If all is ok, you should be seeing something like:
+
+```
+CONTAINER ID   IMAGE     COMMAND   CREATED   STATUS    PORTS     NAMES
+```
+
+## Git
+
+1. Setup your GitHub user configs
+
+```
+git config --global user.name "your_github_user"
+git config --global user.email "your_github_email"
+```
+
+2. Create a GitHub [personal access token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens#creating-a-personal-access-token-classic).
+
+3. Set `GH_TOKEN` environment variable. 
+
+- You can use `nano` or any other editor to edit the files.
+
+For bash (Linux):
+```
+nano ~/.bashrc
+```
+
+For zshrc (MacOS):
+```
+nano ~/.zshrc
+```
+
+- When the file opens, add the environment variable in a new line:
+
+```
+export GH_TOKEN=my_github_personal_access_token_here`
+```
+
+- Reinitialize the configuration file to apply the changes to the current session:
+
+`source ~/.bashrc` or `source ~/.zshrc`
+
+- Test your new config: 
+
+```
+echo $GH_TOKEN
+```
+
+
+## Build Taxonomy Development Tools (Optional)
+
+Users are suggested to use the [Get Taxonomy Development Tools](#get-taxonomy-development-tools) step to have a TDT Docker Image. But, alternatively, you can build TDT docker image in your local. Checkout the project and run given command in the project root folder:
 
 ```
-docker build -t "ghcr.io/brain-bican/taxonomy-development-tools" .
+docker build --no-cache -t "ghcr.io/brain-bican/taxonomy-development-tools" .
 ```

docs/NewRepo.md

@@ -7,17 +7,7 @@ instructions here.
 
 We will walk you though the steps to make a new ontology project
 
-## 1. Install requirements
-
-- [docker](https://www.docker.com/get-docker): Install Docker and make sure its runnning properly, for example by typing `docker ps` in your terminal or command line (CMD). If all is ok, you should be seeing something like:
-
-```
-CONTAINER ID   IMAGE     COMMAND   CREATED   STATUS    PORTS     NAMES
-```
-
-- git, for example bundled with [GitHub Desktop](https://desktop.github.com/)
-
-## 2. Download the wrapper script and pull latest ODK version
+## 1. Download the wrapper script and pull latest ODK version
 
 - Linux/Mac: [seed-via-docker.sh](https://raw.githubusercontent.com/brain-bican/taxonomy-development-tools/main/seed-via-docker.sh)
 - PC: [seed-via-docker.bat](https://raw.githubusercontent.com/brain-bican/taxonomy-development-tools/main/seed-via-docker.bat)

examples/nhp_basal_ganglia/AIT115_annotation_sheet_delete.tsv

@@ -0,0 +1,5 @@
+cluster_id	cluster_name	level 3 (subclass)	level 2 (neighborhood)	level1 (class)	region.info (Frequency)	NSForest markers (Combo)
+1	1_MSN	D1-Matrix	D1-MSN	MSN	PuR(0.52) | CaH(0.39)	EPYC, RELN, GULP1
+2	2_MSN	D1-Matrix	D1-MSN	MSN	CaH(0.95)	SEMA3E, TOX3, RELN, RAP1GAP
+3	3_MSN	D1-Matrix	D1-MSN	MSN	CaH(0.59) | PuR(0.38)	RELN, FGGY, CDH10
+4	4_MSN	D1-Matrix	D1-MSN	MSN	PuR(0.91) | CaH(0.08)	EVC, RXFP2, ETV5, SEMA3E

examples/nhp_basal_ganglia/CCN20230601_project_config.yaml

@@ -1,6 +1,6 @@
 id: CCN20230601
 title: NHP Basal Ganglia taxonomy
-description: Atlas of human primary motor cortex (M1), developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN).
+description: Atlas of non-human primate basal ganglia, developed in collaboration with the BRAIN Initiative Cell Census Network (BICCN).
 github_org: hkir-dev
 repo: nhp_basal_ganglia_taxonomy
 author: https://orcid.org/0000-0002-7073-9172

nanobot/nanobot.toml

@@ -95,4 +95,10 @@ commands = [
   ["git", "pull"],
   ["git", "-c", "color.ui=always", "status"],
   ["gh", "release", "create", "--tag", "'{tag}'"],
+]
+
+[actions.purl]
+label = "Publish PURL"
+commands = [
+  ["tdta", "purl-publish", "-i", "./", "-t", "$$TAXONOMY_ID$$", "-u", "'{username}'"]
 ]