Adding download geneset cli tutorial

docs/tutorial/downloading_geneset_command_line.md

@@ -0,0 +1,69 @@
+# Downloading a Geneset From the Command Line
+This guide will walk you through how to download a geneset from Geneweaver on the 
+command line. This can be useful if you want to automate the downloading of genesets
+from Geneweaver, or if you want to use the geneset data in a local analysis tool,
+or if you want to access Geneweaver data from somewhere without a web browser.
+
+### Step 0: Install the `gweave` Command Line Tool
+
+##### Optional (But Recommended)
+Create a virtual environment for the `geneweaver-client` package.
+```
+python3 -m venv geneweaver-client
+source geneweaver-client/bin/activate
+```
+
+```
+pip install geneweaver-client
+```
+
+### Step 1: Login to Geneweaver
+```
+gweaver beta auth login --reauth
+```
+
+
+### Step 2: Download Geneset Data
+```
+gweave -p alpha api genesets get 1234 --gene-id-type=Wormbase
+```
+
+The `-p` flag will format the results in a way that is easier to read.
+
+#### Pretty Printing
+You can save the results to a file by using the `>` operator.
+```
+gweave -p alpha api genesets get 1234 --gene-id-type=Wormbase > geneset_123.json
+```
+
+#### Specifying Gene ID Type
+The `--gene-id` flag is optional. If you do not specify a gene ID type, the default 
+will be whatever the geneset was originally uploaded as.
+
+You can specify any gene ID type that is available in Geneweaver, specifically any of the
+`GeneIdentifier` types available in the geneweaver.core.enum module 
+(`geneweaver-core` package).
+
+##### GeneIdentifier Types
+
+!!! warning
+    The `GeneIdentifier` types are reproduced here for convenience, but the most 
+    up-to-date list can be found in the `geneweaver-core` package by using the
+    `geneweaver.core.enum.GeneIdentifier` class.
+
+- "Entrez"
+- "Ensemble Gene"
+- "Ensemble Protein"
+- "Ensemble Transcript"
+- "Unigene"
+- "Gene Symbol"
+- "Unannotated"
+- "MGI"
+- "HGNC"
+- "RGD"
+- "ZFIN"
+- "FlyBase"
+- "Wormbase"
+- "SGD"
+- "miRBase"
+- "CGNC"

mkdocs.yml

@@ -81,7 +81,8 @@ nav:
       - tutorial/index.md
       - Client Login: tutorial/geneweaver_client_login.ipynb
       - NCI-60 Example Workflow: tutorial/nci_60_example_01.ipynb
-      - Download Genesets: tutorial/download_genesets.ipynb
+      - Download Geneset (CLI): tutorial/download_geneset_command_line.md
+#      - Download Genesets: tutorial/download_genesets.ipynb
 #      - Accessing Geneweaver Data: tutorial/accessing-geneweaver-data.md
 #      - Running a Local Database: tutorial/running-a-local-database.md
 #      - Creating New Tools: tutorial/creating-new-tools.md