First commit of cli docs for data setup

.github/workflows/pull_request.yml

@@ -1,6 +1,10 @@
 name: Pull Request
 
-on: pull_request
+# on: pull_request
+on:
+  push:
+    branches:
+      - cli_data_setup_docs
 
 jobs:
   build:

docs/data_setup/cli.md

@@ -0,0 +1,119 @@
+<!-- vim-markdown-toc GFM -->
+
+* [Setup a user profile](#setup-a-user-profile)
+* [Features shared across most commands](#features-shared-across-most-commands)
+* [Add, delete, view assemblies](#add-delete-view-assemblies)
+* [Import and delete features](#import-and-delete-features)
+
+<!-- vim-markdown-toc -->
+
+These instructions describe how to add data such assemblies and features to an
+Apollo instance using the command line
+interface ([cli](https://github.com/GMOD/Apollo3/tree/cli-misc/packages/apollo-cli)).
+
+# Setup a user profile
+
+This is a one-time setup to enable a user to connect to Apollo. The following
+command will start a guided, interactive process to setup a new user profile:
+
+```
+apollo config
+```
+
+Alternatively, for non-interactive setup use key/value pairs. For example,
+setup a profile called `my-profile`:
+
+```
+apollo config --profile my-profile address http://localhost:3999
+apollo config --profile my-profile accessType google
+```
+
+Or to setup a root profile named admin, non-interactively:
+
+```
+apollo config --profile admin address http://localhost:3999
+apollo config --profile admin accessType root
+apollo config --profile admin rootCredentials.username myName
+apollo config --profile admin rootCredentials.password myPassword
+```
+
+Once the profile is setup, login to store the access token:
+
+```
+apollo login --profile my-profile
+```
+
+*TO FIX/TO DOCUMENT:* If you login from within the host machine, you will get a
+`Error: listen EADDRINUSE: address already in use :::3000`
+
+# Features shared across most commands
+
+* The default profile is `default`. If you setup a profile with a different
+  name, remember to add the option `--profile my-profile` to your commands.
+
+* For commands that take as input an assembly or a reference sequence, you can
+  use the human readable name (e.g. `Homo_sapiens`, `chr1`, possibly
+  non-unique) or the 24 letter unique identifier assigned by Apollo.
+
+* Commands that query the database print results to standard output in json
+  format (you can parse it with *e.g.*, [jq](https://jqlang.github.io/jq/))
+
+# Add, delete, view assemblies
+
+With one of the following commands we add an assembly and assign a name with
+`-a/--assembly`. If an assembly with the same name already exists, the commands
+will exit with an error unless you set `--force/-f` which will delete the
+existing assembly before importing.
+
+* **Add** from a local fasta file:
+
+```
+apollo assembly add-fasta -i genome.fa -a myGenome
+```
+
+* **Add** from an external source:
+
+```
+apollo assembly add-fasta -a myGenome \
+    -i https://path/to/genome.fa \
+    -x https://path/to/genome.fa.fai
+```
+
+* **Add** from a GFF file which includes sequences (remove flag `--omit-features`
+  if you want to add sequences *and* features):
+
+```
+apollo assembly add-gff -i genome.gff -a myGenome --omit-features 
+```
+
+* **Delete** one or more assemblies:
+
+```
+apollo assembly delete -a assembly1 assembly2
+```
+
+* **View** list of assemblies:
+
+```
+apollo assembly get
+```
+
+# Import and delete features
+
+Import features from a gff file into assembly `myGenome`:
+
+```
+apollo feature import -i annotation.gff -a myGenome
+```
+
+By default, `import` adds features to the current assembly. To delete the
+existing features before importing, use flag `-d/--delete-existing`.
+
+To delete features:
+
+```
+apollo feature delete -i featureA featureB ...
+```
+
+where `featureA`, `featureB` are feature identifiers (since these are unique
+there is no need to specify assembly or reference sequence).

packages/apollo-collaboration-server/package.json

@@ -21,7 +21,7 @@
     "test:cov": "jest --coverage",
     "test:debug": "node --inspect-brk -r tsconfig-paths/register -r ts-node/register node_modules/.bin/jest --runInBand",
     "test:e2e": "jest --config ./test/jest-e2e.json",
-    "cypress:start": "GUEST_USER_ROLE=admin MONGODB_URI=\"mongodb://localhost:27017/apolloTestDb?directConnection=true\" LOG_LEVELS=error,warn yarn start"
+    "cypress:start": "CORS=true GUEST_USER_ROLE=admin MONGODB_URI=\"mongodb://localhost:27017/apolloTestDb?directConnection=true\" LOG_LEVELS=error,warn yarn start"
   },
   "dependencies": {
     "@emotion/react": "^11.10.6",