Feat/extend creds setup (#70)

* Update .gitignore

* Update script

* Update getting started doc

* Tag maintainer in help docs

.gitignore

@@ -1,6 +1,7 @@
 # Creds
 creds.json
 schematic_service_account_creds.json
+.synapseConfig
 
 # Tests and template files generated locally
 *.schema.json

getting_started.md

@@ -20,15 +20,15 @@ You may need to wait a bit for the container to install tools and finish other s
 
 This is the command-line equivalent of using the schematic API or using the DCA UI to generate a template.
 
-1. For generating templates, you need creds. (You only need to do this once with a new codespace. Locally, we can keep the `creds.json` In the command line and gitignore it so it is not committed to the repo.) Run this simple bash script at the codespace command line: `./scripts/setup_creds.sh`. You should see a `creds.json` file at the root of the repo, next to the `.jsonld` file, etc. Feel free to skim the bash script and the `.json` file.
+1. For generating templates, you need creds. You only need to do this once when starting up a new codespace. Run this simple bash script at the codespace command line: `./scripts/setup_creds.sh`. You should see a `creds.json` and `.synapseConfig` file at the root of the repo, next to the `.jsonld` file. Locally, we can keep these files around but .gitignore them so they are **not committed to the repo**. Also, for local use, you may want to set up `.synapseConfig` using your own credentials. Feel free to skim the bash script and creds files.
 
 2. Generate a blank Excel template for e.g. scRNAseq-Level1 by running `./scripts/gen_template.sh ImagingLevel2`. This generates an Excel template by default. Try replacing with another template ID. Try also copy-pasting contents of the script to the command-line to run schematic command natively, replacing variables as needed.
 
-TODO - update script for these steps
+TODO - adapt script to allow these steps @cconrad8
 
 3. Generate a blank Google template.
 
-4. Generate a *filled-in* Google or Excel template for existing files on Synapse.
+4. Generate a *filled-in* Google or Excel template for existing files on Synapse. An example for where this would apply is the public ScRNA-seqLevel1 dataset `syn26560315`.
 
 
 ## Validate manifest

scripts/setup_creds.sh

@@ -1,6 +1,7 @@
 #!/bin/bash
 
 CREDS=creds.json
+SYNAPSE_CONFIG=.synapseConfig
 
 if [ -f "$CREDS" ]; then
   echo "✓ $CREDS already present."
@@ -12,3 +13,15 @@ else
   exit 1
 fi
 
+if [ -f "$SYNAPSE_CONFIG" ]; then
+  echo "✓ $SYNAPSE_CONFIG already present."
+elif [ -n "${SYNAPSE_AUTH_TOKEN}" ]; then
+  echo "[authentication]" > $SYNAPSE_CONFIG
+  echo "authtoken = ${SYNAPSE_AUTH_TOKEN}" >> $SYNAPSE_CONFIG
+  echo "✓ Created $SYNAPSE_CONFIG"
+else
+  echo "✗ Failed to access stored creds."
+  exit 1
+fi
+
+