Updates to documentation

.gitignore

@@ -1,5 +1,5 @@
 __pycache__/
-.DS_Store
+**.DS_Store
 .ruff_cache/
 .vscode/
 *.orig
@@ -12,9 +12,10 @@ dist/
 jquery/
 Pipfile
 Pipfile.lock
-run_dir/genosqlrc.yaml
+**genosqlrc.yaml
 run_dir/qc_reports/
 run_dir/settings.yaml
 run_dir/settings/
 status.egg-info/
 tests/test_items.yaml
+**orderportal_cred.yaml

README.md

@@ -2,38 +2,86 @@
 
 Genomics Status is a Tornado web app for visualizing information and statistics regarding operations by NGI Stockholm at SciLifeLab.
 
-Genomics Status interfaces with StatusDB; the CouchDB database instance used to store metadata in various forms. Documentation about CouchDB can be found [here](http://guide.couchdb.org/).
+Genomics Status interfaces with StatusDB, which is a [CouchDB](http://guide.couchdb.org/) database instance used to store metadata in various forms.
 
 ## Installing and running genomics status
 
-**NOTE**: These steps assume that:
+### Requirements
+
 * you're either running a python virtualenv or you do have root permissions.
 * you're running python version 3.6 or later (dicts are ordered by default)
 * you have access to both StatusDB and Genologics LIMS
 
-1 - Clone the repository with the `--recursive` option (this will also download [nvd3](http://nvd3.org/) library):
+### Installation
 
-```
+Clone the repository with the `--recursive` option (this will also download [nvd3](http://nvd3.org/) library):
+
+```bash
 git clone --recursive https://github.com/NationalGenomicsInfrastructure/genomics-status.git
 ```
 
-2 - Install the package (the `pip install -r requirements_dev.txt` can be skipped on a production server)
+<details>
+
+<summary>Note on `conda` environments</summary>
+
+#### Create the environment with the correct dependencies
+
+If you decide to use a conda environment, create one making sure to use the `conda_requirements.yml` file with the following command:
+
+```bash
+conda env create -n <env_name> -f conda_requirements.yml
+```
+
+where `<env_name>` is the name of the environment you want to create.  Then, activate the environment with:
 
+```bash
+conda activate <env_name>
 ```
-cd status
+
+</details>
+
+Install the dependencies and the package (the `pip install -r requirements_dev.txt` can be skipped on a production server)
+
+```bash
 pip install -r requirements.txt
 pip install -r requirements_dev.txt
 python setup.py install
 ```
 
-3 - You'll need to install genologics package separately:
+<details>
+
+<summary>Note on MacOS installations</summary>
+
+### Fix library issues
+
+If you are using MacOS, you might run into some issues with the libraries when running the app. 
 
+In case you get the `OSError: cannot load library 'gobject-2.0-0'` error (or similar), install `glib` and `pango` via [Homebrew](https://brew.sh/):
+
+```bash
+brew install glib
+brew install pango
 ```
-pip install git+https://github.com/SciLifeLab/genologics.git
+
+and then symlink the libraries to `/usr/local/lib`:
+
+```bash
+sudo ln -s /opt/homebrew/opt/glib/lib/libgobject-2.0.0.dylib /usr/local/lib/gobject-2.0
+sudo ln -s /opt/homebrew/opt/pango/lib/libpango-1.0.dylib /usr/local/lib/pango-1.0
+sudo ln -s /opt/homebrew/opt/harfbuzz/lib/libharfbuzz.dylib /usr/local/lib/harfbuzz
+sudo ln -s /opt/homebrew/opt/fontconfig/lib/libfontconfig.1.dylib /usr/local/lib/fontconfig-1
+sudo ln -s /opt/homebrew/opt/pango/lib/libpangoft2-1.0.dylib /usr/local/lib/pangoft2-1.0
 ```
 
-4 - For running, it requires a `settings.yaml` file which points to the CouchDB server to use, and which port to
-serve the web app to. You will also need a .genologicsrc file with the API credentials for our Genologics LIMS. The files should look like these:
+</details>
+
+
+### Configuration
+
+Before running the app, you need to configure it. This is done by creating the`settings.yaml` file, which points to 
+the CouchDB server to use and defines which port to serve the web app to. You will also need to create a `.genologicsrc`
+file with the API credentials for our Genologics LIMS, and a `orderportal_cred.yaml` file with the credentials for the 
+order portal. The files should look like these:
 
 `<status_dir>/run_dir/settings.yaml`:
 ```yaml
@@ -42,68 +90,98 @@ username: <tools_username> # same as input above
 password: <tools_password> # same as input above
 port: 9761
 redirect_uri: http://localhost:9761/login
+cookie_secret: 
+couch_url: https://ngi-statusdb-dev.scilifelab.se
+
+# Data Centre's pro subscription
+font_awesome_url: https://kit.fontawesome.com/<subscription_id>.js
+
+lims_backend_credential_location: <genologicsrc_location>
+
+order_portal_credential_location: orderportal_cred.yaml
 
-# This can be left like this as long as --testing_mode is used
 google_oauth:
-    key_old: write
-    key: anything
-    secret: here
+    key: <google_oauth_key>
+    secret: <google_oauth_secret>
 
 zendesk:
-    url: any
-    username: thing
-    token: goes
+    url: https://ngisweden.zendesk.com
+    username: <zendesk_username>
+    token: <zendesk_token>
 
-sftp:
-    login: will
-    password: code
-
-contact_person: [email protected]
+contact_person: <contact_person_email>
 
 instruments:
     HiSeq:
-        INSTRUMENT_ID: INSTRUMENT_NAME
+        INSTRUMENT_ID: <Instrument_Name>
     MiSeq:
-        INSTRUMENT_ID: INSTRUMENT_NAME
+        INSTRUMENT_ID: <Instrument_Name>
+
+slack:
+    token: <slack_token>
+
+jira:
+    url: https://scilifelab.atlassian.net
+    user: <jira_user>
+    api_token: <jira_api_token>
+    project_key: NSD
+
+# Trello suggestion box update log
+sb_log: suggestion_box.log # Optional
 
-password_seed: not_needed_for_development
+psul_log: /home/hiseq.bioinfo/log/LIMS2DB/lims2db_projects.log
+charon:
+    url: https://charon-dev.scilifelab.se
+    api_token:  
 
-# You Trello API credentials, you need a board named "Suggestion Box"
-trello:
-    api_key: <trello_api_key>
-    api_secret: <trello_api_secret>
-    token: <trello_token>
+# LIMS Dashboard
+lims_dashboard_url: https://lims-dashboard.scilifelab.se
 
-uppmax_projects
-    - proj_id1
-    - proj_id2
+server_status:
+    instruments:
+        <instrument_address>: <instrument_name>
+        <instrument_address>: <instrument_name>
+        <instrument_address>: <instrument_name>
+
+reports_path: <reports_path>
 ```
 
-`~/.genologicsrc`:
+`.genologicsrc`:
 ```yaml
 [genologics]
 BASEURI=https://ngi-lims-stage.scilifelab.se:8443
 USERNAME=<lims_api_username>
 PASSWORD=<lims_api_password>
 ```
-5 - Run the tornado app from run_dir :
+
+`orderportal_cred.yaml`:
+```yaml
+order_portal:
+    api_get_order_url: 'https://ngisweden.scilifelab.se/orders/api/v1/order'
+    api_token: <order_portal_api_token>
 ```
+
+### Usage
+
+Run the tornado app from `run_dir`:
+```bash
 cd run_dir
 python ../status_app.py --testing_mode
 ```
 
-`--testing_mode` will skip the google authentication, which is convenient for testing
+The `--testing_mode` flag will skip the google authentication, which is convenient for testing.
 
 The status web app both provides the HTML web interface, and a RESTful api for accessing the data being
 visualized on the various pages.
 
 If you've used the `settings.yaml` template above, you should now be able to access the site at `http://localhost:9761/` or `http://localhost:9761/login`
 
+
 ## Generating the custom bootstrap css file
 The bootstrap css file is customised to use a smaller font size.
 To replicate this, use the following snippet:
 
-```
+```bash
 conda create -n nodejs
 conda activate nodejs
 conda install nodejs
@@ -114,7 +192,7 @@ cd run_dir/static/scss
 
 Then modify the `custom.scss` file, especially the hard-coded path according to your needs, and run the compilation:
 
-```
+```bash
 sass custom.scss custom-bootstrap-5-alpha.css
 ```
 
@@ -171,6 +249,7 @@ On Genomics Status, templates are located in `status/run_dir/design`
 
 
 TODO:
+
     - [ ] Fix links to old project page vs new project page
     - [ ] Add link to project cards from menu and front page
 

status_app.py

@@ -524,10 +524,6 @@ def __init__(self, settings):
         # Load password seed
         self.password_seed = settings.get("password_seed")
 
-        # load logins for the genologics sftp
-        self.genologics_login = settings["sftp"]["login"]
-        self.genologics_pw = settings["sftp"]["password"]
-
         # Location of the psul log
         self.psul_log = settings.get("psul_log")