CAMd web-apps

Web-apps for:

• C2DB
• CMR-projects
• QPOD
• BiDB
• CRYSP
• OQMD12345 (CrystalBank)

Contents

• Important links
• URLs
• Installation
• Command-line interface
• CMR-app for old projects
• C2DB-app
  • Testing the C2DB-app
• Development
• Deployment
• How it works
  • Objects

Important links

• Bottle
• uWSGI
• Plotly
• Bootstrap
• WSGI
• HTMX
• ASE
• CMR-projects
• CMR-repo
• ASR-repo
• Scaling to many users
• OPTIMADE

URLs

Forwarding to https://fysik-cmr02.fysik.dtu.dk:<port>:

Link	port
C2DB	8081
CMR-projects	8082
QPOD	8083
BiDB	8084
CRYSP	8085
OQMD12345	8086
OPTIMADE
OPTIMADE

Installation

CAMd-web needs Python version 3.9 or later.

$ python -m venv venv
$ source venv/bin/activate
$ git clone git@gitlab.com:ase/ase
$ pip install -e ase
$ git clone git@gitlab.com:asr-dev/asr
$ pip install -e asr
$ git clone git@gitlab.com:camd/camd-web
$ pip install -e camd-web[test,optimade]

Command-line interface

usage: camd-web [-h] filename [filename ...]

positional arguments:

filename Filename of atomic structure file.

options:

-h, --help

show this help message and exit

CMR-app for old projects

$ python -m camdweb.cmr.app *.db

C2DB-app

$ python -m camdweb.c2db.copy ~cmr/C2DB-ASR "tree/*/*/*/" ...
$ python -m camdweb.c2db.app A*/

Folder structure for UIDs 1MoS2-1 and 1MoS2-2:

AB2/1MoS2/1/data.json
            structure.xyz
            results-asr.<property1>.json
            results-asr.<property2>.json
            ...
            ...
          2/data.json
            structure.xyz
            ...
oqmd123.json.gz
convex-hulls/MoS.json
             Mo.json
             S.json

Testing the C2DB-app

For development work, just copy one or a few meterial folders from Niflheim to your local machine:

$ mkdir C2DB-test
$ ssh sylg
$ cd /home/niflheim2/cmr/C2DB-ASR/tree/AB2/MoS2
$ scp -r MoS2-b3b4685fb6e1 <your-machine>:C2DB-test/
$ ^D

Then you can play with those files like this:

$ cd C2DB-test
$ python -m camdweb.c2db.copy . "MoS2*/"
$ python -m camdweb.c2db.app AB2

Development

Please run the following checks on your code:

$ cd <root-of-repo>
$ mypy
$ flake8 camdweb
$ camd-web-coverage

If 100 % coverage is not possible then you can make CI pass by adding # pragma: no cover or # pragma: no branch comments.

Deployment

On the fysik-cmr02 server run uWSGI like this:

$ uwsgi -w "camdweb.c2db.app:create_app()" --http :8081 --master --threads=2 --enable-threads --daemonize=c2db.log
$ uwsgi -w "camdweb.cmr.app:create_app()" --http :8082 --master --threads=2 --enable-threads --daemonize=cmr.log
$ uwsgi -w "camdweb.bidb.app:create_app()" --http :8084 --master --threads=2 --enable-threads --daemonize=bidb.log
$ uwsgi -w "camdweb.oqmd12345.app:create_app()" --http :8086 --master --threads=2 --enable-threads --daemonize=oqmd12345.log

How it works

In the picture below, camd.app is the WSGI app:

camd
  |
  v
+---------+
| CAMDApp |   app   +------------+
|         |-------->| bottle.App |
|   and   |         +------------+
|   sub-  |
| classes |   sessions   +----------+
|         |------------->| Sessions |
|         |              +----------+
+---------+
   |
   |materials
   |
   v
+------------+  index   +-------+
| Materials  |--------->| Index |
|            |          +-------+
|  --------  |
| |Material| |
|  --------  |   panels   +--------------+
| |Material| |----------->| list[Panel]  |
|  --------  |            |              |
|     :      |            |  ----------  |
|     :      |            | |AtomsPanel| |
+------------+            |  ----------  |
                          | |OtherPanel| |
                          |  ----------  |
                          |      :       |
                          |      :       |
                          +--------------+

Objects

bottle.App:	WSGI app. Defines the end-points / and /material/<uid>/.
Material:	Attributes: uid: str, atoms: Atoms, folder: Path columns: dict[str, bool | int | float | str] and count: dict[str, int]. The columns dictionary stores key-value pairs for displaying in the landing-page table. The count dictionary stores the number of each species present.
Panel:	Has a get_data(material) method that can produce a PanelData object (html, title, pop-up text, javascript and possibly sub-panels) to be assembled in the /material/<uid>/ end-point.
Index:	Handles efficient filtering of materials using the values in Material.columns and Material.count.
Materials:	Keeps track of all the Panel and Material objects (materials[uid] will give you the material with the given uid and for material in materials: will loop over them all). Also handles two dictionaries that it shares with the panels: column_descriptions: dict[str, str] for longer descriptions of the short column names. html_column_formatters: dict[str, Callable[..., str]] for converting bool, int, float and str values to HTML strings.
Sessions:	Handles Session objects for clients (one for each browser-tab).
Session:	Remembers selected columns, sorting information, ...