rcsb.app.file 0.24

RCSB File Access Service Application

RCSB File Access API Application

A FastAPI File Access Service Application

Installation

Download the library source software from the project repository:

git clone https://github.com/rcsb/py-rcsb_app_file.git

Optionally, run test suite (Python 3.9) using setuptools or tox:

python setup.py test

or simply run

tox

Installation is via the program pip.

pip3 install rcsb.app.file

or from the local repository directory:

pip3 install .

Configuration

Edit variables in rcsb/app/config/config.yml.

In particular, edit paths (SESSION_DIR_PATH, REPOSITORY_DIR_PATH, SHARED_LOCK_PATH, PDBX_REPOSITORY).

Also edit SERVER_HOST_AND_PORT.

Other files may require configuration.

Edit url in LAUNCH_GUNICORN.sh or port in Dockerfile.stage if necessary.

Edit url variables to match server url in example-upload.html, example-download.html, and example-list.html.

Endpoints and forwarding

The repository has one upload endpoint, one download endpoint, and one list-directory endpoint, among others.

To upload a file in chunks, use the 'file-v2/upload' endpoint.

To upload the entire file in one request, configure the parameters to treat the file as one chunk.

Upload requires some setup by invoking the 'file-v2/getUploadParameters' endpoint first, then passing the results as parameters.

To maintain sequential order, the client must wait for each response before sending the next chunk.

The repository saves chunks to a temporary file that is named after the upload id and begins with "._" which is configurable from the getTempFilePath function in both uploadRequest and IoUtils.

The download endpoint is found at 'file-v1/download'.

The list directory endpoint is found at 'file-v1/list-dir'.

For streamlining, the upload function has been partly duplicated in uploadRequest and IoUtils, so changes to one should be performed in the other.

To skip endpoints and forward a server-side chunk or file from Python, use functions by the same names in IoUtils.py.

Uploads and downloads

HTML examples

The example-upload.html, example-download.html, and example-list.html files demonstrate requests to the endpoints from HTML.

Python client

In a separate shell (also from the base repository directory) run client.py or gui.py

Gui.py is launched from the shell

Client.py usage

python3 client.py
[-h (help)]
[--upload source_file repo_type id content_type milestone part format version]
[--download target_file repo_type id content_type milestone part format version]
[--list repo_type dep_id (list directory)]
[-s (chunk file sequentially)]
[-r (chunk file resumably)]
[-o (overwrite files with same name)]
[-z (zip files prior to upload)]
[-x (expand files after upload)]

Hashing and compression

Should hashing be performed before or after compression/decompression? From the client side, the API first compresses, then hashes the complete file, then uploads. From the server side, the API saves, then hashes the complete file, then decompresses.

Testing and deployment

Testing is easiest without Docker and using a Sqlite database.

For production, use a Docker container with a Redis database.

Deployment on local server without docker

For launching without docker, edit url in deploy/LAUNCH_GUNICORN.sh

From base repository directory (in py-rcsb_app_file/), start app with:

./deploy/LAUNCH_GUNICORN.sh

Sqlite3

When uploading resumable chunks, server processes coordinate through a database named KV (key-value)

If KV_MODE is set to sqlite in rcsb/app/config/config.yml, chunk information is coordinated with a sqlite3 database

To view or remove Sqlite variables

Find KV_FILE_PATH in rcsb/app/config/config.yml

Connect to sqlite and use SQL commands, then ctrl-d to exit

sqlite3 path/to/kv.sqlite
.table
select * from sessions;
select * from log;

However, if files API is running in Docker, sqlite will not save to path specified in config.yml

Instead, to view or remove Sqlite variables, find kv.sqlite with

find / -name kv.sqlite

Redis

If KV_MODE is set to redis in rcsb/app/config/config.yml, resumable chunks coordinate through a Redis database

Install Redis

apt install redis
apt install redis-server
apt install redis-tools

Start the Redis server

/usr/bin/redis-server (preferred)
or
service redis start

To test Redis

redis-cli
ping
(should respond PONG)

To stop Redis

redis-cli
shutdown
(or service redis stop, but not if Redis was started with /usr/bin/redis-server)

To view Redis variables

redis-cli
KEYS *
exit

To remove all variables

redis-cli
FLUSHALL
exit

Redis on same machine as files API and without Redis in Docker

Change Redis host to 'localhost' in rcsb/app/config/config.yml, then save.

self.kV = redis.Redis(host='localhost', decode_responses=True)

Then, from the base directory, reinstall with pip3

pip3 install .

Connecting to Redis remotely

If Redis runs on a different machine than the files API, then the host must be set to a url

Change Redis host to '#:#:#:#' and port 6379 in rcsb/app/config/config.yml.

For example

self.kV = redis.Redis(host='1.2.3.4', port=6379, decode_responses=True)

Remote Redis requires changing the config file settings on the machine with Redis

From root

vim /etc/redis/redis.conf
(comment out the 'bind' statement)
(change 'protected-mode' from 'yes' to 'no')

Then start Redis and add the config file as a parameter

/usr/bin/redis-server /etc/redis/redis.conf

Redis in Docker

If the file access API is running in Docker, then Redis must also run in Docker.

Redis is run from a separate Docker container.

Download Redis image and start container

docker run --name redis-container -d redis
or (if connecting remotely to Redis container on different server)
docker run --name redis-container -p 6379:6379 -d redis

If the Redis container runs on the same machine as the files API, change Redis host to 'redis' in rcsb/app/config/config.yml.

self.kV = redis.Redis(host='redis', decode_responses=True)

Or, if connecting remotely to Redis container on different server, change Redis host to '#:#:#:#' and port 6379 in rcsb/app/config/config.yml.

For example

self.kV = redis.Redis(host='1.2.3.4', port=6379, decode_responses=True)

To view Redis variables

docker run -it --name redis-viewer --link redis-container:redis --rm redis redis-cli -h redis -p 6379
KEYS *
exit

To remove all variables

docker run -it --name redis-viewer --link redis-container:redis --rm redis redis-cli -h redis -p 6379
FLUSHALL
exit

Docker

Build Docker Container

In directory that contains Dockerfile.stage:

docker build --build-arg USER_ID=<user_id> --build-arg GROUP_ID=<group_id> -t fileapp -f Dockerfile.stage .

Run docker container

docker run --name fileapp -p 8000:8000 fileapp

or, if also running a Redis container on the same machine

docker run --name fileapp -p 8000:8000 --link redis-container:redis fileapp

or, if mounting folders, change paths in rcsb/app/config/config.yml (SESSION_DIR_PATH, REPOSITORY_DIR_PATH, SHARED_LOCK_PATH, PDBX_REPOSITORY), enable full permissions for target folder, then

docker run --mount type=bind,source=/path/to/file/system,target=/path/to/file/system --name fileapp -p 8000:8000 fileapp

or, if also linking to redis container running on same server

docker run --mount type=bind,source=/path/to/file/system,target=/path/to/file/system --name fileapp -p 8000:8000 --link redis-container:redis fileapp

(observe that the link attribute is not necessary for connecting to Redis running in a container on a different server)

-d runs container in the background (for production)

–-rm removes the container after it is stopped (only for development testing)

–-name allows user to choose a name for the container

-p allows user to choose a port, 8000:8000 is used in this case, as the port 8000 is exposed in the current dockerfile

--link connects to a Redis container if the container is running on the same machine as the files API

Error handling

Errors related to 'shared locks' are generally fixed by deleting the 'shared-locks' directory and, if necessary, restarting.

For production, Redis variables are set to expire periodically. However, hidden files are not, so a cron job should be run periodically to remove lingering hidden files from the deposit or archive directories.

After development testing with a Sqlite database, open the kv.sqlite file and delete the tables, and delete hidden files from the deposit or archives directories.

After development testing with Redis, open the redis-cli and delete the variables, and delete hidden files from the deposit or archives directories.

The hidden files to be deleted are those that start with the value configured in getTempFilePath, referred to above, after checking that the file modification time is beyond a specified threshold.