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Merge pull request #139 from jbernal0019/master
Implement filesystem storage for PFCON in-network
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,91 @@ | ||
| """ | ||
| Handle filesystem-based (eg. mount directory) storage. This is used when pfcon is | ||
| in-network and configured to directly copy the data from a filesystem. | ||
| """ | ||
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| import logging | ||
| import datetime | ||
| import os | ||
| import json | ||
| import io | ||
| import shutil | ||
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| from .base_storage import BaseStorage | ||
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| logger = logging.getLogger(__name__) | ||
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| class FileSystemStorage(BaseStorage): | ||
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| def __init__(self, config): | ||
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| super().__init__(config) | ||
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| self.base_dir = config.get('FILESYSTEM_BASEDIR') | ||
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| def store_data(self, job_id, job_incoming_dir, data, **kwargs): | ||
| """ | ||
| Copy all the files/folders under each input folder in the specified data list | ||
| into the specified incoming directory. | ||
| """ | ||
| nfiles = 0 | ||
| for rel_path in data: | ||
| abs_path = os.path.join(self.base_dir, rel_path.strip('/')) | ||
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| for root, dirs, files in os.walk(abs_path): | ||
| local_path = root.replace(abs_path, job_incoming_dir, 1) | ||
| os.makedirs(local_path, exist_ok=True) | ||
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| for filename in files: | ||
| fs_file_path = os.path.join(root, filename) | ||
| try: | ||
| shutil.copy(fs_file_path, local_path) | ||
| except Exception as e: | ||
| logger.error(f'Failed to copy file {fs_file_path} for ' | ||
| f'job {job_id}, detail: {str(e)}') | ||
| raise | ||
| nfiles += 1 | ||
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| logger.info(f'{nfiles} files copied from file system for job {job_id}') | ||
| return { | ||
| 'jid': job_id, | ||
| 'nfiles': nfiles, | ||
| 'timestamp': f'{datetime.datetime.now()}', | ||
| 'path': job_incoming_dir | ||
| } | ||
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| def get_data(self, job_id, job_outgoing_dir, **kwargs): | ||
| """ | ||
| Copy output files/folders from the specified outgoing directory into the folder | ||
| specified by job_output_path keyword argument (relative to the FS base dir). | ||
| Then create job json file ready for transmission to a remote origin. The json | ||
| file contains the job_output_path prefix and the list of relative file paths. | ||
| """ | ||
| job_output_path = kwargs['job_output_path'] | ||
| fs_output_path = os.path.join(self.base_dir, job_output_path) | ||
| fs_rel_file_paths = [] | ||
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| for root, dirs, files in os.walk(job_outgoing_dir): | ||
| rel_path = os.path.relpath(root, job_outgoing_dir) | ||
| if rel_path == '.': | ||
| rel_path = '' | ||
| fs_path = os.path.join(fs_output_path, rel_path) | ||
| os.makedirs(fs_path, exist_ok=True) | ||
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| for filename in files: | ||
| local_file_path = os.path.join(root, filename) | ||
| if not os.path.islink(local_file_path): | ||
| try: | ||
| shutil.copy(local_file_path, fs_path) | ||
| except Exception as e: | ||
| logger.error(f'Failed to copy file {local_file_path} for ' | ||
| f'job {job_id}, detail: {str(e)}') | ||
| raise | ||
| fs_rel_file_paths.append(os.path.join(rel_path, filename)) | ||
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| data = {'job_output_path': job_output_path, | ||
| 'rel_file_paths': fs_rel_file_paths} | ||
| return io.BytesIO(json.dumps(data).encode()) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,73 @@ | ||
| # https://docs.docker.com/compose/yml/ | ||
| # Each service defined in docker-compose.yml must specify exactly one of | ||
| # image or build. Other keys are optional, and are analogous to their | ||
| # docker run command-line counterparts. | ||
| # | ||
| # As with docker run, options specified in the Dockerfile (e.g., CMD, | ||
| # EXPOSE, VOLUME, ENV) are respected by default - you don't need to | ||
| # specify them again in docker-compose.yml. | ||
| # | ||
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| version: '3.7' | ||
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| services: | ||
| pfcon: | ||
| image: localhost:5000/fnndsc/pfcon:dev | ||
| build: | ||
| context: .. | ||
| args: | ||
| ENVIRONMENT: local | ||
| stdin_open: true # docker run -i | ||
| tty: true # docker run -t | ||
| # We need to mount a physical dir in the HOST onto the key store in pfcon. This dir | ||
| # is given by the STOREBASE env variable substitution. The keystore can be specified | ||
| # by the --storeBase flag during development. | ||
| command: ["python", "-m", "pfcon"] | ||
| environment: | ||
| - APPLICATION_MODE=development | ||
| - PFCON_INNETWORK=true | ||
| - STORAGE_ENV=filesystem | ||
| volumes: | ||
| - fs_storage_dev:/filesystem | ||
| - ${STOREBASE:?}:/var/local/storeBase:z | ||
| - ../pfcon:/app/pfcon:z | ||
| - ../tests:/app/tests:z | ||
| ports: | ||
| - "30006:5005" | ||
| depends_on: | ||
| - pman | ||
| - swift_service | ||
| networks: | ||
| - remote | ||
| labels: | ||
| name: "pfcon" | ||
| role: "pfcon service" | ||
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| pman: | ||
| image: ${PMANREPO:?}/pman | ||
| # Since pman spins off containers of its own it needs to mount storeBase dir (where | ||
| # pfcon shares the data) into the spawned container. This directory is passed in the | ||
| # STOREBASE env variable. | ||
| environment: | ||
| - STORAGE_TYPE=host | ||
| - STOREBASE | ||
| - SECRET_KEY="w1kxu^l=@pnsf!5piqz6!!5kdcdpo79y6jebbp+2244yjm*#+k" | ||
| - CONTAINER_ENV=swarm | ||
| volumes: | ||
| - /var/run/docker.sock:/var/run/docker.sock:z | ||
| deploy: | ||
| placement: | ||
| constraints: | ||
| - "node.role==manager" | ||
| networks: | ||
| - remote | ||
| labels: | ||
| name: "pman" | ||
| role: "pman service" | ||
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| networks: | ||
| remote: | ||
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| volumes: | ||
| fs_storage_dev: |
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