Skip to content

Fix harvester container in the docker compose #59

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
vemonet wants to merge 1 commit into
base: main
Choose a base branch
from
+10 −3
Open

Fix harvester container in the docker compose #59

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 9 additions & 3 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,7 +57,7 @@ To run the containers:
- load XML data from `scripts/postgres_data/data` (populates table `harvest_events`):
```sh
uv run import_data.py
```
```

- transform data from `scripts/postgres_data/data` to a local dir
(to test transformation, alternative to using the Celery process):
Expand Down Expand Up @@ -99,9 +99,9 @@ and the harvest run is then closed. Note that a transformation can only be perfo
```

- To obtain a harvest run id and status for a given endpoint (https://dabar.srce.hr/oai):
```sh
```sh
http://127.0.0.1:8080/harvest_run?harvest_url=https%3A%2F%2Fdabar.srce.hr%2Foai
```
```

- start transformation process:
```sh
Expand All @@ -112,3 +112,9 @@ and the harvest run is then closed. Note that a transformation can only be perfo
http://127.0.0.1:5555/tasks
```

After starting the stack with `docker compose up`, you can run the harvester for a given repository URL, e.g.:

```sh
docker compose run harvester https://lifesciences.datastations.nl/oai
Copy link
Collaborator

@tobiasschweizer tobiasschweizer Feb 11, 2026

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

if this is run by crontab, this might require an absolute path to the docker compose file: docker compose --project-directory /abs/path/to/dir run harvester https://lifesciences.datastations.nl/oai

```

1 change: 1 addition & 0 deletions docker-compose.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -228,6 +228,7 @@ services:
# https://github.com/EOSC-Data-Commons/metadata-crawlers/pkgs/container/metadata-crawlers
harvester:
image: ghcr.io/eosc-data-commons/metadata-crawlers:latest
profiles: ["manual"]
env_file:
- .env
volumes:
Expand Down