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| Original file line number | Diff line number | Diff line change |
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| # sda-pipeline: finalize | ||
| # finalize Service | ||
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| Handles the so-called _Accession ID (stable ID)_ to filename mappings from Central EGA. | ||
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| At the same time the service fulfills the replication requirement of having distinct backup copies. | ||
| For more information see [Federated EGA Node Operations v2](https://ega-archive.org/assets/files/EGA-Node-Operations-v2.pdf) document. | ||
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| ## Configuration | ||
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| There are a number of options that can be set for the finalize service. | ||
| There are a number of options that can be set for the `finalize` service. | ||
| These settings can be set by mounting a yaml-file at `/config.yaml` with settings. | ||
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| ex. | ||
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| ```yaml | ||
| log: | ||
| level: "debug" | ||
| format: "json" | ||
| ``` | ||
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| They may also be set using environment variables like: | ||
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| ```bash | ||
| export LOG_LEVEL="debug" | ||
| export LOG_FORMAT="json" | ||
| ``` | ||
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| ### RabbitMQ broker settings | ||
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| These settings control how finalize connects to the RabbitMQ message broker. | ||
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| - `BROKER_HOST`: hostname of the rabbitmq server | ||
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| - `BROKER_PORT`: rabbitmq broker port (commonly `5671` with TLS and `5672` without) | ||
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| - `BROKER_QUEUE`: message queue to read messages from (commonly `accessionIDs`) | ||
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| - `BROKER_ROUTINGKEY`: message queue to write success messages to (commonly `backup`) | ||
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| - `BROKER_USER`: username to connect to rabbitmq | ||
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| - `BROKER_PASSWORD`: password to connect to rabbitmq | ||
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| - `BROKER_PREFETCHCOUNT`: Number of messages to pull from the message server at the time (default to 2) | ||
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| ### PostgreSQL Database settings: | ||
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| - `DB_HOST`: hostname for the postgresql database | ||
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| - `DB_PORT`: database port (commonly 5432) | ||
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| - `DB_USER`: username for the database | ||
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| - `DB_PASSWORD`: password for the database | ||
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| - `DB_DATABASE`: database name | ||
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| - `DB_SSLMODE`: The TLS encryption policy to use for database connections. | ||
| Valid options are: | ||
| - `disable` | ||
| - `allow` | ||
| - `prefer` | ||
| - `require` | ||
| - `verify-ca` | ||
| - `verify-full` | ||
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| More information is available | ||
| [in the postgresql documentation](https://www.postgresql.org/docs/current/libpq-ssl.html#LIBPQ-SSL-PROTECTION) | ||
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| Note that if `DB_SSLMODE` is set to anything but `disable`, then `DB_CACERT` needs to be set, | ||
| and if set to `verify-full`, then `DB_CLIENTCERT`, and `DB_CLIENTKEY` must also be set | ||
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| - `DB_CLIENTKEY`: key-file for the database client certificate | ||
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| - `DB_CLIENTCERT`: database client certificate file | ||
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| - `DB_CACERT`: Certificate Authority (CA) certificate for the database to use | ||
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| ### Logging settings: | ||
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| - `LOG_FORMAT` can be set to “json” to get logs in json format. | ||
| All other values result in text logging | ||
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| - `LOG_LEVEL` can be set to one of the following, in increasing order of severity: | ||
| - `trace` | ||
| - `debug` | ||
| - `info` | ||
| - `warn` (or `warning`) | ||
| - `error` | ||
| - `fatal` | ||
| - `panic` | ||
| These settings control how `finalize` connects to the RabbitMQ message broker. | ||
|
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| - `BROKER_HOST`: hostname of the RabbitMQ server | ||
| - `BROKER_PORT`: RabbitMQ broker port (commonly: `5671` with TLS and `5672` without) | ||
| - `BROKER_QUEUE`: message queue to read messages from (commonly: `accession`) | ||
| - `BROKER_ROUTINGKEY`: Routing key for publishing messages (commonly: `completed`) | ||
| - `BROKER_USER`: username to connect to RabbitMQ | ||
| - `BROKER_PASSWORD`: password to connect to RabbitMQ | ||
| - `BROKER_PREFETCHCOUNT`: Number of messages to pull from the message server at the time (default to `2`) | ||
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| ### PostgreSQL Database settings | ||
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| - `DB_HOST`: hostname for the postgresql database | ||
| - `DB_PORT`: database port (commonly: `5432`) | ||
| - `DB_USER`: username for the database | ||
| - `DB_PASSWORD`: password for the database | ||
| - `DB_DATABASE`: database name | ||
| - `DB_SSLMODE`: The TLS encryption policy to use for database connections, valid options are: | ||
| - `disable` | ||
| - `allow` | ||
| - `prefer` | ||
| - `require` | ||
| - `verify-ca` | ||
| - `verify-full` | ||
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| More information is available | ||
| [in the postgresql documentation](https://www.postgresql.org/docs/current/libpq-ssl.html#LIBPQ-SSL-PROTECTION) | ||
|
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| Note that if `DB_SSLMODE` is set to anything but `disable`, then `DB_CACERT` needs to be set, | ||
| and if set to `verify-full`, then `DB_CLIENTCERT`, and `DB_CLIENTKEY` must also be set. | ||
|
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| - `DB_CLIENTKEY`: key-file for the database client certificate | ||
| - `DB_CLIENTCERT`: database client certificate file | ||
| - `DB_CACERT`: Certificate Authority (CA) certificate for the database to use | ||
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| ### Logging settings | ||
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| - `LOG_FORMAT` can be set to `json` to get logs in JSON format. All other values result in text logging. | ||
| - `LOG_LEVEL` can be set to one of the following, in increasing order of severity: | ||
| - `trace` | ||
| - `debug` | ||
| - `info` | ||
| - `warn` (or `warning`) | ||
| - `error` | ||
| - `fatal` | ||
| - `panic` | ||
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| ### Storage settings | ||
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| Storage backend is defined by the `ARCHIVE_TYPE`, and `BACKUP_TYPE` variables. | ||
| Valid values for these options are `S3` or `POSIX` | ||
| (Defaults to `POSIX` on unknown values). | ||
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| The value of these variables define what other variables are read. | ||
| The same variables are available for all storage types, differing by prefix (`ARCHIVE_`, or `BACKUP_`) | ||
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| if `*_TYPE` is `S3` then the following variables are available: | ||
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| - `*_URL`: URL to the S3 system | ||
| - `*_ACCESSKEY`: The S3 access and secret key are used to authenticate to S3, | ||
| [more info at AWS](https://docs.aws.amazon.com/general/latest/gr/aws-sec-cred-types.html#access-keys-and-secret-access-keys) | ||
| - `*_SECRETKEY`: The S3 access and secret key are used to authenticate to S3, | ||
| [more info at AWS](https://docs.aws.amazon.com/general/latest/gr/aws-sec-cred-types.html#access-keys-and-secret-access-keys) | ||
| - `*_BUCKET`: The S3 bucket to use as the storage root | ||
| - `*_PORT`: S3 connection port (default: `443`) | ||
| - `*_REGION`: S3 region (default: `us-east-1`) | ||
| - `*_CHUNKSIZE`: S3 chunk size for multipart uploads. | ||
| - `*_CACERT`: Certificate Authority (CA) certificate for the storage system, this is only needed if the S3 server has a certificate signed by a private entity | ||
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| and if `*_TYPE` is `POSIX`: | ||
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| - `*_LOCATION`: POSIX path to use as storage root | ||
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| ## Service Description | ||
| Finalize adds stable, shareable _Accession ID_'s to archive files. | ||
| When running, finalize reads messages from the configured RabbitMQ queue (default "accessionIDs"). | ||
| For each message, these steps are taken (if not otherwise noted, errors halt progress and the service moves on to the next message): | ||
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| 1. The message is validated as valid JSON that matches the "ingestion-accession" schema (defined in sda-common). | ||
| If the message can’t be validated it is discarded with an error message in the logs. | ||
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| 1. if the type of the `DecryptedChecksums` field in the message is `sha256`, the value is stored. | ||
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| 1. A new RabbitMQ "complete" message is created and validated against the "ingestion-completion" schema. | ||
| If the validation fails, an error message is written to the logs. | ||
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| 1. The file accession ID in the message is marked as "ready" in the database. | ||
| On error the service sleeps for up to 5 minutes to allow for database recovery, after 5 minutes the message is Nacked, re-queued and an error message is written to the logs. | ||
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| 1. The complete message is sent to RabbitMQ. On error, a message is written to the logs. | ||
| `Finalize` adds stable, shareable _Accession ID_'s to archive files. | ||
| If a backup location is configured it will perform backup of a file. | ||
| When running, `finalize` reads messages from the configured RabbitMQ queue (commonly: `accession`). | ||
| For each message, these steps are taken (if not otherwise noted, errors halt progress and the service moves on to the next message): | ||
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| 1. The original RabbitMQ message is Ack'ed. | ||
| 1. The message is validated as valid JSON that matches the `ingestion-accession` schema. If the message can’t be validated it is discarded with an error message in the logs. | ||
| 2. If the service is configured to perform backups i.e. the `ARCHIVE_` and `BACKUP_` storage backend are set. Archived files will be copied to the backup location. | ||
| 1. The file size on disk is requested from the storage system. | ||
| 2. The database file size is compared against the disk file size. | ||
| 3. A file reader is created for the archive storage file, and a file writer is created for the backup storage file. | ||
| 3. The file data is copied from the archive file reader to the backup file writer. | ||
| 4. If the type of the `DecryptedChecksums` field in the message is `sha256`, the value is stored. | ||
| 5. A new RabbitMQ `complete` message is created and validated against the `ingestion-completion` schema. If the validation fails, an error message is written to the logs. | ||
| 6. The file accession ID in the message is marked as *ready* in the database. On error the service sleeps for up to 5 minutes to allow for database recovery, after 5 minutes the message is Nacked, re-queued and an error message is written to the logs. | ||
| 7. The complete message is sent to RabbitMQ. On error, a message is written to the logs. | ||
| 8. The original RabbitMQ message is Ack'ed. | ||
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| ## Communication | ||
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| - Finalize reads messages from one rabbitmq queue (default `accessionIDs`). | ||
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| - Finalize writes messages to one rabbitmq queue (default `backup`). | ||
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| - Finalize assigns the accession ID to a file in the database using the `SetAccessionID` function. | ||
| - `Finalize` reads messages from one RabbitMQ queue (commonly: `accession`). | ||
| - `Finalize` publishes messages with one routing key (commonly: `completed`). | ||
| - `Finalize` assigns the accession ID to a file in the database using the `SetAccessionID` function. |
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