Skip to content

Configuration

To configure the Fractal Server one must define some environment variables. Some of them are required, and the server will not start unless they are set. Some are optional and sensible defaults are provided.

The required variables are the following

JWT_SECRET_KEY
FRACTAL_TASKS_DIR
FRACTAL_RUNNER_WORKING_BASE_DIR
POSTGRES_DB

OAuthClientConfig

Bases: BaseModel

OAuth Client Config Model

This model wraps the variables that define a client against an Identity Provider. As some providers are supported by the libraries used within the server, some attributes are optional.

Attributes:

Name Type Description
CLIENT_NAME str

The name of the client

CLIENT_ID str

ID of client

CLIENT_SECRET str

Secret to authorise against the identity provider

OIDC_CONFIGURATION_ENDPOINT Optional[str]

OpenID configuration endpoint, allowing to discover the required endpoints automatically

REDIRECT_URL Optional[str]

String to be used as redirect_url argument for fastapi_users.get_oauth_router, and then in httpx_oauth.integrations.fastapi.OAuth2AuthorizeCallback.

Source code in fractal_server/config.py
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
class OAuthClientConfig(BaseModel):
    """
    OAuth Client Config Model

    This model wraps the variables that define a client against an Identity
    Provider. As some providers are supported by the libraries used within the
    server, some attributes are optional.

    Attributes:
        CLIENT_NAME:
            The name of the client
        CLIENT_ID:
            ID of client
        CLIENT_SECRET:
            Secret to authorise against the identity provider
        OIDC_CONFIGURATION_ENDPOINT:
            OpenID configuration endpoint,
            allowing to discover the required endpoints automatically
        REDIRECT_URL:
            String to be used as `redirect_url` argument for
            `fastapi_users.get_oauth_router`, and then in
            `httpx_oauth.integrations.fastapi.OAuth2AuthorizeCallback`.
    """

    CLIENT_NAME: str
    CLIENT_ID: str
    CLIENT_SECRET: str
    OIDC_CONFIGURATION_ENDPOINT: Optional[str]
    REDIRECT_URL: Optional[str] = None

    @root_validator
    def check_configuration(cls, values):
        if values.get("CLIENT_NAME") not in ["GOOGLE", "GITHUB"]:
            if not values.get("OIDC_CONFIGURATION_ENDPOINT"):
                raise FractalConfigurationError(
                    f"Missing OAUTH_{values.get('CLIENT_NAME')}"
                    "_OIDC_CONFIGURATION_ENDPOINT"
                )
        return values

Settings

Bases: BaseSettings

Contains all the configuration variables for Fractal Server

The attributes of this class are set from the environtment.

Source code in fractal_server/config.py
 86
 87
 88
 89
 90
 91
 92
 93
 94
 95
 96
 97
 98
 99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
class Settings(BaseSettings):
    """
    Contains all the configuration variables for Fractal Server

    The attributes of this class are set from the environtment.
    """

    class Config:
        case_sensitive = True

    PROJECT_NAME: str = "Fractal Server"
    PROJECT_VERSION: str = fractal_server.__VERSION__

    ###########################################################################
    # AUTH
    ###########################################################################

    OAUTH_CLIENTS_CONFIG: list[OAuthClientConfig] = Field(default_factory=list)

    # JWT TOKEN
    JWT_EXPIRE_SECONDS: int = 180
    """
    JWT token lifetime, in seconds.
    """

    JWT_SECRET_KEY: Optional[str]
    """
    JWT secret

    ⚠️ **IMPORTANT**: set this variable to a secure string, and do not disclose
    it.
    """

    # COOKIE TOKEN
    COOKIE_EXPIRE_SECONDS: int = 86400
    """
    Cookie token lifetime, in seconds.
    """

    @root_validator(pre=True)
    def collect_oauth_clients(cls, values):
        """
        Automatic collection of OAuth Clients

        This method collects the environment variables relative to a single
        OAuth client and saves them within the `Settings` object in the form
        of an `OAuthClientConfig` instance.

        Fractal can support an arbitrary number of OAuth providers, which are
        automatically detected by parsing the environment variable names. In
        particular, to set the provider `FOO`, one must specify the variables

            OAUTH_FOO_CLIENT_ID
            OAUTH_FOO_CLIENT_SECRET
            ...

        etc (cf. OAuthClientConfig).
        """
        oauth_env_variable_keys = [
            key for key in environ.keys() if key.startswith("OAUTH_")
        ]
        clients_available = {
            var.split("_")[1] for var in oauth_env_variable_keys
        }

        values["OAUTH_CLIENTS_CONFIG"] = []
        for client in clients_available:
            prefix = f"OAUTH_{client}"
            oauth_client_config = OAuthClientConfig(
                CLIENT_NAME=client,
                CLIENT_ID=getenv(f"{prefix}_CLIENT_ID", None),
                CLIENT_SECRET=getenv(f"{prefix}_CLIENT_SECRET", None),
                OIDC_CONFIGURATION_ENDPOINT=getenv(
                    f"{prefix}_OIDC_CONFIGURATION_ENDPOINT", None
                ),
                REDIRECT_URL=getenv(f"{prefix}_REDIRECT_URL", None),
            )
            values["OAUTH_CLIENTS_CONFIG"].append(oauth_client_config)
        return values

    ###########################################################################
    # DATABASE
    ###########################################################################
    DB_ECHO: bool = False
    """
    If `True`, make database operations verbose.
    """
    POSTGRES_USER: Optional[str]
    """
    User to use when connecting to the PostgreSQL database.
    """
    POSTGRES_PASSWORD: Optional[str]
    """
    Password to use when connecting to the PostgreSQL database.
    """
    POSTGRES_HOST: Optional[str] = "localhost"
    """
    URL to the PostgreSQL server or path to a UNIX domain socket.
    """
    POSTGRES_PORT: Optional[str] = "5432"
    """
    Port number to use when connecting to the PostgreSQL server.
    """
    POSTGRES_DB: Optional[str]
    """
    Name of the PostgreSQL database to connect to.
    """

    @property
    def DATABASE_ASYNC_URL(self) -> URL:
        url = URL.create(
            drivername="postgresql+psycopg",
            username=self.POSTGRES_USER,
            password=self.POSTGRES_PASSWORD,
            host=self.POSTGRES_HOST,
            port=self.POSTGRES_PORT,
            database=self.POSTGRES_DB,
        )
        return url

    @property
    def DATABASE_SYNC_URL(self):
        return self.DATABASE_ASYNC_URL.set(drivername="postgresql+psycopg")

    ###########################################################################
    # FRACTAL SPECIFIC
    ###########################################################################

    FRACTAL_DEFAULT_ADMIN_EMAIL: str = "admin@fractal.xy"
    """
    Admin default email, used upon creation of the first superuser during
    server startup.

    ⚠️  **IMPORTANT**: After the server startup, you should always edit the
    default admin credentials.
    """

    FRACTAL_DEFAULT_ADMIN_PASSWORD: str = "1234"
    """
    Admin default password, used upon creation of the first superuser during
    server startup.

    ⚠️ **IMPORTANT**: After the server startup, you should always edit the
    default admin credentials.
    """

    FRACTAL_DEFAULT_ADMIN_USERNAME: str = "admin"
    """
    Admin default username, used upon creation of the first superuser during
    server startup.

    ⚠️ **IMPORTANT**: After the server startup, you should always edit the
    default admin credentials.
    """

    FRACTAL_TASKS_DIR: Optional[Path]
    """
    Directory under which all the tasks will be saved (either an absolute path
    or a path relative to current working directory).
    """

    @validator("FRACTAL_TASKS_DIR", always=True)
    def make_FRACTAL_TASKS_DIR_absolute(cls, v):
        """
        If `FRACTAL_TASKS_DIR` is a non-absolute path, make it absolute (based
        on the current working directory).
        """
        if v is None:
            return None
        FRACTAL_TASKS_DIR_path = Path(v)
        if not FRACTAL_TASKS_DIR_path.is_absolute():
            FRACTAL_TASKS_DIR_path = FRACTAL_TASKS_DIR_path.resolve()
            logging.warning(
                f'FRACTAL_TASKS_DIR="{v}" is not an absolute path; '
                f'converting it to "{str(FRACTAL_TASKS_DIR_path)}"'
            )
        return FRACTAL_TASKS_DIR_path

    @validator("FRACTAL_RUNNER_WORKING_BASE_DIR", always=True)
    def make_FRACTAL_RUNNER_WORKING_BASE_DIR_absolute(cls, v):
        """
        (Copy of make_FRACTAL_TASKS_DIR_absolute)
        If `FRACTAL_RUNNER_WORKING_BASE_DIR` is a non-absolute path,
        make it absolute (based on the current working directory).
        """
        if v is None:
            return None
        FRACTAL_RUNNER_WORKING_BASE_DIR_path = Path(v)
        if not FRACTAL_RUNNER_WORKING_BASE_DIR_path.is_absolute():
            FRACTAL_RUNNER_WORKING_BASE_DIR_path = (
                FRACTAL_RUNNER_WORKING_BASE_DIR_path.resolve()
            )
            logging.warning(
                f'FRACTAL_RUNNER_WORKING_BASE_DIR="{v}" is not an absolute '
                "path; converting it to "
                f'"{str(FRACTAL_RUNNER_WORKING_BASE_DIR_path)}"'
            )
        return FRACTAL_RUNNER_WORKING_BASE_DIR_path

    FRACTAL_RUNNER_BACKEND: Literal[
        "local",
        "local_experimental",
        "slurm",
        "slurm_ssh",
    ] = "local"
    """
    Select which runner backend to use.
    """

    FRACTAL_RUNNER_WORKING_BASE_DIR: Optional[Path]
    """
    Base directory for running jobs / workflows. All artifacts required to set
    up, run and tear down jobs are placed in subdirs of this directory.
    """

    FRACTAL_LOGGING_LEVEL: int = logging.INFO
    """
    Logging-level threshold for logging

    Only logs of with this level (or higher) will appear in the console logs;
    see details [here](../internals/logs/).
    """

    FRACTAL_LOCAL_CONFIG_FILE: Optional[Path]
    """
    Path of JSON file with configuration for the local backend.
    """

    FRACTAL_API_MAX_JOB_LIST_LENGTH: int = 50
    """
    Number of ids that can be stored in the `jobsV1` and `jobsV2` attributes of
    `app.state`.
    """

    FRACTAL_GRACEFUL_SHUTDOWN_TIME: int = 30
    """
    Waiting time for the shutdown phase of executors
    """

    FRACTAL_SLURM_CONFIG_FILE: Optional[Path]
    """
    Path of JSON file with configuration for the SLURM backend.
    """

    FRACTAL_SLURM_WORKER_PYTHON: Optional[str] = None
    """
    Absolute path to Python interpreter that will run the jobs on the SLURM
    nodes. If not specified, the same interpreter that runs the server is used.
    """

    @validator("FRACTAL_SLURM_WORKER_PYTHON", always=True)
    def absolute_FRACTAL_SLURM_WORKER_PYTHON(cls, v):
        """
        If `FRACTAL_SLURM_WORKER_PYTHON` is a relative path, fail.
        """
        if v is None:
            return None
        elif not Path(v).is_absolute():
            raise FractalConfigurationError(
                f"Non-absolute value for FRACTAL_SLURM_WORKER_PYTHON={v}"
            )
        else:
            return v

    FRACTAL_TASKS_PYTHON_DEFAULT_VERSION: Optional[
        Literal["3.9", "3.10", "3.11", "3.12"]
    ] = None
    """
    Default Python version to be used for task collection. Defaults to the
    current version. Requires the corresponding variable (e.g
    `FRACTAL_TASKS_PYTHON_3_10`) to be set.
    """

    FRACTAL_TASKS_PYTHON_3_9: Optional[str] = None
    """
    Absolute path to the Python 3.9 interpreter that serves as base for virtual
    environments tasks. Note that this interpreter must have the `venv` module
    installed. If set, this must be an absolute path. If the version specified
    in `FRACTAL_TASKS_PYTHON_DEFAULT_VERSION` is `"3.9"` and this attribute is
    unset, `sys.executable` is used as a default.
    """

    FRACTAL_TASKS_PYTHON_3_10: Optional[str] = None
    """
    Same as `FRACTAL_TASKS_PYTHON_3_9`, for Python 3.10.
    """

    FRACTAL_TASKS_PYTHON_3_11: Optional[str] = None
    """
    Same as `FRACTAL_TASKS_PYTHON_3_9`, for Python 3.11.
    """

    FRACTAL_TASKS_PYTHON_3_12: Optional[str] = None
    """
    Same as `FRACTAL_TASKS_PYTHON_3_9`, for Python 3.12.
    """

    @root_validator(pre=True)
    def check_tasks_python(cls, values) -> None:
        """
        Perform multiple checks of the Python-intepreter variables.

        1. Each `FRACTAL_TASKS_PYTHON_X_Y` variable must be an absolute path,
            if set.
        2. If `FRACTAL_TASKS_PYTHON_DEFAULT_VERSION` is unset, use
            `sys.executable` and set the corresponding
            `FRACTAL_TASKS_PYTHON_X_Y` (and unset all others).
        """

        # `FRACTAL_TASKS_PYTHON_X_Y` variables can only be absolute paths
        for version in ["3_9", "3_10", "3_11", "3_12"]:
            key = f"FRACTAL_TASKS_PYTHON_{version}"
            value = values.get(key)
            if value is not None and not Path(value).is_absolute():
                raise FractalConfigurationError(
                    f"Non-absolute value {key}={value}"
                )

        default_version = values.get("FRACTAL_TASKS_PYTHON_DEFAULT_VERSION")

        if default_version is not None:
            # "production/slurm" branch
            # If a default version is set, then the corresponding interpreter
            # must also be set
            default_version_undescore = default_version.replace(".", "_")
            key = f"FRACTAL_TASKS_PYTHON_{default_version_undescore}"
            value = values.get(key)
            if value is None:
                msg = (
                    f"FRACTAL_TASKS_PYTHON_DEFAULT_VERSION={default_version} "
                    f"but {key}={value}."
                )
                logging.error(msg)
                raise FractalConfigurationError(msg)

        else:
            # If no default version is set, then only `sys.executable` is made
            # available
            _info = sys.version_info
            current_version = f"{_info.major}_{_info.minor}"
            current_version_dot = f"{_info.major}.{_info.minor}"
            values[
                "FRACTAL_TASKS_PYTHON_DEFAULT_VERSION"
            ] = current_version_dot
            logging.info(
                "Setting FRACTAL_TASKS_PYTHON_DEFAULT_VERSION to "
                f"{current_version_dot}"
            )

            # Unset all existing intepreters variable
            for _version in ["3_9", "3_10", "3_11", "3_12"]:
                key = f"FRACTAL_TASKS_PYTHON_{_version}"
                if _version == current_version:
                    values[key] = sys.executable
                    logging.info(f"Setting {key} to {sys.executable}.")
                else:
                    value = values.get(key)
                    if value is not None:
                        logging.info(
                            f"Setting {key} to None (given: {value}), "
                            "because FRACTAL_TASKS_PYTHON_DEFAULT_VERSION was "
                            "not set."
                        )
                    values[key] = None
        return values

    FRACTAL_SLURM_POLL_INTERVAL: int = 5
    """
    Interval to wait (in seconds) before checking whether unfinished job are
    still running on SLURM (see `SlurmWaitThread` in
    [`clusterfutures`](https://github.com/sampsyo/clusterfutures/blob/master/cfut/__init__.py)).
    """

    FRACTAL_SLURM_SBATCH_SLEEP: float = 0
    """
    Interval to wait (in seconds) between two subsequent `sbatch` calls, when
    running a task that produces multiple SLURM jobs.
    """

    FRACTAL_SLURM_ERROR_HANDLING_INTERVAL: int = 5
    """
    Interval to wait (in seconds) when the SLURM backend does not find an
    output pickle file - which could be due to several reasons (e.g. the SLURM
    job was cancelled or failed, or writing the file is taking long). If the
    file is still missing after this time interval, this leads to a
    `JobExecutionError`.
    """

    FRACTAL_API_SUBMIT_RATE_LIMIT: int = 2
    """
    Interval to wait (in seconds) to be allowed to call again
    `POST api/v1/{project_id}/workflow/{workflow_id}/apply/`
    with the same path and query parameters.
    """

    FRACTAL_RUNNER_TASKS_INCLUDE_IMAGE: str = (
        "Copy OME-Zarr structure;Convert Metadata Components from 2D to 3D"
    )
    """
    `;`-separated list of names for task that require the `metadata["image"]`
    attribute in their input-arguments JSON file.
    """

    FRACTAL_API_V1_MODE: Literal[
        "include", "include_read_only", "exclude"
    ] = "include"
    """
    Whether to include the v1 API.
    """

    FRACTAL_MAX_PIP_VERSION: str = "24.0"
    """
    Maximum value at which to update `pip` before performing task collection.
    """

    ###########################################################################
    # BUSINESS LOGIC
    ###########################################################################
    def check_db(self) -> None:
        """
        Checks that db environment variables are properly set.
        """
        if not self.POSTGRES_DB:
            raise FractalConfigurationError("POSTGRES_DB cannot be None.")

    def check_runner(self) -> None:

        if not self.FRACTAL_RUNNER_WORKING_BASE_DIR:
            raise FractalConfigurationError(
                "FRACTAL_RUNNER_WORKING_BASE_DIR cannot be None."
            )

        info = f"FRACTAL_RUNNER_BACKEND={self.FRACTAL_RUNNER_BACKEND}"
        if self.FRACTAL_RUNNER_BACKEND == "slurm":

            from fractal_server.app.runner.executors.slurm._slurm_config import (  # noqa: E501
                load_slurm_config_file,
            )

            if not self.FRACTAL_SLURM_CONFIG_FILE:
                raise FractalConfigurationError(
                    f"Must set FRACTAL_SLURM_CONFIG_FILE when {info}"
                )
            else:
                if not self.FRACTAL_SLURM_CONFIG_FILE.exists():
                    raise FractalConfigurationError(
                        f"{info} but FRACTAL_SLURM_CONFIG_FILE="
                        f"{self.FRACTAL_SLURM_CONFIG_FILE} not found."
                    )

                load_slurm_config_file(self.FRACTAL_SLURM_CONFIG_FILE)
                if not shutil.which("sbatch"):
                    raise FractalConfigurationError(
                        f"{info} but `sbatch` command not found."
                    )
                if not shutil.which("squeue"):
                    raise FractalConfigurationError(
                        f"{info} but `squeue` command not found."
                    )
        elif self.FRACTAL_RUNNER_BACKEND == "slurm_ssh":
            if self.FRACTAL_SLURM_WORKER_PYTHON is None:
                raise FractalConfigurationError(
                    f"Must set FRACTAL_SLURM_WORKER_PYTHON when {info}"
                )

            from fractal_server.app.runner.executors.slurm._slurm_config import (  # noqa: E501
                load_slurm_config_file,
            )

            if not self.FRACTAL_SLURM_CONFIG_FILE:
                raise FractalConfigurationError(
                    f"Must set FRACTAL_SLURM_CONFIG_FILE when {info}"
                )
            else:
                if not self.FRACTAL_SLURM_CONFIG_FILE.exists():
                    raise FractalConfigurationError(
                        f"{info} but FRACTAL_SLURM_CONFIG_FILE="
                        f"{self.FRACTAL_SLURM_CONFIG_FILE} not found."
                    )

                load_slurm_config_file(self.FRACTAL_SLURM_CONFIG_FILE)
                if not shutil.which("ssh"):
                    raise FractalConfigurationError(
                        f"{info} but `ssh` command not found."
                    )
        else:  # i.e. self.FRACTAL_RUNNER_BACKEND == "local"
            if self.FRACTAL_LOCAL_CONFIG_FILE:
                if not self.FRACTAL_LOCAL_CONFIG_FILE.exists():
                    raise FractalConfigurationError(
                        f"{info} but FRACTAL_LOCAL_CONFIG_FILE="
                        f"{self.FRACTAL_LOCAL_CONFIG_FILE} not found."
                    )

    def check(self):
        """
        Make sure that required variables are set

        This method must be called before the server starts
        """

        if not self.JWT_SECRET_KEY:
            raise FractalConfigurationError("JWT_SECRET_KEY cannot be None")

        if not self.FRACTAL_TASKS_DIR:
            raise FractalConfigurationError("FRACTAL_TASKS_DIR cannot be None")

        self.check_db()
        self.check_runner()

    def get_sanitized(self) -> dict:
        def _must_be_sanitized(string) -> bool:
            if not string.upper().startswith("FRACTAL") or any(
                s in string.upper()
                for s in ["PASSWORD", "SECRET", "PWD", "TOKEN"]
            ):
                return True
            else:
                return False

        sanitized_settings = {}
        for k, v in self.dict().items():
            if _must_be_sanitized(k):
                sanitized_settings[k] = "***"
            else:
                sanitized_settings[k] = v

        return sanitized_settings

COOKIE_EXPIRE_SECONDS: int = 86400 class-attribute instance-attribute

Cookie token lifetime, in seconds.

DB_ECHO: bool = False class-attribute instance-attribute

If True, make database operations verbose.

FRACTAL_API_MAX_JOB_LIST_LENGTH: int = 50 class-attribute instance-attribute

Number of ids that can be stored in the jobsV1 and jobsV2 attributes of app.state.

FRACTAL_API_SUBMIT_RATE_LIMIT: int = 2 class-attribute instance-attribute

Interval to wait (in seconds) to be allowed to call again POST api/v1/{project_id}/workflow/{workflow_id}/apply/ with the same path and query parameters.

FRACTAL_API_V1_MODE: Literal['include', 'include_read_only', 'exclude'] = 'include' class-attribute instance-attribute

Whether to include the v1 API.

FRACTAL_DEFAULT_ADMIN_EMAIL: str = 'admin@fractal.xy' class-attribute instance-attribute

Admin default email, used upon creation of the first superuser during server startup.

⚠️ IMPORTANT: After the server startup, you should always edit the default admin credentials.

FRACTAL_DEFAULT_ADMIN_PASSWORD: str = '1234' class-attribute instance-attribute

Admin default password, used upon creation of the first superuser during server startup.

⚠️ IMPORTANT: After the server startup, you should always edit the default admin credentials.

FRACTAL_DEFAULT_ADMIN_USERNAME: str = 'admin' class-attribute instance-attribute

Admin default username, used upon creation of the first superuser during server startup.

⚠️ IMPORTANT: After the server startup, you should always edit the default admin credentials.

FRACTAL_GRACEFUL_SHUTDOWN_TIME: int = 30 class-attribute instance-attribute

Waiting time for the shutdown phase of executors

FRACTAL_LOCAL_CONFIG_FILE: Optional[Path] instance-attribute

Path of JSON file with configuration for the local backend.

FRACTAL_LOGGING_LEVEL: int = logging.INFO class-attribute instance-attribute

Logging-level threshold for logging

Only logs of with this level (or higher) will appear in the console logs; see details here.

FRACTAL_MAX_PIP_VERSION: str = '24.0' class-attribute instance-attribute

Maximum value at which to update pip before performing task collection.

FRACTAL_RUNNER_BACKEND: Literal['local', 'local_experimental', 'slurm', 'slurm_ssh'] = 'local' class-attribute instance-attribute

Select which runner backend to use.

FRACTAL_RUNNER_TASKS_INCLUDE_IMAGE: str = 'Copy OME-Zarr structure;Convert Metadata Components from 2D to 3D' class-attribute instance-attribute

;-separated list of names for task that require the metadata["image"] attribute in their input-arguments JSON file.

FRACTAL_RUNNER_WORKING_BASE_DIR: Optional[Path] instance-attribute

Base directory for running jobs / workflows. All artifacts required to set up, run and tear down jobs are placed in subdirs of this directory.

FRACTAL_SLURM_CONFIG_FILE: Optional[Path] instance-attribute

Path of JSON file with configuration for the SLURM backend.

FRACTAL_SLURM_ERROR_HANDLING_INTERVAL: int = 5 class-attribute instance-attribute

Interval to wait (in seconds) when the SLURM backend does not find an output pickle file - which could be due to several reasons (e.g. the SLURM job was cancelled or failed, or writing the file is taking long). If the file is still missing after this time interval, this leads to a JobExecutionError.

FRACTAL_SLURM_POLL_INTERVAL: int = 5 class-attribute instance-attribute

Interval to wait (in seconds) before checking whether unfinished job are still running on SLURM (see SlurmWaitThread in clusterfutures).

FRACTAL_SLURM_SBATCH_SLEEP: float = 0 class-attribute instance-attribute

Interval to wait (in seconds) between two subsequent sbatch calls, when running a task that produces multiple SLURM jobs.

FRACTAL_SLURM_WORKER_PYTHON: Optional[str] = None class-attribute instance-attribute

Absolute path to Python interpreter that will run the jobs on the SLURM nodes. If not specified, the same interpreter that runs the server is used.

FRACTAL_TASKS_DIR: Optional[Path] instance-attribute

Directory under which all the tasks will be saved (either an absolute path or a path relative to current working directory).

FRACTAL_TASKS_PYTHON_3_10: Optional[str] = None class-attribute instance-attribute

Same as FRACTAL_TASKS_PYTHON_3_9, for Python 3.10.

FRACTAL_TASKS_PYTHON_3_11: Optional[str] = None class-attribute instance-attribute

Same as FRACTAL_TASKS_PYTHON_3_9, for Python 3.11.

FRACTAL_TASKS_PYTHON_3_12: Optional[str] = None class-attribute instance-attribute

Same as FRACTAL_TASKS_PYTHON_3_9, for Python 3.12.

FRACTAL_TASKS_PYTHON_3_9: Optional[str] = None class-attribute instance-attribute

Absolute path to the Python 3.9 interpreter that serves as base for virtual environments tasks. Note that this interpreter must have the venv module installed. If set, this must be an absolute path. If the version specified in FRACTAL_TASKS_PYTHON_DEFAULT_VERSION is "3.9" and this attribute is unset, sys.executable is used as a default.

FRACTAL_TASKS_PYTHON_DEFAULT_VERSION: Optional[Literal['3.9', '3.10', '3.11', '3.12']] = None class-attribute instance-attribute

Default Python version to be used for task collection. Defaults to the current version. Requires the corresponding variable (e.g FRACTAL_TASKS_PYTHON_3_10) to be set.

JWT_EXPIRE_SECONDS: int = 180 class-attribute instance-attribute

JWT token lifetime, in seconds.

JWT_SECRET_KEY: Optional[str] instance-attribute

JWT secret

⚠️ IMPORTANT: set this variable to a secure string, and do not disclose it.

POSTGRES_DB: Optional[str] instance-attribute

Name of the PostgreSQL database to connect to.

POSTGRES_HOST: Optional[str] = 'localhost' class-attribute instance-attribute

URL to the PostgreSQL server or path to a UNIX domain socket.

POSTGRES_PASSWORD: Optional[str] instance-attribute

Password to use when connecting to the PostgreSQL database.

POSTGRES_PORT: Optional[str] = '5432' class-attribute instance-attribute

Port number to use when connecting to the PostgreSQL server.

POSTGRES_USER: Optional[str] instance-attribute

User to use when connecting to the PostgreSQL database.

absolute_FRACTAL_SLURM_WORKER_PYTHON(v)

If FRACTAL_SLURM_WORKER_PYTHON is a relative path, fail.

Source code in fractal_server/config.py
336
337
338
339
340
341
342
343
344
345
346
347
348
@validator("FRACTAL_SLURM_WORKER_PYTHON", always=True)
def absolute_FRACTAL_SLURM_WORKER_PYTHON(cls, v):
    """
    If `FRACTAL_SLURM_WORKER_PYTHON` is a relative path, fail.
    """
    if v is None:
        return None
    elif not Path(v).is_absolute():
        raise FractalConfigurationError(
            f"Non-absolute value for FRACTAL_SLURM_WORKER_PYTHON={v}"
        )
    else:
        return v

check()

Make sure that required variables are set

This method must be called before the server starts

Source code in fractal_server/config.py
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
def check(self):
    """
    Make sure that required variables are set

    This method must be called before the server starts
    """

    if not self.JWT_SECRET_KEY:
        raise FractalConfigurationError("JWT_SECRET_KEY cannot be None")

    if not self.FRACTAL_TASKS_DIR:
        raise FractalConfigurationError("FRACTAL_TASKS_DIR cannot be None")

    self.check_db()
    self.check_runner()

check_db()

Checks that db environment variables are properly set.

Source code in fractal_server/config.py
504
505
506
507
508
509
def check_db(self) -> None:
    """
    Checks that db environment variables are properly set.
    """
    if not self.POSTGRES_DB:
        raise FractalConfigurationError("POSTGRES_DB cannot be None.")

check_tasks_python(values)

Perform multiple checks of the Python-intepreter variables.

  1. Each FRACTAL_TASKS_PYTHON_X_Y variable must be an absolute path, if set.
  2. If FRACTAL_TASKS_PYTHON_DEFAULT_VERSION is unset, use sys.executable and set the corresponding FRACTAL_TASKS_PYTHON_X_Y (and unset all others).
Source code in fractal_server/config.py
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
@root_validator(pre=True)
def check_tasks_python(cls, values) -> None:
    """
    Perform multiple checks of the Python-intepreter variables.

    1. Each `FRACTAL_TASKS_PYTHON_X_Y` variable must be an absolute path,
        if set.
    2. If `FRACTAL_TASKS_PYTHON_DEFAULT_VERSION` is unset, use
        `sys.executable` and set the corresponding
        `FRACTAL_TASKS_PYTHON_X_Y` (and unset all others).
    """

    # `FRACTAL_TASKS_PYTHON_X_Y` variables can only be absolute paths
    for version in ["3_9", "3_10", "3_11", "3_12"]:
        key = f"FRACTAL_TASKS_PYTHON_{version}"
        value = values.get(key)
        if value is not None and not Path(value).is_absolute():
            raise FractalConfigurationError(
                f"Non-absolute value {key}={value}"
            )

    default_version = values.get("FRACTAL_TASKS_PYTHON_DEFAULT_VERSION")

    if default_version is not None:
        # "production/slurm" branch
        # If a default version is set, then the corresponding interpreter
        # must also be set
        default_version_undescore = default_version.replace(".", "_")
        key = f"FRACTAL_TASKS_PYTHON_{default_version_undescore}"
        value = values.get(key)
        if value is None:
            msg = (
                f"FRACTAL_TASKS_PYTHON_DEFAULT_VERSION={default_version} "
                f"but {key}={value}."
            )
            logging.error(msg)
            raise FractalConfigurationError(msg)

    else:
        # If no default version is set, then only `sys.executable` is made
        # available
        _info = sys.version_info
        current_version = f"{_info.major}_{_info.minor}"
        current_version_dot = f"{_info.major}.{_info.minor}"
        values[
            "FRACTAL_TASKS_PYTHON_DEFAULT_VERSION"
        ] = current_version_dot
        logging.info(
            "Setting FRACTAL_TASKS_PYTHON_DEFAULT_VERSION to "
            f"{current_version_dot}"
        )

        # Unset all existing intepreters variable
        for _version in ["3_9", "3_10", "3_11", "3_12"]:
            key = f"FRACTAL_TASKS_PYTHON_{_version}"
            if _version == current_version:
                values[key] = sys.executable
                logging.info(f"Setting {key} to {sys.executable}.")
            else:
                value = values.get(key)
                if value is not None:
                    logging.info(
                        f"Setting {key} to None (given: {value}), "
                        "because FRACTAL_TASKS_PYTHON_DEFAULT_VERSION was "
                        "not set."
                    )
                values[key] = None
    return values

collect_oauth_clients(values)

Automatic collection of OAuth Clients

This method collects the environment variables relative to a single OAuth client and saves them within the Settings object in the form of an OAuthClientConfig instance.

Fractal can support an arbitrary number of OAuth providers, which are automatically detected by parsing the environment variable names. In particular, to set the provider FOO, one must specify the variables

OAUTH_FOO_CLIENT_ID
OAUTH_FOO_CLIENT_SECRET
...

etc (cf. OAuthClientConfig).

Source code in fractal_server/config.py
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
@root_validator(pre=True)
def collect_oauth_clients(cls, values):
    """
    Automatic collection of OAuth Clients

    This method collects the environment variables relative to a single
    OAuth client and saves them within the `Settings` object in the form
    of an `OAuthClientConfig` instance.

    Fractal can support an arbitrary number of OAuth providers, which are
    automatically detected by parsing the environment variable names. In
    particular, to set the provider `FOO`, one must specify the variables

        OAUTH_FOO_CLIENT_ID
        OAUTH_FOO_CLIENT_SECRET
        ...

    etc (cf. OAuthClientConfig).
    """
    oauth_env_variable_keys = [
        key for key in environ.keys() if key.startswith("OAUTH_")
    ]
    clients_available = {
        var.split("_")[1] for var in oauth_env_variable_keys
    }

    values["OAUTH_CLIENTS_CONFIG"] = []
    for client in clients_available:
        prefix = f"OAUTH_{client}"
        oauth_client_config = OAuthClientConfig(
            CLIENT_NAME=client,
            CLIENT_ID=getenv(f"{prefix}_CLIENT_ID", None),
            CLIENT_SECRET=getenv(f"{prefix}_CLIENT_SECRET", None),
            OIDC_CONFIGURATION_ENDPOINT=getenv(
                f"{prefix}_OIDC_CONFIGURATION_ENDPOINT", None
            ),
            REDIRECT_URL=getenv(f"{prefix}_REDIRECT_URL", None),
        )
        values["OAUTH_CLIENTS_CONFIG"].append(oauth_client_config)
    return values

make_FRACTAL_RUNNER_WORKING_BASE_DIR_absolute(v)

(Copy of make_FRACTAL_TASKS_DIR_absolute) If FRACTAL_RUNNER_WORKING_BASE_DIR is a non-absolute path, make it absolute (based on the current working directory).

Source code in fractal_server/config.py
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
@validator("FRACTAL_RUNNER_WORKING_BASE_DIR", always=True)
def make_FRACTAL_RUNNER_WORKING_BASE_DIR_absolute(cls, v):
    """
    (Copy of make_FRACTAL_TASKS_DIR_absolute)
    If `FRACTAL_RUNNER_WORKING_BASE_DIR` is a non-absolute path,
    make it absolute (based on the current working directory).
    """
    if v is None:
        return None
    FRACTAL_RUNNER_WORKING_BASE_DIR_path = Path(v)
    if not FRACTAL_RUNNER_WORKING_BASE_DIR_path.is_absolute():
        FRACTAL_RUNNER_WORKING_BASE_DIR_path = (
            FRACTAL_RUNNER_WORKING_BASE_DIR_path.resolve()
        )
        logging.warning(
            f'FRACTAL_RUNNER_WORKING_BASE_DIR="{v}" is not an absolute '
            "path; converting it to "
            f'"{str(FRACTAL_RUNNER_WORKING_BASE_DIR_path)}"'
        )
    return FRACTAL_RUNNER_WORKING_BASE_DIR_path

make_FRACTAL_TASKS_DIR_absolute(v)

If FRACTAL_TASKS_DIR is a non-absolute path, make it absolute (based on the current working directory).

Source code in fractal_server/config.py
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
@validator("FRACTAL_TASKS_DIR", always=True)
def make_FRACTAL_TASKS_DIR_absolute(cls, v):
    """
    If `FRACTAL_TASKS_DIR` is a non-absolute path, make it absolute (based
    on the current working directory).
    """
    if v is None:
        return None
    FRACTAL_TASKS_DIR_path = Path(v)
    if not FRACTAL_TASKS_DIR_path.is_absolute():
        FRACTAL_TASKS_DIR_path = FRACTAL_TASKS_DIR_path.resolve()
        logging.warning(
            f'FRACTAL_TASKS_DIR="{v}" is not an absolute path; '
            f'converting it to "{str(FRACTAL_TASKS_DIR_path)}"'
        )
    return FRACTAL_TASKS_DIR_path