-
Notifications
You must be signed in to change notification settings - Fork 4
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* initial config * passes tests, but does it work? * rename config funcs and bugfix * initial config * passes tests, but does it work? * rename config funcs and bugfix * test and continue site_utils work * add env variable for default datastack name * tests and tweaks
- Loading branch information
Showing
12 changed files
with
406 additions
and
138 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,5 @@ | ||
| from nglui.easyviewer import EasyViewer | ||
| from . import parser, segmentprops, statebuilder | ||
|
|
||
| from . import parser, segmentprops, statebuilder | ||
|
|
||
| __version__ = "3.5.2" |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,222 @@ | ||
| import logging | ||
| import os | ||
| from typing import Literal, Optional | ||
|
|
||
| import attrs | ||
| import caveclient | ||
|
|
||
| logger = logging.getLogger(__name__) | ||
|
|
||
| MAINLINE_NAMES = ["spelunker", "mainline", "cave-explorer"] | ||
| SEUNGLAB_NAMES = ["seunglab"] | ||
| default_seunglab_neuroglancer_base = "https://neuromancer-seung-import.appspot.com/" | ||
| default_mainline_neuroglancer_base = "https://spelunker.cave-explorer.org/" | ||
|
|
||
| DEFAULT_TARGET_SITE = os.environ.get("NGLUI_DEFAULT_TARGET_SITE", "seunglab") | ||
| DEFAULT_URL = os.environ.get("NGLUI_DEFAULT_TARGET_URL", None) | ||
| DEFAULT_DATASTACK_NAME = os.environ.get("NGLUI_DEFAULT_DATASTACK_NAME", None) | ||
|
|
||
| __all__ = [ | ||
| "is_mainline", | ||
| "is_seunglab", | ||
| "check_target_site", | ||
| "set_default_config", | ||
| "get_default_config", | ||
| "reset_default_config", | ||
| MAINLINE_NAMES, | ||
| SEUNGLAB_NAMES, | ||
| ] | ||
|
|
||
|
|
||
| def is_mainline(target_name): | ||
| return target_name in MAINLINE_NAMES | ||
|
|
||
|
|
||
| def is_seunglab(target_name): | ||
| return target_name in SEUNGLAB_NAMES | ||
|
|
||
|
|
||
| def check_target_site(ngl_url, client): | ||
| """ | ||
| Check neuroglancer info to determine which kind of site a neuroglancer URL is. | ||
| """ | ||
| ngl_info = client.state.get_neuroglancer_info(ngl_url) | ||
| if len(ngl_info) == 0: | ||
| return SEUNGLAB_NAMES[0] | ||
| else: | ||
| return MAINLINE_NAMES[0] | ||
|
|
||
|
|
||
| @attrs.define | ||
| class NGLUIConfig: | ||
| target_site = attrs.field(type=str) | ||
| target_url = attrs.field(type=str) | ||
| seunglab_fallback_url = attrs.field( | ||
| default=default_seunglab_neuroglancer_base, type=str | ||
| ) | ||
| mainline_fallback_url = attrs.field( | ||
| default=default_mainline_neuroglancer_base, type=str | ||
| ) | ||
| caveclient = attrs.field(default=None) | ||
| datastack_name = attrs.field(default=DEFAULT_DATASTACK_NAME, type=str) | ||
|
|
||
| def __attrs_post_init__(self): | ||
| # validate target site | ||
| if ( | ||
| self.target_site not in MAINLINE_NAMES + SEUNGLAB_NAMES | ||
| and self.target_site is not None | ||
| ): | ||
| raise ValueError( | ||
| f"target_site must be one of {MAINLINE_NAMES + SEUNGLAB_NAMES}" | ||
| ) | ||
| # Set and validate caveclient if info is provided | ||
| if self.caveclient is None and self.datastack_name is not None: | ||
| try: | ||
| self.caveclient = caveclient.CAVEclient(self.datastack_name) | ||
| except Exception as e: | ||
| msg = f"Could not create CAVEclient with datastack_name {self.datastack_name}: {e}" | ||
| logger.error(msg) | ||
| if self.caveclient is not None and self.datastack_name is None: | ||
| self.datastack_name = self.caveclient.datastack_name | ||
| if self.datastack_name is not None and self.caveclient is not None: | ||
| if self.caveclient.datastack_name != self.datastack_name: | ||
| raise ValueError( | ||
| f"CAVEclient datastack_name {self.caveclient.datastack_name} does not match provided datastack_name {self.datastack_name}" | ||
| ) | ||
|
|
||
| # Set and validate target_url if target_site is provided | ||
| if self.target_url is not None and self.target_site is None: | ||
| self.target_site = check_target_site(self.target_url, self.caveclient) | ||
| if self.target_site is not None and self.target_url is None: | ||
| if is_seunglab(self.target_site): | ||
| self.target_url = self.seunglab_fallback_url | ||
| else: | ||
| self.target_url = self.mainline_fallback_url | ||
| if self.target_site is not None and self.target_url is not None: | ||
| if self.caveclient is not None: | ||
| url_based_site = check_target_site(self.target_url, self.caveclient) | ||
| if is_mainline(url_based_site) != is_mainline(self.target_site): | ||
| logging.warning( | ||
| f"target_site {self.target_site} does not match target_url {self.target_url}. Assuming manual setting is correct." | ||
| ) | ||
|
|
||
|
|
||
| default_config = NGLUIConfig( | ||
| target_site=DEFAULT_TARGET_SITE, | ||
| target_url=DEFAULT_URL, | ||
| ) | ||
| default_key = "default" | ||
| NGL_CONFIG = {default_key: default_config} # type: dict[str, NGLUIConfig] | ||
|
|
||
|
|
||
| def get_default_config(config_key: str = None): | ||
| """Get the current configuration for nglui viewers and statebuilders. | ||
| Parameters | ||
| ---------- | ||
| config_key : str, optional | ||
| Key for the configuration setting, by default "default" | ||
| """ | ||
| if config_key is None: | ||
| config_key = default_key | ||
| return attrs.asdict(NGL_CONFIG[config_key]) | ||
|
|
||
|
|
||
| def set_default_config( | ||
| target_site: Optional[ | ||
| Literal["seunglab", "mainline", "cave-explorer", "spelunker"] | ||
| ] = None, | ||
| target_url: str = None, | ||
| seunglab_fallback_url: str = None, | ||
| mainline_fallback_url: str = None, | ||
| datastack_name: str = None, | ||
| caveclient: "caveclient.CAVEclient" = None, | ||
| url_from_client: bool = False, | ||
| config_key: str = "default", | ||
| ): | ||
| """Set default configuration for nglui viewers and statebuilders. | ||
| Parameters | ||
| ---------- | ||
| target_site : str, optional | ||
| Target site for the neuroglancer viewer, by default None | ||
| target_url : str, optional | ||
| Target URL for the neuroglancer viewer, by default None | ||
| seunglab_url : str, optional | ||
| URL for the seunglab neuroglancer viewer, by default None | ||
| mainline_url : str, optional | ||
| URL for the mainline neuroglancer viewer, by default None | ||
| datastack_name : str, optional | ||
| Name of the datastack, by default None | ||
| caveclient : caveclient.CAVEclient, optional | ||
| CAVEclient object, by default None. | ||
| """ | ||
| if config_key in NGL_CONFIG: | ||
| curr_config = get_default_config(config_key) | ||
| else: | ||
| curr_config = attrs.asdict(default_config) | ||
| if target_site is not None or target_url is not None: | ||
| curr_config["target_site"] = target_site | ||
| curr_config["target_url"] = target_url | ||
| if seunglab_fallback_url is not None: | ||
| curr_config["seunglab_fallback_url"] = seunglab_fallback_url | ||
| if mainline_fallback_url is not None: | ||
| curr_config["mainline_fallback_url"] = mainline_fallback_url | ||
| if caveclient is not None or datastack_name is not None: | ||
| curr_config["caveclient"] = caveclient | ||
| curr_config["datastack_name"] = datastack_name | ||
| if url_from_client: | ||
| curr_config["target_site"] = None | ||
| curr_config["target_url"] = caveclient.info.viewer_site() | ||
| NGL_CONFIG[config_key] = NGLUIConfig(**curr_config) | ||
|
|
||
|
|
||
| def reset_config( | ||
| config_key: str = "default", | ||
| ): | ||
| """Reset the configuration for nglui viewers and statebuilders to the default. | ||
| Parameters | ||
| ---------- | ||
| config_key : str, optional | ||
| Key for the configuration setting, by default "default" | ||
| """ | ||
| NGL_CONFIG[config_key] = default_config | ||
|
|
||
|
|
||
| def neuroglancer_url( | ||
| url: Optional[str] = None, | ||
| target_site: Optional[str] = None, | ||
| config_key: str = "default", | ||
| ): | ||
| """ | ||
| Check neuroglancer info to determine which kind of site a neuroglancer URL is. | ||
| If either url or target_site are provided, it will use these values, looking up target site | ||
| from the fallback values in the config. Otherwise, it falls back to the value of | ||
| "target_url" in the config. | ||
| Parameters | ||
| ---------- | ||
| url : str, optional | ||
| URL to check, by default None | ||
| target_site : str, optional | ||
| Target site to check, by default None | ||
| Returns | ||
| ------- | ||
| str | ||
| URL of the neuroglancer viewer | ||
| """ | ||
| if url is not None: | ||
| return url | ||
| if target_site is None: | ||
| url = get_default_config(config_key)["target_url"] | ||
| elif is_seunglab(target_site): | ||
| url = get_default_config(config_key)["seunglab_fallback_url"] | ||
| else: | ||
| url = get_default_config(config_key)["mainline_fallback_url"] | ||
| return url | ||
|
|
||
|
|
||
| def reset_default_config(): | ||
| NGL_CONFIG[default_key] = default_config |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.