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9089fc98f2
* Switch logic from `--annotations` to `--disable-annotations * Rename `--annotations-file` --> `--annotations-input-file` and remove `experimental` * update docs * update makefile * update tests * Disable annotations on standard client smoke test * Update docs/posts/annotations.md Co-Authored-By: Matt Weiden <538456+mweiden@users.noreply.github.com> * Update docs/posts/annotations.md * Renaming * Docs * Update tests * Pesky typo -_- Co-authored-by: Matt Weiden <538456+mweiden@users.noreply.github.com>
134 lines
4.0 KiB
Python
134 lines
4.0 KiB
Python
# -*- coding: utf-8 -*-
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from server import __version__ as cellxgene_version
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class AppFeature(object):
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def __init__(self, path, available=False, method="POST", extra={}):
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self.path = path
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self.available = available
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self.method = method
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self.extra = extra
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for k, v in extra.items():
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setattr(self, k, v)
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def todict(self):
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d = dict(available=self.available, method=self.method, path=self.path)
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d.update(self.extra)
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return d
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class AppConfig(object):
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def __init__(self, **kw):
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super().__init__()
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# app inputs
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self.datapath = None
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self.dataroot = None
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self.title = ""
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self.about = None
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self.scripts = []
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self.layout = []
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self.max_category_items = 100
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self.diffexp_lfc_cutoff = 0.01
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self.disable_diffexp = False
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self.enable_reembedding = False
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self.anndata_backed = False
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# TODO these options may not apply to all datasets in the multi dataset.
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# may need to invent a way to associate these config parameters with
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# specific datasets.
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self.obs_names = None
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self.var_names = None
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# parameters
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self.diffexp_may_be_slow = False
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inputs = [
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"datapath",
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"dataroot",
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"title",
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"about",
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"scripts",
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"layout",
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"max_category_items",
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"diffexp_lfc_cutoff",
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"obs_names",
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"var_names",
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"anndata_backed",
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"disable_diffexp",
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"enable_reembedding",
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]
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self.update(inputs, kw)
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def update(self, inputs, kw):
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for k, v in kw.items():
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if k in inputs:
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setattr(self, k, v)
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else:
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raise RuntimeError(f"unknown config parameter {k}.")
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def get_title(self, data_adaptor):
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return self.title if self.title else data_adaptor.get_title()
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def get_about(self, data_adaptor):
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return self.about if self.about else data_adaptor.get_about()
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def get_config(self, data_adaptor, annotation=None):
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# FIXME The current set of config is not consistently presented:
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# we have camalCase, hyphen-text, and underscore_text
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# features
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features = [f.todict() for f in data_adaptor.get_features(annotation)]
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# display_names
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title = self.get_title(data_adaptor)
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about = self.get_about(data_adaptor)
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display_names = dict(engine=data_adaptor.get_name(), dataset=title)
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# library_versions
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library_versions = {}
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library_versions.update(data_adaptor.get_library_versions())
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library_versions["cellxgene"] = cellxgene_version
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# links
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links = {"about-dataset": about}
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# parameters
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parameters = {
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"layout": self.layout,
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"max-category-items": self.max_category_items,
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"obs_names": self.obs_names,
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"var_names": self.var_names,
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"diffexp_lfc_cutoff": self.diffexp_lfc_cutoff,
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"backed": self.anndata_backed,
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"disable-diffexp": self.disable_diffexp,
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"enable-reembedding": self.enable_reembedding,
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"annotations": False,
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"annotations_file": None,
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"annotations_dir": None,
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"annotations_cell_ontology_enabled": False,
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"annotations_cell_ontology_obopath": None,
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"annotations_cell_ontology_terms": None,
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"diffexp-may-be-slow": False,
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}
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data_adaptor.update_parameters(parameters)
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if annotation:
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annotation.update_parameters(parameters, data_adaptor)
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# gather it all together
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c = {}
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config = c["config"] = {}
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config["features"] = features
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config["displayNames"] = display_names
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config["library_versions"] = library_versions
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config["links"] = links
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config["parameters"] = parameters
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return c
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