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https://github.com/chanzuckerberg/cellxgene.git
synced 2026-10-06 07:48:11 +08:00
refactor config to support different config options for datasets in different dataroots. (#1596)
This will give us the ability to specify different config options for different dataroots. the key of the dataroot dictionary is no longer the same as the dataroot_url. Previously key==dataroot_url, and now those are separated. Added an "is_multi_dataset" function to simplify logic where it branched on single vs multi. Simplified the rest.py interface by no longer passing in the user annotations object, since that can be retrieved from the dataset.
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@@ -24,11 +24,10 @@ class CxgAdaptor(DataAdaptor):
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{"sm.tile_cache_size": 8 * 1024 * 1024 * 1024, "sm.num_reader_threads": 32, "vfs.s3.region": "us-east-1"}
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)
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def __init__(self, data_locator, config=None):
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super().__init__(config)
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def __init__(self, data_locator, app_config=None, dataset_config=None):
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super().__init__(data_locator, app_config, dataset_config)
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self.lock = threading.Lock()
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self.data_locator = data_locator
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self.url = data_locator.uri_or_path
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if self.url[-1] != "/":
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self.url += "/"
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@@ -66,8 +65,8 @@ class CxgAdaptor(DataAdaptor):
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return 0
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@staticmethod
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def open(data_locator, args):
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return CxgAdaptor(data_locator, args)
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def open(data_locator, app_config, dataset_config=None):
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return CxgAdaptor(data_locator, app_config, dataset_config)
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def get_about(self):
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return self.about if self.about else super().get_about()
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@@ -75,12 +74,6 @@ class CxgAdaptor(DataAdaptor):
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def get_title(self):
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return self.title if self.title else super().get_title()
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def get_location(self):
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return self.url
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def get_data_locator(self):
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return self.data_locator
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def get_name(self):
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return "cellxgene cxg adaptor version"
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@@ -196,9 +189,9 @@ class CxgAdaptor(DataAdaptor):
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def compute_diffexp_ttest(self, maskA, maskB, top_n=None, lfc_cutoff=None):
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if top_n is None:
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top_n = self.config.diffexp__top_n
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top_n = self.dataset_config.diffexp__top_n
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if lfc_cutoff is None:
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lfc_cutoff = self.config.diffexp__lfc_cutoff
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lfc_cutoff = self.dataset_config.diffexp__lfc_cutoff
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return diffexp_cxg.diffexp_ttest(self, maskA, maskB, top_n, lfc_cutoff)
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def get_colors(self):
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