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Code Issues Packages Projects Releases Wiki Activity

initial support for corpora schema conventions (#1676)

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* initial support for corpora schema conventions

* remove debugging print

* add corpora util module

* tests

* lint

* PR review edits

* PR changes

* more PR changes

* more PR chnages

* PR fixes

* formatting

* PR updates

* lint

* PR review
This commit is contained in:
Bruce Martin
2020-07-28 17:32:27 -07:00
committed by GitHub
parent 5285556415
commit 59f989d26f
12 changed files with 450 additions and 104 deletions
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server/data_cxg/cxg_adaptor.py
+12 -4
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@@ -74,6 +74,9 @@ class CxgAdaptor(DataAdaptor):
def get_title(self):
return self.title if self.title else super().get_title()
def get_corpora_props(self):
return self.corpora_props if self.corpora_props else super().get_corpora_props()
def get_name(self):
return "cellxgene cxg adaptor version"
@@ -144,26 +147,31 @@ class CxgAdaptor(DataAdaptor):
* version 0.1 -- metadata attache to cxg_group_metadata array.
Same as 0, except it adds group metadata.
"""
title = None
about = None
corpora_props = None
if self.has_array("cxg_group_metadata"):
# version >0
gmd = self.open_array("cxg_group_metadata")
cxg_version = gmd.meta["cxg_version"]
if cxg_version == "0.1":
# version 0.1 used a malformed/shorthand semver string.
if cxg_version == "0.1" or cxg_version == "0.2.0":
cxg_properties = json.loads(gmd.meta["cxg_properties"])
title = cxg_properties.get("title", None)
about = cxg_properties.get("about", None)
if cxg_version == "0.2.0":
corpora_props = json.loads(gmd.meta["corpora"]) if "corpora" in gmd.meta else None
else:
# version 0
cxg_version = "0.0"
title = None
about = None
if cxg_version not in ["0.0", "0.1"]:
if cxg_version not in ["0.0", "0.1", "0.2.0"]:
raise DatasetAccessError(f"cxg matrix is not valid: {self.url}")
self.title = title
self.about = about
self.cxg_version = cxg_version
self.corpora_props = corpora_props
@staticmethod
def _open_array(uri, tiledb_ctx):