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Code Issues Packages Projects Releases Wiki Activity

config refactor (#1854)

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* split out config

* add tests for base and app config, refactor client config out of app config

* refactor default config retrieval

* create config test class and helper functions

* move default_config into server to fix import issue
This commit is contained in:
Madison Dunitz
2020-09-29 16:42:46 -05:00
committed by GitHub
parent 1145f61c78
commit af3c6e1d8e
57 changed files with 2667 additions and 1599 deletions
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server/common/annotations/hosted_tiledb.py
+9 -8
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@@ -31,7 +31,8 @@ class AnnotationsHostedTileDB(Annotations):
unsanitary_original_category_names = set(original_category_names).difference(sanitized_category_names)
if unsanitary_original_category_names:
raise AnnotationCategoryNameError(
f"{unsanitary_original_category_names} are not valid category names, please resubmit")
f"{unsanitary_original_category_names} are not valid category names, please resubmit"
)
def is_safe_collection_name(self, name):
"""
@@ -68,11 +69,11 @@ class AnnotationsHostedTileDB(Annotations):
index_dims = None
schema_hints = json.loads(schema_hints)
if '__pandas_attribute_repr' in tileDBArray.meta:
if "__pandas_attribute_repr" in tileDBArray.meta:
# backwards compatibility... unsure if necessary at this point
repr_meta = json.loads(tileDBArray.meta['__pandas_attribute_repr'])
if '__pandas_index_dims' in tileDBArray.meta:
index_dims = json.loads(tileDBArray.meta['__pandas_index_dims'])
repr_meta = json.loads(tileDBArray.meta["__pandas_attribute_repr"])
if "__pandas_index_dims" in tileDBArray.meta:
index_dims = json.loads(tileDBArray.meta["__pandas_index_dims"])
data = tileDBArray[:]
indexes = list()
@@ -80,12 +81,12 @@ class AnnotationsHostedTileDB(Annotations):
for col_name, col_val in data.items():
# If the column values are byte literals, decode them
if isinstance(col_val[0], bytes):
col_val = [value.decode('utf-8') for value in col_val]
col_val = [value.decode("utf-8") for value in col_val]
if schema_hints and col_name in schema_hints:
type = schema_hints.get(col_name).get("type")
if type and type == "categorical":
new_col = pd.Series(col_val, dtype='category')
new_col = pd.Series(col_val, dtype="category")
data[col_name] = new_col
elif repr_meta and col_name in repr_meta:
new_col = pd.Series(col_val, dtype=repr_meta[col_name])
@@ -127,7 +128,7 @@ class AnnotationsHostedTileDB(Annotations):
tiledb_uri=uri,
user_id=user_id,
dataset_id=str(dataset_id),
schema_hints=json.dumps(dataframe_schema_type_hints)
schema_hints=json.dumps(dataframe_schema_type_hints),
)
if not df.empty:
self.check_category_names(df)