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3ebbb0ccbf
* move common code into server, update tests and makefile remove backend directory, refactor update smoke tests
91 lines
2.9 KiB
Python
91 lines
2.9 KiB
Python
from abc import ABCMeta, abstractmethod
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from server.common.errors import DisabledFeatureError
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from server.common.utils.type_conversion_utils import get_schema_type_hint_of_array
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from server.common.genesets import write_gene_sets_tidycsv
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class Annotations(metaclass=ABCMeta):
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"""baseclass for annotations and gene sets"""
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def __init__(self, config={}):
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self.config = config
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def user_annotations_enabled(self):
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return self.config.get("user-annotations", False)
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def gene_sets_save_enabled(self):
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return self.config.get("genesets-save", False)
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def check_user_annotations_enabled(self):
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if not self.user_annotations_enabled():
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raise DisabledFeatureError("User annotations are disabled.")
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def check_gene_sets_save_enabled(self):
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if not self.gene_sets_save_enabled():
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raise DisabledFeatureError("User gene sets save is disabled.")
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def get_schema(self, data_adaptor):
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schema = []
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labels = self.read_labels(data_adaptor)
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if labels is not None and not labels.empty:
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for col in labels.columns:
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col_schema = dict(name=col, writable=True)
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col_schema.update(get_schema_type_hint_of_array(labels[col]))
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schema.append(col_schema)
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return schema
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@abstractmethod
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def set_collection(self, name):
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"""set or create a new annotation collection"""
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pass
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@abstractmethod
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def read_labels(self, data_adaptor):
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"""Return the labels as a pandas.DataFrame"""
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pass
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@abstractmethod
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def write_labels(self, df, data_adaptor):
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"""Write the labels (df) to a persistent storage such that it can later be read"""
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pass
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@abstractmethod
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def read_gene_sets(self, data_adaptor):
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"""Return the gene sets from persistent storage"""
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pass
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@abstractmethod
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def write_gene_sets(self, gs, data_adaptor):
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"""Write the gene sets (gs) to a persistent storage such that it can later be read"""
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pass
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@abstractmethod
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def update_parameters(self, parameters, data_adaptor):
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"""Update configuration parameters that describe information about the annotations feature"""
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pass
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@staticmethod
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def gene_sets_to_csv(genesets):
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"""
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Convert the internal gene sets format (returned by read_gene_set) into
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the simple Tidy CSV.
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"""
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from io import StringIO
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if isinstance(genesets, dict):
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genesets = genesets.values()
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with StringIO() as sio:
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write_gene_sets_tidycsv(sio, genesets)
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return sio.getvalue()
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@staticmethod
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def gene_sets_to_response(genesets):
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"""
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Convert the internal gene sets format (returned by read_gene_set) into
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the dict expected by the JSON REST API
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"""
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return list(genesets.values())
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