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hosted gene sets routes, plus a few bug fixes (#2155)

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* first cut at hosted gs routes

* lint

* update tests to match csv parser changes

* update tests to new API

* update gene set name validation rules to match requirements

* add path mapping from dataset to geneset

* add test cases for geneset GET route

* fix test assertion

* remove debugging code

* update gene set uri mapping function

* fix error message

* allow extra user-specified headers in gene set csv file

* clarify comment
This commit is contained in:
Bruce Martin
2021-04-27 13:58:58 -07:00
committed by GitHub
parent ebeb1c8818
commit f2e9aecebe
19 changed files with 702 additions and 267 deletions
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backend/server/data_common/data_adaptor.py
+2 -89
View File
@@ -1,6 +1,5 @@
from abc import ABCMeta, abstractmethod
from os.path import basename, splitext
import re
import numpy as np
import pandas as pd
from scipy import sparse
@@ -11,6 +10,7 @@ from backend.common.constants import Axis
from backend.common.errors import FilterError, JSONEncodingValueError, ExceedsLimitError, UnsupportedSummaryMethod
from backend.common.utils.utils import jsonify_numpy
from backend.common.fbs.matrix import encode_matrix_fbs
from backend.common.genesets import validate_gene_sets
class DataAdaptor(metaclass=ABCMeta):
@@ -263,95 +263,8 @@ class DataAdaptor(metaclass=ABCMeta):
return labels_df
def check_new_gene_sets(self, genesets, context=None):
"""
Check validity of gene sets, return if correct, else raise error.
May also modify the gene set for conditions that should be resolved,
but which do not warrant a hard error.
Argument genesets may be either the REST OTA format (list of dicts) or the internal
format (dict of dicts, keyed by the geneset name).
Will return a modified genesets (eg, remove dups) of the same type as the
provided argument. Ie, dict->dict, list->list
Rules:
0. all geneset names must be unique.
1. All geneset names must be comprised of legal characters, meaning:
* no leading or trailing white space
* no multi-space runs
* no tab, vertical tab, newline or return
Where "space" means ASCII 32. Generates hard error.
2. Gene symbols must be part of the current var_index. If symbol not in var_index,
will generate a warning and the symbol removed.
3. Duplicate gene symbols are silently de-duped.
"""
messagefn = context["messagefn"] if context else (lambda x: None)
# accept genesets args as either the internal (dict) or REST (list) format,
# as they are identical except for the dict being keyed by geneset_name.
if not isinstance(genesets, dict) and not isinstance(genesets, list):
raise ValueError("Genesets must be either dict or list.")
genesets_iterable = genesets if isinstance(genesets, list) else genesets.values()
# 0. check for uniqueness of geneset names
geneset_names = [gs["geneset_name"] for gs in genesets_iterable]
if len(set(geneset_names)) != len(geneset_names):
raise KeyError("All geneset names must be unique.")
# 1. check gene set character set and format
illegal_name = re.compile(r"^\s| |[\v\t\r\n]|\s$")
for name in geneset_names:
if type(name) != str or len(name) == 0:
raise KeyError("Geneset names must be non-null string.")
if illegal_name.search(name):
messagefn(
"Error: "
f"Geneset name {name} "
"is not valid. Leading, trailing, and multiple spaces within a name are not allowed."
)
raise KeyError(
"Geneset name is not valid. Leading, trailing, and multiple spaces within a name are not allowed."
)
# 2. & 3. check for duplicate gene symbols, and those not present in the dataset. They will
# generate a warning and be removed.
var_names = set(self.query_var_array(self.parameters.get("var_names")))
for geneset in genesets_iterable:
if not isinstance(geneset, dict):
raise ValueError("Each geneset must be a dict.")
geneset_name = geneset["geneset_name"]
genes = geneset["genes"]
if not isinstance(genes, list):
raise ValueError("Geneset genes field must be a list")
geneset.setdefault("geneset_description", "")
gene_symbol_already_seen = set()
new_genes = []
for gene in genes:
gene_symbol = gene["gene_symbol"]
if not isinstance(gene_symbol, str) or len(gene_symbol) == 0:
raise ValueError("Gene symbol must be non-null string.")
if gene_symbol in gene_symbol_already_seen:
# duplicate check
messagefn(
f"Warning: a duplicate of gene {gene_symbol} was found in geneset {geneset_name}, "
"and will be ignored."
)
continue
if gene_symbol not in var_names:
messagefn(
f"Warning: {gene_symbol}, used in geneset {geneset_name}, "
"was not found in the dataset and will be ignored."
)
continue
gene_symbol_already_seen.add(gene_symbol)
gene.setdefault("gene_description", "")
new_genes.append(gene)
geneset["genes"] = new_genes
return genesets
return validate_gene_sets(genesets, var_names)
def data_frame_to_fbs_matrix(self, filter, axis):
"""