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Merge branch 'v.1.2.6'
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@dthoward96
dthoward96 committed Dec 11, 2024
2 parents cf993be + 90c723a commit c01da2e
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Showing 7 changed files with 52 additions and 308 deletions.
170 changes: 18 additions & 152 deletions config/genbank/genbank_flu_src_schema.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,16 +12,6 @@
description="Altitude in metres above or below sea level of where the sample was collected.",
title="Altitude",
),
"src-Authority": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="The author or authors of the organism name from which sequence was obtained.",
title="Authority",
),
"src-Bio_material": Column(
dtype="object",
checks=None,
Expand All @@ -32,26 +22,6 @@
description="An identifier for the biological material from which the nucleotide sequence was obtained, with optional institution code and collection code for the place where it is currently stored. This should be provided using the following format 'institution-code:collection-code:material_id'. material_id is mandatory, institution-code and collection-code are optional; institution-code is mandatory when collection-code is present. This qualifier should be used to annotate the identifiers of material in biological collections which include zoos and aquaria, stock centers, seed banks, germplasm repositories and DNA banks.",
title="Bio_material",
),
"src-Biotype": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="Variety of a species (usually a fungus, bacteria, or virus) characterized by some specific biological property (often geographical, ecological, or physiological). Same as biotype.",
title="Biotype",
),
"src-Biovar": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="See biotype",
title="Biovar",
),
"src-Breed": Column(
dtype="object",
checks=None,
Expand Down Expand Up @@ -82,16 +52,6 @@
description="Type of cell from which sequence was obtained.",
title="Cell_type",
),
"src-Chemovar": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="Variety of a species (usually a fungus, bacteria, or virus) characterized by its biochemical properties.",
title="Chemovar",
),
"src-Clone": Column(
dtype="object",
checks=None,
Expand All @@ -112,15 +72,17 @@
description="Name of person who collected the sample.",
title="Collected_by",
),
"src-Country": Column(
"src-geo_loc_name": Column(
dtype="object",
checks=None,
nullable=True,
checks=[
Check.str_matches(r"^(?!\s*$).+"),
],
nullable=False,
unique=False,
coerce=False,
required=False,
description="The country where the sequence's organism was located. May also be an ocean or major sea. Additional region or locality information must be after the country name and separated by a ':'. For example: USA: Riverview Park, Ripkentown, MD",
title="Country",
required=True,
description="Geographical origin of the sample; use the appropriate name from this list http://www.insdc.org/documents/country-qualifier-vocabulary. Use a colon to separate the country or ocean from more detailed information about the location, eg \"Canada: Vancouver\" or \"Germany: halfway down Zugspitze, Alps\".",
title="Geographic_location",
),
"src-Cultivar": Column(
dtype="object",
Expand Down Expand Up @@ -162,26 +124,6 @@
description="The named ecotype (population adapted to a local habitat) from which sequence was obtained (customarily applied to populations of Arabidopsis thaliana).",
title="Ecotype",
),
"src-Forma": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="The forma (lowest taxonomic unit governed by the nomenclatural codes) of organism from which sequence was obtained. This term is usually applied to plants and fungi.",
title="Forma",
),
"src-Forma_specialis": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="The physiologically distinct form from which sequence was obtained (usually restricted to certain parasitic fungi).",
title="Forma_specialis",
),
"src-Fwd_primer_name": Column(
dtype="object",
checks=None,
Expand Down Expand Up @@ -234,31 +176,25 @@
),
"src-Host": Column(
dtype="object",
checks=None,
nullable=True,
checks=[
Check.str_matches(r"^(?!\s*$).+"),
],
nullable=False,
unique=False,
coerce=False,
required=False,
required=True,
description="When the sequence submission is from an organism that exists in a symbiotic, parasitic, or other special relationship with some second organism, the 'host' modifier can be used to identify the name of the host species.",
title="Host",
),
"src-Identified_by": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="name of the person or persons who identified by taxonomic name the organism from which the sequence was obtained",
title="Identified_by",
),
"src-Isolate": Column(
dtype="object",
checks=None,
nullable=True,
checks=[
Check.str_matches(r"^(?!\s*$).+"),
],
nullable=False,
unique=False,
coerce=False,
required=False,
required=True,
description="Identification or description of the specific individual from which this sequence was obtained.",
title="Isolate",
),
Expand Down Expand Up @@ -302,26 +238,6 @@
description="Any additional information that you wish to provide about the sequence.",
title="Note",
),
"src-Pathovar": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="Variety of a species (usually a fungus, bacteria or virus) characterized by the biological target of the pathogen. Examples include Pseudomonas syringae pathovar tomato and Pseudomonas syringae pathovar tabaci.",
title="Pathovar",
),
"src-Pop_variant": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="name of the population variant from which the sequence was obtained",
title="Pop_variant",
),
"src-Rev_primer_name": Column(
dtype="object",
checks=None,
Expand Down Expand Up @@ -352,16 +268,6 @@
description="name of viral or phage segment sequenced",
title="Segment",
),
"src-Serogroup": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="Variety of a species (usually a fungus, bacteria, or virus) characterized by its antigenic properties. Same as serogroup and serovar.",
title="Serogroup",
),
"src-Serotype": Column(
dtype="object",
checks=None,
Expand Down Expand Up @@ -422,36 +328,6 @@
description="Subspecies of organism from which sequence was obtained.",
title="Sub_species",
),
"src-Subclone": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="Name of subclone from which sequence was obtained.",
title="Subclone",
),
"src-Subtype": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="Subtype of organism from which sequence was obtained.",
title="Subtype",
),
"src-Substrain": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="Sub-strain of organism from which sequence was obtained.",
title="Substrain",
),
"src-Tissue_lib": Column(
dtype="object",
checks=None,
Expand All @@ -472,16 +348,6 @@
description="Type of tissue from which sequence was obtained.",
title="Tissue_type",
),
"src-Type": Column(
dtype="object",
checks=None,
nullable=True,
unique=False,
coerce=False,
required=False,
description="Type of organism from which sequence was obtained.",
title="Type",
),
"src-Variety": Column(
dtype="object",
checks=None,
Expand Down
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