-
Notifications
You must be signed in to change notification settings - Fork 46
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #70 from openvar/develop_2_0
begin creating fast validation endpoints - currently variants in jour…
- Loading branch information
Showing
5 changed files
with
289 additions
and
4 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,282 @@ | ||
| # Import modules | ||
| from flask_restplus import Namespace, Resource | ||
| from . import request_parser | ||
| from . import representations | ||
|
|
||
| # Import variantFormatter | ||
| import VariantFormatter | ||
| import VariantFormatter.simpleVariantFormatter | ||
| import VariantValidator | ||
| vval = VariantValidator.Validator() | ||
|
|
||
| """ | ||
| Create a list containing common warnings which are not errors | ||
| """ | ||
| my_warnings = [ | ||
| "A more recent version of the selected reference sequence", | ||
| "No transcripts found that fully overlap the described variation", | ||
| "is pending therefore changes may be made to the LRG reference sequence", | ||
| "This coding sequence variant description spans at least one intron", | ||
| "RefSeqGene record not available", | ||
| "automapped to equivalent RefSeq record", | ||
| "Protein level variant descriptions are not fully supported", | ||
| "is HGVS compliant and contains a valid reference amino acid description" | ||
| ] | ||
|
|
||
|
|
||
| """ | ||
| Create a parser object locally | ||
| """ | ||
| parser = request_parser.parser | ||
|
|
||
| api = Namespace('VariantsInJournals', description='Endpoints to ensure variants submitted to journals are validated') | ||
|
|
||
|
|
||
| @api.route("/transcript_descriptions/<string:genome_build>/<string:variant_description>") | ||
| @api.param("variant_description", "***HGVS***\n" | ||
| "> - NM_000088.3:c.589G>T\n" | ||
| "> - LRG_1t1:c.589G>T\n" | ||
| "> - *Recommended maximum is 60 variants per submission*\n") | ||
| @api.param("genome_build", "***Accepted:***\n" | ||
| "> - GRCh37\n" | ||
| "> - GRCh38\n" | ||
| "> - hg19\n" | ||
| "> - hg38") | ||
| class VariantValidatorClass(Resource): | ||
| # Add documentation about the parser | ||
| @api.expect(parser, validate=True) | ||
| def get(self, genome_build, variant_description): | ||
|
|
||
| # List the submitted descriptions and the allowed reference sequence types | ||
| description_list = variant_description.split() | ||
| allowed_references = ["NM_", | ||
| "NR_", | ||
| "ENST", | ||
| "NP_", | ||
| "ENSP", | ||
| "t", | ||
| "p"] | ||
|
|
||
| # Check correct variant type (Currently transcript but also accepts Protein | ||
| # even though we do not advertise this | ||
| variant_description_outs = [] | ||
| for description in description_list: | ||
| for reference in allowed_references: | ||
| if reference in description: | ||
| variant_description_outs.append(description) | ||
| variant_description = "|".join(variant_description_outs) | ||
|
|
||
| # Refresh the content | ||
| refreshed_content = {} | ||
| if variant_description is "": | ||
| refreshed_content = {"error": "Unsupported variant type"} | ||
| else: | ||
| # Validate using the VariantValidator Python Library | ||
| validate = vval.validate(variant_description, genome_build, select_transcripts='all') | ||
| content = validate.format_as_dict(with_meta=True) | ||
|
|
||
| # Collect Arguments | ||
| args = parser.parse_args() | ||
| for k, v in content.items(): | ||
| if k is "metadata": | ||
| refreshed_content[k] = v | ||
| elif k is "flag": | ||
| continue | ||
| else: | ||
| refreshed_content[v["submitted_variant"]] = {} | ||
| refreshed_content[v["submitted_variant"]]['pass'] = False | ||
| refreshed_content[v["submitted_variant"]]['errors'] = [] | ||
| refreshed_content[v["submitted_variant"]]['correction'] = None | ||
|
|
||
| # Handle transcript variant inputs | ||
| if "p." not in v["submitted_variant"]: | ||
| # Filter the errors/warnings i.e. removing any warnings that are not actual errors | ||
| # Warnings which are not errors are contained in the my_warnings list | ||
| error_found = [] | ||
| if v["validation_warnings"] is not []: | ||
| for warning in v["validation_warnings"]: | ||
| safe_found = False | ||
| for safe in my_warnings: | ||
| if safe in warning: | ||
| safe_found = True | ||
| break | ||
| if safe_found is False: | ||
| error_found.append(warning) | ||
| refreshed_content[v["submitted_variant"]]['errors'] = error_found | ||
|
|
||
| # Is the input == to the output? | ||
| if "LRG" not in v["submitted_variant"]: | ||
| if v["submitted_variant"] == v["hgvs_transcript_variant"]: | ||
| refreshed_content[v["submitted_variant"]]['pass'] = True | ||
| else: | ||
| refreshed_content[v["submitted_variant"]]['correction'] = v["hgvs_transcript_variant"] | ||
| else: | ||
| if v["submitted_variant"] == v["hgvs_lrg_transcript_variant"]: | ||
| refreshed_content[v["submitted_variant"]]['pass'] = True | ||
| else: | ||
| refreshed_content[v["submitted_variant"]]['correction'] = v["hgvs_lrg_transcript" | ||
| "_variant"] | ||
|
|
||
| else: | ||
| # Filter the errors/warnings i.e. removing any warnings that are not actual errors | ||
| # Warnings which are not errors are contained in the my_warnings list | ||
| error_found = [] | ||
| if v["validation_warnings"] is not []: | ||
| for warning in v["validation_warnings"]: | ||
| safe_found = False | ||
| for safe in my_warnings: | ||
| if safe in warning: | ||
| safe_found = True | ||
| break | ||
| if safe_found is False: | ||
| error_found.append(warning) | ||
| refreshed_content[v["submitted_variant"]]['errors'] = error_found | ||
|
|
||
| # Is the input == to the output? | ||
| if "LRG" not in v["submitted_variant"]: | ||
| if v["submitted_variant"] == v["hgvs_predicted_protein_consequence"]["tlr"]: | ||
| refreshed_content[v["submitted_variant"]]['pass'] = True | ||
| elif v["submitted_variant"] == v["hgvs_predicted_protein_consequence"]["slr"]: | ||
| refreshed_content[v["submitted_variant"]]['pass'] = True | ||
| else: | ||
| if v["hgvs_predicted_protein_consequence"]["tlr"] != "": | ||
| refreshed_content[v["submitted_variant"]]['correction'] = v[ | ||
| "hgvs_predicted_protein_consequence"]["tlr"] | ||
| else: | ||
| refreshed_content[v["submitted_variant"]]['correction'] = None | ||
| else: | ||
| if v["submitted_variant"] == v["hgvs_predicted_protein_consequence"]["lrg_tlr"]: | ||
| refreshed_content[v["submitted_variant"]]['pass'] = True | ||
| elif v["submitted_variant"] == v["hgvs_predicted_protein_consequence"]["lrg_slr"]: | ||
| refreshed_content[v["submitted_variant"]]['pass'] = True | ||
| else: | ||
| if v["hgvs_predicted_protein_consequence"]["lrg_tlr"] != "": | ||
| refreshed_content[v["submitted_variant"]]['correction'] = v[ | ||
| "hgvs_predicted_protein_consequence"]["lrg_tlr"] | ||
| else: | ||
| refreshed_content[v["submitted_variant"]]['correction'] = None | ||
|
|
||
| # Overrides the default response route so that the standard HTML URL can return any specified format | ||
| if args['content-type'] == 'application/json': | ||
| # example: http://127.0.0.1:5000.....bob?content-type=application/json | ||
| return representations.application_json(refreshed_content, 200, None) | ||
| # example: http://127.0.0.1:5000.....?content-type=application/xml | ||
| elif args['content-type'] == 'application/xml': | ||
| return representations.xml(refreshed_content, 200, None) | ||
| else: | ||
| # Return the api default output | ||
| return refreshed_content | ||
|
|
||
|
|
||
| @api.route("/genomic_descriptions/<string:genome_build>/<string:variant_description>/<string:transcript_model>") | ||
| @api.param("variant_description", "***Genomic HGVS***\n" | ||
| "> - NC_000017.10:g.48275363C>A\n" | ||
| "> - *Recommended maximum is 60 variants per submission*\n") | ||
| @api.param("transcript_model", "***Accepted:***\n" | ||
| "> - refseq (return data for RefSeq transcript models)\n" | ||
| "> - all (currently refseq only)") | ||
| @api.param("genome_build", "***Accepted:***\n" | ||
| "> - GRCh37\n" | ||
| "> - GRCh38\n" | ||
| "> - hg19\n" | ||
| "> - hg38\n") | ||
| class LOVDClass(Resource): | ||
| # Add documentation about the parser | ||
| @api.expect(parser, validate=True) | ||
| def get(self, genome_build, variant_description, transcript_model): | ||
| if transcript_model == 'None' or transcript_model == 'none': | ||
| transcript_model = None | ||
| select_transcripts = None | ||
| checkonly = True | ||
| liftover = False | ||
|
|
||
| # List the submitted descriptions and the allowed reference sequence types | ||
| description_list = variant_description.split() | ||
| allowed_references = ["NC_", | ||
| "NG_"] | ||
|
|
||
| # Check correct variant type (Currently transcript but also accepts Protein | ||
| # even though we do not advertise this | ||
| variant_description_outs = [] | ||
| for description in description_list: | ||
| for reference in allowed_references: | ||
| if reference in description: | ||
| variant_description_outs.append(description) | ||
| variant_description = "|".join(variant_description_outs) | ||
|
|
||
| # Refresh the content | ||
| refreshed_content = {} | ||
| if variant_description is "": | ||
| refreshed_content = {"error": "Unsupported variant type"} | ||
| else: | ||
| # Validate using the VariantValidator Python Library | ||
| content = VariantFormatter.simpleVariantFormatter.format(variant_description, | ||
| genome_build, | ||
| transcript_model, | ||
| select_transcripts, | ||
| checkonly, | ||
| liftover) | ||
|
|
||
| # Collect Arguments | ||
| args = parser.parse_args() | ||
| for k, v in content.items(): | ||
| if k is "metadata": | ||
| refreshed_content[k] = v | ||
| else: | ||
| for k2, v2 in v.items(): | ||
| if k2 is "flag" or k2 is "errors": | ||
| continue | ||
|
|
||
| # else | ||
| refreshed_content[k2] = {} | ||
| refreshed_content[k2]['pass'] = False | ||
| refreshed_content[k2]['errors'] = [] | ||
| refreshed_content[k2]['correction'] = None | ||
|
|
||
| # Filter the errors/warnings i.e. removing any warnings that are not actual errors | ||
| # Warnings which are not errors are contained in the my_warnings list | ||
| error_found = [] | ||
| if v2["genomic_variant_error"] is not None: | ||
| safe_found = False | ||
| for safe in my_warnings: | ||
| if safe in v2["genomic_variant_error"]: | ||
| safe_found = True | ||
| break | ||
| if safe_found is False: | ||
| error_found.append(v2["genomic_variant_error"]) | ||
| refreshed_content[k2]['errors'] = error_found | ||
|
|
||
| # Populate the rest of the output | ||
| if k2 == v2["g_hgvs"]: | ||
| refreshed_content[k2]["pass"] = True | ||
| else: | ||
| refreshed_content[k2]["correction"] = v2["g_hgvs"] | ||
|
|
||
| # Overrides the default response route so that the standard HTML URL can return any specified format | ||
| if args['content-type'] == 'application/json': | ||
| # example: http://127.0.0.1:5000.....bob?content-type=application/json | ||
| return representations.application_json(refreshed_content, 200, None) | ||
| # example: http://127.0.0.1:5000.....?content-type=application/xml | ||
| elif args['content-type'] == 'application/xml': | ||
| return representations.xml(refreshed_content, 200, None) | ||
| else: | ||
| # Return the api default output | ||
| return refreshed_content | ||
|
|
||
|
|
||
| # <LICENSE> | ||
| # Copyright (C) 2016-2021 VariantValidator Contributors | ||
| # | ||
| # This program is free software: you can redistribute it and/or modify | ||
| # it under the terms of the GNU Affero General Public License as | ||
| # published by the Free Software Foundation, either version 3 of the | ||
| # License, or (at your option) any later version. | ||
| # | ||
| # This program is distributed in the hope that it will be useful, | ||
| # but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| # GNU Affero General Public License for more details. | ||
| # | ||
| # You should have received a copy of the GNU Affero General Public License | ||
| # along with this program. If not, see <https://www.gnu.org/licenses/>. | ||
| # </LICENSE> |