diff options
| -rw-r--r-- | gn3/computations/slink.py | 2 | ||||
| -rw-r--r-- | gn3/db/datasets.py | 251 | ||||
| -rw-r--r-- | gn3/db/traits.py | 329 | ||||
| -rw-r--r-- | gn3/function_helpers.py | 36 | ||||
| -rw-r--r-- | tests/unit/db/test_datasets.py | 133 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 200 |
6 files changed, 798 insertions, 153 deletions
diff --git a/gn3/computations/slink.py b/gn3/computations/slink.py index 23d3d88..5953e6b 100644 --- a/gn3/computations/slink.py +++ b/gn3/computations/slink.py @@ -7,7 +7,7 @@ slink: TODO: Describe what the function does... """ import logging -from typing import List, Tuple, Union, Sequence +from typing import Union, Sequence NumType = Union[int, float] SeqOfNums = Sequence[NumType] diff --git a/gn3/db/datasets.py b/gn3/db/datasets.py new file mode 100644 index 0000000..3ad50f6 --- /dev/null +++ b/gn3/db/datasets.py @@ -0,0 +1,251 @@ +from typing import Any, Dict, Union + +def retrieve_probeset_trait_dataset_name( + threshold: int, name: str, connection: Any): + query = ( + "SELECT Id, Name, FullName, ShortName, DataScale " + "FROM ProbeSetFreeze " + "WHERE " + "public > %(threshold)s " + "AND " + "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)") + with connection.cursor() as cursor: + cursor.execute( + query, + { + "threshold": threshold, + "name": name + }) + return dict(zip( + ["dataset_id", "dataset_name", "dataset_fullname", + "dataset_shortname", "dataset_datascale"], + cursor.fetchone)) + +def retrieve_publish_trait_dataset_name(threshold: int, name: str, connection: Any): + query = ( + "SELECT Id, Name, FullName, ShortName " + "FROM PublishFreeze " + "WHERE " + "public > %(threshold)s " + "AND " + "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)") + with connection.cursor() as cursor: + cursor.execute( + query, + { + "threshold": threshold, + "name": name + }) + return dict(zip( + ["dataset_id", "dataset_name", "dataset_fullname", + "dataset_shortname"], + cursor.fetchone)) + +def retrieve_geno_trait_dataset_name(threshold: int, name: str, connection: Any): + query = ( + "SELECT Id, Name, FullName, ShortName " + "FROM GenoFreeze " + "WHERE " + "public > %(threshold)s " + "AND " + "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)") + with connection.cursor() as cursor: + cursor.execute( + query, + { + "threshold": threshold, + "name": name + }) + return dict(zip( + ["dataset_id", "dataset_name", "dataset_fullname", + "dataset_shortname"], + cursor.fetchone)) + +def retrieve_temp_trait_dataset_name(threshold: int, name: str, connection: Any): + query = ( + "SELECT Id, Name, FullName, ShortName " + "FROM TempFreeze " + "WHERE " + "public > %(threshold)s " + "AND " + "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)") + with connection.cursor() as cursor: + cursor.execute( + query, + { + "threshold": threshold, + "name": name + }) + return dict(zip( + ["dataset_id", "dataset_name", "dataset_fullname", + "dataset_shortname"], + cursor.fetchone)) + +def retrieve_dataset_name( + trait_type: str, threshold: int, trait_name: str, dataset_name: str, + conn: Any): + """ + Retrieve the name of a trait given the trait's name + + This is extracted from the `webqtlDataset.retrieveName` function as is + implemented at + https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-L169 + """ + fn_map = { + "ProbeSet": retrieve_probeset_trait_dataset_name, + "Publish": retrieve_publish_trait_dataset_name, + "Geno": retrieve_geno_trait_dataset_name, + "Temp": retrieve_temp_trait_dataset_name} + if trait_type == "Temp": + return retrieve_temp_trait_dataset_name(threshold, trait_name, conn) + return fn_map[trait_type](threshold, dataset_name, conn) + + +def retrieve_geno_riset_fields(name, conn): + """ + Retrieve the RISet, and RISetID values for various Geno trait types. + """ + query = ( + "SELECT InbredSet.Name, InbredSet.Id " + "FROM InbredSet, GenoFreeze " + "WHERE GenoFreeze.InbredSetId = InbredSet.Id " + "AND GenoFreeze.Name = %(name)s") + with conn.cursor() as cursor: + cursor.execute(query, {"name": name}) + return dict(zip(["riset", "risetid"], cursor.fetchone())) + return {} + +def retrieve_publish_riset_fields(name, conn): + """ + Retrieve the RISet, and RISetID values for various Publish trait types. + """ + query = ( + "SELECT InbredSet.Name, InbredSet.Id " + "FROM InbredSet, PublishFreeze " + "WHERE PublishFreeze.InbredSetId = InbredSet.Id " + "AND PublishFreeze.Name = %(name)s") + with conn.cursor() as cursor: + cursor.execute(query, {"name": name}) + return dict(zip(["riset", "risetid"], cursor.fetchone())) + return {} + +def retrieve_probeset_riset_fields(name, conn): + """ + Retrieve the RISet, and RISetID values for various ProbeSet trait types. + """ + query = ( + "SELECT InbredSet.Name, InbredSet.Id " + "FROM InbredSet, ProbeSetFreeze, ProbeFreeze " + "WHERE ProbeFreeze.InbredSetId = InbredSet.Id " + "AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId " + "AND ProbeSetFreeze.Name = %(name)s") + with conn.cursor() as cursor: + cursor.execute(query, {"name": name}) + return dict(zip(["riset", "risetid"], cursor.fetchone())) + return {} + +def retrieve_temp_riset_fields(name, conn): + query = ( + "SELECT InbredSet.Name, InbredSet.Id " + "FROM InbredSet, Temp " + "WHERE Temp.InbredSetId = InbredSet.Id " + "AND Temp.Name = %(name)s") + with conn.cursor() as cursor: + cursor.execute(query, {"name": name}) + return dict(zip(["riset", "risetid"], cursor.fetchone())) + return {} + +def retrieve_riset_fields(trait_type, trait_name, dataset_info, conn): + """ + Retrieve the RISet, and RISetID values for various trait types. + """ + riset_fns_map = { + "Geno": retrieve_geno_riset_fields, + "Publish": retrieve_publish_riset_fields, + "ProbeSet": retrieve_probeset_riset_fields + } + + if trait_type == "Temp": + riset_info = retrieve_temp_riset_fields(trait_name, conn) + else: + riset_info = riset_fns_map[trait_type](dataset_info["dataset_name"], conn) + + return { + **dataset_info, + **riset_info, + "riset": ( + "BXD" if riset_info.get("riset") == "BXD300" + else riset_info.get("riset", "")) + } + +def retrieve_temp_trait_dataset(): + return { + "searchfield": ["name", "description"], + "disfield": ["name", "description"], + "type": "Temp", + "dataset_id": 1, + "fullname": "Temporary Storage", + "shortname": "Temp" + } + +def retrieve_geno_trait_dataset(): + return { + "searchfield": ["name","chr"], + "disfield": ["name","chr","mb", "source2", "sequence"], + "type": "Geno" + } + +def retrieve_publish_trait_dataset(): + return { + "searchfield": [ + "name", "post_publication_description", "abstract", "title", + "authors"], + "disfield": [ + "name","pubmed_id", "pre_publication_description", + "post_publication_description", "original_description", + "pre_publication_abbreviation", "post_publication_abbreviation", + "lab_code", "submitter", "owner", "authorized_users", + "authors","title","abstract", "journal","volume","pages","month", + "year","sequence", "units", "comments"], + "type": "Publish" + } + +def retrieve_probeset_trait_dataset(): + return { + "searchfield": [ + "name", "description", "probe_target_description", "symbol", + "alias", "genbankid", "unigeneid", "omim", "refseq_transcriptid", + "probe_set_specificity", "probe_set_blat_score"], + "disfield": [ + "name", "symbol", "description", "probe_target_description", "chr", + "mb", "alias", "geneid", "genbankid", "unigeneid", "omim", + "refseq_transcriptid", "blatseq", "targetseq", "chipid", "comments", + "strand_probe", "strand_gene", "probe_set_target_region", + "proteinid", "probe_set_specificity", "probe_set_blat_score", + "probe_set_blat_mb_start", "probe_set_blat_mb_end", + "probe_set_strand", "probe_set_note_by_rw", "flag"], + "type": "ProbeSet" + } + +def retrieve_trait_dataset(trait_type, trait, threshold, conn): + dataset_fns = { + "Temp": retrieve_temp_trait_dataset, + "Geno": retrieve_geno_trait_dataset, + "Publish": retrieve_publish_trait_dataset, + "ProbeSet": retrieve_probeset_trait_dataset + } + dataset_name_info = { + "dataset_id": None, + "dataset_name": trait["db"]["dataset_name"], + **retrieve_dataset_name( + trait_type, threshold, trait["trait_name"], trait["db"]["dataset_name"], + conn) + } + riset = retrieve_riset_fields( + trait_type, trait["trait_name"], dataset_name_info, conn) + return { + "display_name": dataset_name_info["dataset_name"], + **dataset_name_info, + **dataset_fns[trait_type](), + **riset + } diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 61bc94d..f66ead3 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,5 +1,7 @@ """This class contains functions relating to trait data manipulation""" from typing import Any, Dict, Union +from gn3.function_helpers import compose +from gn3.db.datasets import retrieve_trait_dataset def get_trait_csv_sample_data(conn: Any, @@ -76,159 +78,294 @@ def update_sample_data(conn: Any, return (updated_strains, updated_published_data, updated_se_data, updated_n_strains) - -def retrieve_trait_dataset_name( - trait_type: str, threshold: int, name: str, connection: Any): - """ - Retrieve the name of a trait given the trait's name - - This is extracted from the `webqtlDataset.retrieveName` function as is - implemented at - https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlDataset.py#L140-L169 - """ - columns = "Id, Name, FullName, ShortName{}".format( - ", DataScale" if trait_type == "ProbeSet" else "") - query = ( - "SELECT {columns} " - "FROM {trait_type}Freeze " - "WHERE " - "public > %(threshold)s " - "AND " - "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)").format( - columns=columns, trait_type=trait_type) - with connection.cursor() as cursor: - cursor.execute(query, {"threshold": threshold, "name": name}) - return cursor.fetchone() - -PUBLISH_TRAIT_INFO_QUERY = ( - "SELECT " - "PublishXRef.Id, Publication.PubMed_ID, " - "Phenotype.Pre_publication_description, " - "Phenotype.Post_publication_description, " - "Phenotype.Original_description, " - "Phenotype.Pre_publication_abbreviation, " - "Phenotype.Post_publication_abbreviation, " - "Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, " - "Phenotype.Authorized_Users, CAST(Publication.Authors AS BINARY), " - "Publication.Title, Publication.Abstract, Publication.Journal, " - "Publication.Volume, Publication.Pages, Publication.Month, " - "Publication.Year, PublishXRef.Sequence, Phenotype.Units, " - "PublishXRef.comments " - "FROM " - "PublishXRef, Publication, Phenotype, PublishFreeze " - "WHERE " - "PublishXRef.Id = %(trait_name)s AND " - "Phenotype.Id = PublishXRef.PhenotypeId AND " - "Publication.Id = PublishXRef.PublicationId AND " - "PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND " - "PublishFreeze.Id =%(trait_dataset_id)s") - - def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any): """Retrieve trait information for type `Publish` traits. https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L399-L421""" + keys = ( + "Id", "PubMed_ID", "Pre_publication_description", + "Post_publication_description", "Original_description", + "Pre_publication_abbreviation", "Post_publication_abbreviation", + "Lab_code", "Submitter", "Owner", "Authorized_Users", "Authors", + "Title", "Abstract", "Journal", "Volume", "Pages", "Month", "Year", + "Sequence", "Units", "comments") + columns = ( + "PublishXRef.Id, Publication.PubMed_ID, " + "Phenotype.Pre_publication_description, " + "Phenotype.Post_publication_description, " + "Phenotype.Original_description, " + "Phenotype.Pre_publication_abbreviation, " + "Phenotype.Post_publication_abbreviation, " + "Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, " + "Phenotype.Authorized_Users, CAST(Publication.Authors AS BINARY), " + "Publication.Title, Publication.Abstract, Publication.Journal, " + "Publication.Volume, Publication.Pages, Publication.Month, " + "Publication.Year, PublishXRef.Sequence, Phenotype.Units, " + "PublishXRef.comments") + query = ( + "SELECT " + "{columns} " + "FROM " + "PublishXRef, Publication, Phenotype, PublishFreeze " + "WHERE " + "PublishXRef.Id = %(trait_name)s AND " + "Phenotype.Id = PublishXRef.PhenotypeId AND " + "Publication.Id = PublishXRef.PublicationId AND " + "PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND " + "PublishFreeze.Id =%(trait_dataset_id)s").format(columns=columns) with conn.cursor() as cursor: cursor.execute( - PUBLISH_TRAIT_INFO_QUERY, + query, { k:v for k, v in trait_data_source.items() if k in ["trait_name", "trait_dataset_id"] }) - return cursor.fetchone() - -PROBESET_TRAIT_INFO_QUERY = ( - "SELECT " - "ProbeSet.name, ProbeSet.symbol, ProbeSet.description, " - "ProbeSet.probe_target_description, ProbeSet.chr, ProbeSet.mb, " - "ProbeSet.alias, ProbeSet.geneid, ProbeSet.genbankid, ProbeSet.unigeneid, " - "ProbeSet.omim, ProbeSet.refseq_transcriptid, ProbeSet.blatseq, " - "ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, " - "ProbeSet.strand_probe, ProbeSet.strand_gene, " - "ProbeSet.probe_set_target_region, ProbeSet.proteinid, " - "ProbeSet.probe_set_specificity, ProbeSet.probe_set_blat_score, " - "ProbeSet.probe_set_blat_mb_start, ProbeSet.probe_set_blat_mb_end, " - "ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, " - "ProbeSet.flag " - "FROM " - "ProbeSet, ProbeSetFreeze, ProbeSetXRef " - "WHERE " - "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND " - "ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " - "ProbeSetFreeze.Name = %(trait_dataset_name)s AND " - "ProbeSet.Name = %(trait_name)s") + return dict(zip([k.lower() for k in keys], cursor.fetchone())) + +def set_confidential_field(trait_type, trait_info): + """Post processing function for 'Publish' trait types. + + It sets the value for the 'confidential' key.""" + if trait_type == "Publish": + return { + **trait_info, + "confidential": 1 if ( + trait_info.get("pre_publication_description", None) + and not trait_info.get("pubmed_id", None)) else 0} + return trait_info def retrieve_probeset_trait_info(trait_data_source: Dict[str, Any], conn: Any): """Retrieve trait information for type `ProbeSet` traits. https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L424-L435""" + keys = ( + "name", "symbol", "description", "probe_target_description", "chr", + "mb", "alias", "geneid", "genbankid", "unigeneid", "omim", + "refseq_transcriptid", "blatseq", "targetseq", "chipid", "comments", + "strand_probe", "strand_gene", "probe_set_target_region", "proteinid", + "probe_set_specificity", "probe_set_blat_score", + "probe_set_blat_mb_start", "probe_set_blat_mb_end", "probe_set_strand", + "probe_set_note_by_rw", "flag") + query = ( + "SELECT " + "{columns} " + "FROM " + "ProbeSet, ProbeSetFreeze, ProbeSetXRef " + "WHERE " + "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id AND " + "ProbeSetXRef.ProbeSetId = ProbeSet.Id AND " + "ProbeSetFreeze.Name = %(trait_dataset_name)s AND " + "ProbeSet.Name = %(trait_name)s").format( + columns=", ".join(["ProbeSet.{}".format(x) for x in keys])) with conn.cursor() as cursor: cursor.execute( - PROBESET_TRAIT_INFO_QUERY, + query, { k:v for k, v in trait_data_source.items() if k in ["trait_name", "trait_dataset_name"] }) - return cursor.fetchone() - -GENO_TRAIT_INFO_QUERY = ( - "SELECT " - "Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence " - "FROM " - "Geno, GenoFreeze, GenoXRef " - "WHERE " - "GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND " - "GenoFreeze.Name = %(trait_dataset_name)s AND Geno.Name = %(trait_name)s") + return dict(zip(keys, cursor.fetchone())) def retrieve_geno_trait_info(trait_data_source: Dict[str, Any], conn: Any): """Retrieve trait information for type `Geno` traits. https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L438-L449""" + keys = ("name", "chr", "mb", "source2", "sequence") + query = ( + "SELECT " + "{columns} " + "FROM " + "Geno, GenoFreeze, GenoXRef " + "WHERE " + "GenoXRef.GenoFreezeId = GenoFreeze.Id AND GenoXRef.GenoId = Geno.Id AND " + "GenoFreeze.Name = %(trait_dataset_name)s AND " + "Geno.Name = %(trait_name)s").format( + columns=", ".join(["Geno.{}".format(x) for x in keys])) with conn.cursor() as cursor: cursor.execute( - GENO_TRAIT_INFO_QUERY, + query, { k:v for k, v in trait_data_source.items() if k in ["trait_name", "trait_dataset_name"] }) - return cursor.fetchone() - -TEMP_TRAIT_INFO_QUERY = ( - "SELECT name, description FROM Temp " - "WHERE Name = %(trait_name)s") + return dict(zip(keys, cursor.fetchone())) def retrieve_temp_trait_info(trait_data_source: Dict[str, Any], conn: Any): """Retrieve trait information for type `Temp` traits. https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L450-452""" + keys = ("name", "description") + query = ( + "SELECT {columns} FROM Temp " + "WHERE Name = %(trait_name)s").format(columns=", ".join(keys)) with conn.cursor() as cursor: cursor.execute( - TEMP_TRAIT_INFO_QUERY, + query, { k:v for k, v in trait_data_source.items() if k in ["trait_name"] }) - return cursor.fetchone() + return dict(zip(keys, cursor.fetchone())) + +def set_haveinfo_field(trait_info): + """ + Common postprocessing function for all trait types. + + Sets the value for the 'haveinfo' field.""" + return {**trait_info, "haveinfo": 1 if trait_info else 0} + +def set_homologene_id_field_probeset(trait_info, conn): + """ + Postprocessing function for 'ProbeSet' traits. + + Sets the value for the 'homologene' key. + """ + query = ( + "SELECT HomologeneId FROM Homologene, Species, InbredSet" + " WHERE Homologene.GeneId = %(geneid)s AND InbredSet.Name = %(riset)s" + " AND InbredSet.SpeciesId = Species.Id AND" + " Species.TaxonomyId = Homologene.TaxonomyId") + with conn.cursor() as cursor: + cursor.execute( + query, + { + k:v for k, v in trait_info.items() + if k in ["geneid", "riset"] + }) + res = cursor.fetchone() + if res: + return {**trait_info, "homologeneid": res[0]} + return {**trait_info, "homologeneid": None} + +def set_homologene_id_field(trait_type, trait_info, conn): + """ + Common postprocessing function for all trait types. + + Sets the value for the 'homologene' key.""" + set_to_null = lambda ti: {**ti, "homologeneid": None} + functions_table = { + "Temp": set_to_null, + "Geno": set_to_null, + "Publish": set_to_null, + "ProbeSet": lambda ti: set_homologene_id_field_probeset(ti, conn) + } + return functions_table[trait_type](trait_info) + +def load_publish_qtl_info(trait_info, conn): + query = ( + "SELECT PublishXRef.Locus, PublishXRef.LRS, PublishXRef.additive " + "FROM PublishXRef, PublishFreeze " + "WHERE PublishXRef.Id = %(trait_name)s " + "AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId " + "AND PublishFreeze.Id = %(dataset_id)s") + with conn.cursor() as cursor: + cursor.execute() + return dict(zip(["locus", "lrs", "additive"], cursor.fetchone())) + return {"locus": "", "lrs": "", "additive": ""} + +def load_probeset_qtl_info(trait_info, conn): + query = ( + "SELECT ProbeSetXRef.Locus, ProbeSetXRef.LRS, ProbeSetXRef.pValue, " + "ProbeSetXRef.mean, ProbeSetXRef.additive " + "FROM ProbeSetXRef, ProbeSet " + "WHERE ProbeSetXRef.ProbeSetId = ProbeSet.Id " + " AND ProbeSet.Name = %(trait_name)s " + "AND ProbeSetXRef.ProbeSetFreezeId = %(dataset_id)s") + with conn.cursor() as cursor: + cursor.execute() + return dict(zip( + ["locus", "lrs", "pvalue", "mean", "additive"], cursor.fetchone())) + return {"locus": "", "lrs": "", "pvalue": "", "mean": "", "additive": ""} + +def load_qtl_info(qtl, trait_type, trait_info, conn): + if not qtl: + return trait_info + qtl_info_functions = { + "Publish": load_publish_qtl_info, + "ProbeSet": load_probeset_qtl_info + } + if trait_inf["name"] not in qtl_info_functions.keys(): + return trait_info + + return qtl_info_functions[trait_type](trait_info, conn) + +def build_trait_name(trait_fullname): + name_parts = trait_fullname.split("::") + assert len(name_parts) >= 2, "Name format error" + return { + "db": {"dataset_name": name_parts[0]}, + "trait_fullname": trait_fullname, + "trait_name": name_parts[1], + "cellid": name_parts[2] if len(name_parts) == 3 else "" + } + +def retrieve_probeset_sequence(trait, conn): + query = ( + "SELECT ProbeSet.BlatSeq " + "FROM ProbeSet, ProbeSetFreeze, ProbeSetXRef " + "WHERE ProbeSet.Id=ProbeSetXRef.ProbeSetId " + "AND ProbeSetFreeze.Id = ProbeSetXRef.ProbeSetFreezeId " + "AND ProbeSet.Name = %(trait_name)s " + "AND ProbeSetFreeze.Name = %(dataset_name)s") + with conn.cursor() as cursor: + cursor.execute( + query, + { + "trait_name": trait["trait_name"], + "dataset_name": trait["db"]["dataset_name"] + }) + seq = cursor.fetchone() + return {**trait, "sequence": seq[0] if seq else ""} def retrieve_trait_info( - trait_type: str, trait_name: str, trait_dataset_id: int, - trait_dataset_name: str, conn: Any): + trait_type: str, threshold: int, trait_full_name: str, conn: Any, + qtl=None): """Retrieves the trait information. https://github.com/genenetwork/genenetwork1/blob/master/web/webqtl/base/webqtlTrait.py#L397-L456 This function, or the dependent functions, might be incomplete as they are currently.""" + trait = build_trait_name(trait_full_name) trait_info_function_table = { "Publish": retrieve_publish_trait_info, "ProbeSet": retrieve_probeset_trait_info, "Geno": retrieve_geno_trait_info, "Temp": retrieve_temp_trait_info } - return trait_info_function_table[trait_type]( + + common_post_processing_fn = compose( + lambda ti: load_qtl_info(qtl, trait_type, ti, conn), + lambda ti: set_homologene_id_field(trait_type, ti, conn), + lambda ti: {"trait_type": trait_type, **ti}, + lambda ti: {**trait, **ti}, + set_haveinfo_field) + + trait_post_processing_functions_table = { + "Publish": compose( + lambda ti: set_confidential_field(trait_type, ti), + common_post_processing_fn), + "ProbeSet": compose( + lambda ti: retrieve_probeset_sequence(ti, conn), + common_post_processing_fn), + "Geno": common_post_processing_fn, + "Temp": common_post_processing_fn + } + + retrieve_info = compose( + trait_post_processing_functions_table[trait_type], + trait_info_function_table[trait_type]) + + trait_dataset = retrieve_trait_dataset(trait_type, trait, threshold, conn) + trait_info = retrieve_info( { - "trait_name": trait_name, - "trait_dataset_id": trait_dataset_id, - "trait_dataset_name":trait_dataset_name + "trait_name": trait["trait_name"], + "trait_dataset_id": trait_dataset["dataset_id"], + "trait_dataset_name": trait_dataset["dataset_name"] }, conn) + return { + **trait_info, + "db": {**trait["db"], **trait_dataset}, + "riset": trait_dataset["riset"] + } diff --git a/gn3/function_helpers.py b/gn3/function_helpers.py new file mode 100644 index 0000000..397b2da --- /dev/null +++ b/gn3/function_helpers.py @@ -0,0 +1,36 @@ +""" +This module will contain helper functions that should assist in maintaining a +mostly functional way of programming. + +It will also contain miscellaneous functions that can be used globally, and thus +do not fit well in any other module. + +FUNCTIONS: +compose: This function is used to compose multiple functions into a single + function. It passes the results of calling one function to the other until + all the functions to be composed are called. +""" +from functools import reduce + +def compose(*functions): + """Compose multiple functions into a single function. + + The utility in this function is not specific to this module, and as such, + this function can, and probably should, be moved to a more global module. + + DESCRIPTION: + Given `cfn = compose(f_1, f_2, ... f_(n-1), f_n )`, calling + `cfn(arg_1, arg_2, ..., arg_m)` should call `f_n` with the arguments passed + to `cfn` and the results of that should be passed as arguments to `f_(n-1)` + and so on until `f_1` is called with the results of the cumulative calls and + that is the result of the entire chain of calls. + + PARAMETERS: + functions: a variable argument list of function. + """ + def composed_function(*args, **kwargs): + return reduce( + lambda res, fn: fn(res), + reversed(functions[:-1]), + functions[-1](*args, **kwargs)) + return composed_function diff --git a/tests/unit/db/test_datasets.py b/tests/unit/db/test_datasets.py new file mode 100644 index 0000000..34fe7f0 --- /dev/null +++ b/tests/unit/db/test_datasets.py @@ -0,0 +1,133 @@ +from unittest import mock, TestCase + +class TestDatasetsDBFunctions(TestCase): + + def test_retrieve_trait_dataset_name(self): + """Test that the function is called correctly.""" + for trait_type, thresh, trait_dataset_name, columns, table in [ + ["ProbeSet", 9, "testName", + "Id, Name, FullName, ShortName, DataScale", "ProbeSetFreeze"], + ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName", + "GenoFreeze"], + ["Publish", 6, "publishTraitName", + "Id, Name, FullName, ShortName", "PublishFreeze"], + ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName", + "TempFreeze"]]: + db_mock = mock.MagicMock() + with self.subTest(trait_type=trait_type): + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = ( + "testName", "testNameFull", "testNameShort", + "dataScale") + self.assertEqual( + retrieve_trait_dataset_name( + trait_type, thresh, trait_dataset_name, db_mock), + ("testName", "testNameFull", "testNameShort", + "dataScale")) + cursor.execute.assert_called_once_with( + "SELECT %(columns)s " + "FROM %(table)s " + "WHERE public > %(threshold)s AND " + "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format( + cols=columns, ttype=trait_type), + {"threshold": thresh, "name": trait_dataset_name, + "table": table, "columns": columns}) + + def test_set_probeset_riset_fields(self): + """ + Test that the `riset` and `riset_id` fields are retrieved appropriately + for the 'ProbeSet' trait type. + """ + for trait_name, expected in [ + ["testProbeSetName", ()]]: + db_mock = mock.MagicMock() + with self.subTest(trait_name=trait_name, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = () + self.assertEqual( + set_probeset_riset_fields(trait_name, db_mock), expected) + cursor.execute.assert_called_once_with( + ( + "SELECT InbredSet.Name, InbredSet.Id" + " FROM InbredSet, ProbeSetFreeze, ProbeFreeze" + " WHERE ProbeFreeze.InbredSetId = InbredSet.Id" + " AND ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId" + " AND ProbeSetFreeze.Name = %(name)s"), + {"name": trait_name}) + + def test_set_riset_fields(self): + """ + Test that the riset fields are set up correctly for the different trait + types. + """ + for trait_info, expected in [ + [{}, {}], + [{"haveinfo": 0, "type": "Publish"}, + {"haveinfo": 0, "type": "Publish"}], + [{"haveinfo": 0, "type": "ProbeSet"}, + {"haveinfo": 0, "type": "ProbeSet"}], + [{"haveinfo": 0, "type": "Geno"}, + {"haveinfo": 0, "type": "Geno"}], + [{"haveinfo": 0, "type": "Temp"}, + {"haveinfo": 0, "type": "Temp"}], + [{"haveinfo": 1, "type": "Publish", "name": "test"}, + {"haveinfo": 1, "type": "Publish", "name": "test", + "riset": "riset_name", "risetid": 0}], + [{"haveinfo": 1, "type": "ProbeSet", "name": "test"}, + {"haveinfo": 1, "type": "ProbeSet", "name": "test", + "riset": "riset_name", "risetid": 0}], + [{"haveinfo": 1, "type": "Geno", "name": "test"}, + {"haveinfo": 1, "type": "Geno", "name": "test", + "riset": "riset_name", "risetid": 0}], + [{"haveinfo": 1, "type": "Temp", "name": "test"}, + {"haveinfo": 1, "type": "Temp", "name": "test", "riset": None, + "risetid": None}] + ]: + db_mock = mock.MagicMock() + with self.subTest(trait_info=trait_info, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = ("riset_name", 0) + self.assertEqual( + set_riset_fields(trait_info, db_mock), expected) + + def test_set_publish_riset_fields(self): + """ + Test that the `riset` and `riset_id` fields are retrieved appropriately + for the 'Publish' trait type. + """ + for trait_name, expected in [ + ["testPublishName", ()]]: + db_mock = mock.MagicMock() + with self.subTest(trait_name=trait_name, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = () + self.assertEqual( + set_publish_riset_fields(trait_name, db_mock), expected) + cursor.execute.assert_called_once_with( + ( + "SELECT InbredSet.Name, InbredSet.Id" + " FROM InbredSet, PublishFreeze" + " WHERE PublishFreeze.InbredSetId = InbredSet.Id" + " AND PublishFreeze.Name = %(name)s"), + {"name": trait_name}) + + def test_set_geno_riset_fields(self): + """ + Test that the `riset` and `riset_id` fields are retrieved appropriately + for the 'Geno' trait type. + """ + for trait_name, expected in [ + ["testGenoName", ()]]: + db_mock = mock.MagicMock() + with self.subTest(trait_name=trait_name, expected=expected): + with db_mock.cursor() as cursor: + cursor.execute.return_value = () + self.assertEqual( + set_geno_riset_fields(trait_name, db_mock), expected) + cursor.execute.assert_called_once_with( + ( + "SELECT InbredSet.Name, InbredSet.Id" + " FROM InbredSet, GenoFreeze" + " WHERE GenoFreeze.InbredSetId = InbredSet.Id" + " AND GenoFreeze.Name = %(name)s"), + {"name": trait_name}) diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index c8f28b5..7d161bf 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -1,51 +1,20 @@ """Tests for gn3/db/traits.py""" from unittest import mock, TestCase from gn3.db.traits import ( - GENO_TRAIT_INFO_QUERY, - TEMP_TRAIT_INFO_QUERY, - PUBLISH_TRAIT_INFO_QUERY, - PROBESET_TRAIT_INFO_QUERY) -from gn3.db.traits import ( + build_trait_name, + set_haveinfo_field, + update_sample_data, retrieve_trait_info, + set_confidential_field, + set_homologene_id_field, retrieve_geno_trait_info, retrieve_temp_trait_info, - retrieve_trait_dataset_name, retrieve_publish_trait_info, - retrieve_probeset_trait_info, - update_sample_data) - + retrieve_probeset_trait_info) class TestTraitsDBFunctions(TestCase): "Test cases for traits functions" - def test_retrieve_trait_dataset_name(self): - """Test that the function is called correctly.""" - for trait_type, thresh, trait_dataset_name, columns in [ - ["ProbeSet", 9, "testName", - "Id, Name, FullName, ShortName, DataScale"], - ["Geno", 3, "genoTraitName", "Id, Name, FullName, ShortName"], - ["Publish", 6, "publishTraitName", - "Id, Name, FullName, ShortName"], - ["Temp", 4, "tempTraitName", "Id, Name, FullName, ShortName"]]: - db_mock = mock.MagicMock() - with self.subTest(trait_type=trait_type): - with db_mock.cursor() as cursor: - cursor.fetchone.return_value = ( - "testName", "testNameFull", "testNameShort", - "dataScale") - self.assertEqual( - retrieve_trait_dataset_name( - trait_type, thresh, trait_dataset_name, db_mock), - ("testName", "testNameFull", "testNameShort", - "dataScale")) - cursor.execute.assert_called_once_with( - "SELECT {cols} " - "FROM {ttype}Freeze " - "WHERE public > %(threshold)s AND " - "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)".format( - cols=columns, ttype=trait_type), - {"threshold": thresh, "name": trait_dataset_name}) - def test_retrieve_publish_trait_info(self): """Test retrieval of type `Publish` traits.""" db_mock = mock.MagicMock() @@ -54,12 +23,32 @@ class TestTraitsDBFunctions(TestCase): trait_source = { "trait_name": "PublishTraitName", "trait_dataset_id": 1} self.assertEqual( - retrieve_publish_trait_info( - trait_source, - db_mock), - tuple()) + retrieve_publish_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( - PUBLISH_TRAIT_INFO_QUERY, trait_source) + ("SELECT " + "PublishXRef.Id, Publication.PubMed_ID," + " Phenotype.Pre_publication_description," + " Phenotype.Post_publication_description," + " Phenotype.Original_description," + " Phenotype.Pre_publication_abbreviation," + " Phenotype.Post_publication_abbreviation," + " Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner," + " Phenotype.Authorized_Users," + " CAST(Publication.Authors AS BINARY)," + " Publication.Title, Publication.Abstract," + " Publication.Journal," + " Publication.Volume, Publication.Pages, Publication.Month," + " Publication.Year, PublishXRef.Sequence, Phenotype.Units," + " PublishXRef.comments" + " FROM" + " PublishXRef, Publication, Phenotype, PublishFreeze" + " WHERE" + " PublishXRef.Id = %(trait_name)s" + " AND Phenotype.Id = PublishXRef.PhenotypeId" + " AND Publication.Id = PublishXRef.PublicationId" + " AND PublishXRef.InbredSetId = PublishFreeze.InbredSetId" + " AND PublishFreeze.Id =%(trait_dataset_id)s"), + trait_source) def test_retrieve_probeset_trait_info(self): """Test retrieval of type `Probeset` traits.""" @@ -70,9 +59,31 @@ class TestTraitsDBFunctions(TestCase): "trait_name": "ProbeSetTraitName", "trait_dataset_name": "ProbeSetDatasetTraitName"} self.assertEqual( - retrieve_probeset_trait_info(trait_source, db_mock), tuple()) + retrieve_probeset_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( - PROBESET_TRAIT_INFO_QUERY, trait_source) + ( + "SELECT " + "ProbeSet.name, ProbeSet.symbol, ProbeSet.description, " + "ProbeSet.probe_target_description, ProbeSet.chr, " + "ProbeSet.mb, ProbeSet.alias, ProbeSet.geneid, " + "ProbeSet.genbankid, ProbeSet.unigeneid, ProbeSet.omim, " + "ProbeSet.refseq_transcriptid, ProbeSet.blatseq, " + "ProbeSet.targetseq, ProbeSet.chipid, ProbeSet.comments, " + "ProbeSet.strand_probe, ProbeSet.strand_gene, " + "ProbeSet.probe_set_target_region, ProbeSet.proteinid, " + "ProbeSet.probe_set_specificity, " + "ProbeSet.probe_set_blat_score, " + "ProbeSet.probe_set_blat_mb_start, " + "ProbeSet.probe_set_blat_mb_end, " + "ProbeSet.probe_set_strand, ProbeSet.probe_set_note_by_rw, " + "ProbeSet.flag " + "FROM " + "ProbeSet, ProbeSetFreeze, ProbeSetXRef " + "WHERE " + "ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id " + "AND ProbeSetXRef.ProbeSetId = ProbeSet.Id " + "AND ProbeSetFreeze.Name = %(trait_dataset_name)s " + "AND ProbeSet.Name = %(trait_name)s"), trait_source) def test_retrieve_geno_trait_info(self): """Test retrieval of type `Geno` traits.""" @@ -83,9 +94,19 @@ class TestTraitsDBFunctions(TestCase): "trait_name": "GenoTraitName", "trait_dataset_name": "GenoDatasetTraitName"} self.assertEqual( - retrieve_geno_trait_info(trait_source, db_mock), tuple()) + retrieve_geno_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( - GENO_TRAIT_INFO_QUERY, trait_source) + ( + "SELECT " + "Geno.name, Geno.chr, Geno.mb, Geno.source2, Geno.sequence " + "FROM " + "Geno, GenoFreeze, GenoXRef " + "WHERE " + "GenoXRef.GenoFreezeId = GenoFreeze.Id " + "AND GenoXRef.GenoId = Geno.Id " + "AND GenoFreeze.Name = %(trait_dataset_name)s " + "AND Geno.Name = %(trait_name)s"), + trait_source) def test_retrieve_temp_trait_info(self): """Test retrieval of type `Temp` traits.""" @@ -94,26 +115,60 @@ class TestTraitsDBFunctions(TestCase): cursor.fetchone.return_value = tuple() trait_source = {"trait_name": "TempTraitName"} self.assertEqual( - retrieve_temp_trait_info(trait_source, db_mock), tuple()) + retrieve_temp_trait_info(trait_source, db_mock), {}) cursor.execute.assert_called_once_with( - TEMP_TRAIT_INFO_QUERY, trait_source) + "SELECT name, description FROM Temp WHERE Name = %(trait_name)s", + trait_source) + + def test_build_trait_name_with_good_fullnames(self): + for fullname, expected in [ + ["testdb::testname", + {"db": {"dataset_name": "testdb"}, "trait_name": "testname", + "cellid": "", "trait_fullname": "testdb::testname"}], + ["testdb::testname::testcell", + {"db": {"dataset_name": "testdb"}, "trait_name": "testname", + "cellid": "testcell", + "trait_fullname": "testdb::testname::testcell"}]]: + with self.subTest(fullname=fullname): + self.assertEqual(build_trait_name(fullname), expected) + + def test_build_trait_name_with_bad_fullnames(self): + for fullname in ["", "test", "test:test"]: + with self.subTest(fullname=fullname): + with self.assertRaises(AssertionError, msg="Name format error"): + build_trait_name(fullname) def test_retrieve_trait_info(self): """Test that information on traits is retrieved as appropriate.""" - for trait_type, trait_name, trait_dataset_id, trait_dataset_name, in [ - ["Publish", "PublishTraitName", 1, "PublishDatasetTraitName"], - ["ProbeSet", "ProbeSetTraitName", 2, "ProbeSetDatasetTraitName"], - ["Geno", "GenoTraitName", 3, "GenoDatasetTraitName"], - ["Temp", "TempTraitName", 4, "TempDatasetTraitName"]]: + for trait_type, threshold, trait_fullname, expected in [ + ["Publish", 9, "pubDb::PublishTraitName::pubCell", + {"haveinfo": 0, "homologeneid": None, "type": "Publish", + "confidential": 0, "db": {"dataset_name": "pubDb"}, + "trait_name": "PublishTraitName", "cellid": "pubCell", + "trait_fullname": "pubDb::PublishTraitName::pubCell"}], + ["ProbeSet", 5, "prbDb::ProbeSetTraitName::prbCell", + {"haveinfo": 0, "homologeneid": None, "type": "ProbeSet", + "trait_fullname": "prbDb::ProbeSetTraitName::prbCell", + "db": {"dataset_name": "prbDb"}, + "trait_name": "ProbeSetTraitName", "cellid": "prbCell"}], + ["Geno", 12, "genDb::GenoTraitName", + {"haveinfo": 0, "homologeneid": None, "type": "Geno", + "trait_fullname": "genDb::GenoTraitName", + "db": {"dataset_name": "genDb"}, + "trait_name": "GenoTraitName", "cellid": ""}], + ["Temp", 6, "tmpDb::TempTraitName", + {"haveinfo": 0, "homologeneid": None, "type": "Temp", + "trait_fullname": "tmpDb::TempTraitName", + "db": {"dataset_name": "tmpDb"}, + "trait_name": "TempTraitName", "cellid": ""}]]: db_mock = mock.MagicMock() with self.subTest(trait_type=trait_type): with db_mock.cursor() as cursor: cursor.fetchone.return_value = tuple() self.assertEqual( retrieve_trait_info( - trait_type, trait_name, trait_dataset_id, - trait_dataset_name, db_mock), - tuple()) + trait_type, threshold, trait_fullname, db_mock), + expected) def test_update_sample_data(self): """Test that the SQL queries when calling update_sample_data are called with @@ -143,3 +198,36 @@ class TestTraitsDBFunctions(TestCase): mock.call(PUBLISH_SE_SQL, (2.3, 10, 8967049)), mock.call(N_STRAIN_SQL, (2, 10, 8967049))] ) + + def test_set_haveinfo_field(self): + """Test that the `haveinfo` field is set up correctly""" + for trait_info, expected in [ + [{}, {"haveinfo": 0}], + [{"k1": "v1"}, {"k1": "v1", "haveinfo": 1}]]: + with self.subTest(trait_info=trait_info, expected=expected): + self.assertEqual(set_haveinfo_field(trait_info), expected) + + def test_set_homologene_id_field(self): + """Test that the `homologene_id` field is set up correctly""" + for trait_type, trait_info, expected in [ + ["Publish", {}, {"homologeneid": None}], + ["ProbeSet", {}, {"homologeneid": None}], + ["Geno", {}, {"homologeneid": None}], + ["Temp", {}, {"homologeneid": None}]]: + db_mock = mock.MagicMock() + with self.subTest(trait_info=trait_info, expected=expected): + with db_mock.cursor() as cursor: + cursor.fetchone.return_value = () + self.assertEqual( + set_homologene_id_field(trait_type, trait_info, db_mock), expected) + + def test_set_confidential_field(self): + """Test that the `confidential` field is set up correctly""" + for trait_type, trait_info, expected in [ + ["Publish", {}, {"confidential": 0}], + ["ProbeSet", {}, {}], + ["Geno", {}, {}], + ["Temp", {}, {}]]: + with self.subTest(trait_info=trait_info, expected=expected): + self.assertEqual( + set_confidential_field(trait_type, trait_info), expected) |