diff options
Diffstat (limited to 'gn3/db')
| -rw-r--r-- | gn3/db/datasets.py | 251 | ||||
| -rw-r--r-- | gn3/db/traits.py | 171 |
2 files changed, 324 insertions, 98 deletions
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 9f89510..85cccfa 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1,6 +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, @@ -77,41 +78,6 @@ 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 - """ - table_map = { - "ProbeSet": "ProbeSetFreeze", - "Publish": "PublishFreeze", - "Geno": "GenoFreeze", - "Temp": "TempFreeze"} - columns = "Id, Name, FullName, ShortName{}".format( - ", DataScale" if trait_type == "ProbeSet" else "") - query = ( - "SELECT %(columns)s " - "FROM %(table)s " - "WHERE " - "public > %(threshold)s " - "AND " - "(Name = %(name)s OR FullName = %(name)s OR ShortName = %(name)s)") - with connection.cursor() as cursor: - cursor.execute( - query, - { - "table": table_map[trait_type], - "columns": columns, - "threshold": threshold, - "name": name - }) - return cursor.fetchone() - - def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any): """Retrieve trait information for type `Publish` traits. @@ -156,11 +122,11 @@ def retrieve_publish_trait_info(trait_data_source: Dict[str, Any], conn: Any): }) return dict(zip([k.lower() for k in keys], cursor.fetchone())) -def set_confidential_field(trait_info): +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_info["type"] == "Publish": + if trait_type == "Publish": return { **trait_info, "confidential": 1 if ( @@ -271,7 +237,7 @@ def set_homologene_id_field_probeset(trait_info, conn): return {**trait_info, "homologeneid": res[0]} return {**trait_info, "homologeneid": None} -def set_homologene_id_field(trait_info, conn): +def set_homologene_id_field(trait_type, trait_info, conn): """ Common postprocessing function for all trait types. @@ -283,84 +249,83 @@ def set_homologene_id_field(trait_info, conn): "Publish": set_to_null, "ProbeSet": lambda ti: set_homologene_id_field_probeset(ti, conn) } - return functions_table[trait_info["type"]](trait_info) + return functions_table[trait_type](trait_info) -def set_geno_riset_fields(name, conn): - """ - Retrieve the RISet, and RISetID values for various Geno trait types. - """ +def load_publish_qtl_info(trait_info, conn): query = ( - "SELECT InbredSet.Name, InbredSet.Id " - "FROM InbredSet, GenoFreeze " - "WHERE GenoFreeze.InbredSetId = InbredSet.Id " - "AND GenoFreeze.Name = %(name)s") + "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: - return cursor.execute(query, {"name": name}) + cursor.execute() + return dict(zip(["locus", "lrs", "additive"], cursor.fetchone())) + return {"locus": "", "lrs": "", "additive": ""} -def set_publish_riset_fields(name, conn): - """ - Retrieve the RISet, and RISetID values for various Publish trait types. - """ +def load_probeset_qtl_info(trait_info, conn): query = ( - "SELECT InbredSet.Name, InbredSet.Id " - "FROM InbredSet, PublishFreeze " - "WHERE PublishFreeze.InbredSetId = InbredSet.Id " - "AND PublishFreeze.Name = %(name)s") + "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: - return cursor.execute(query, {"name": name}) + cursor.execute() + return dict(zip( + ["locus", "lrs", "pvalue", "mean", "additive"], cursor.fetchone())) + return {"locus": "", "lrs": "", "pvalue": "", "mean": "", "additive": ""} -def set_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: - return cursor.execute(query, {"name": name}) - -def set_riset_fields(trait_info, conn): - """ - Retrieve the RISet, and RISetID values for various trait types. - """ - riset_functions_map = { - "Temp": lambda ti, con: (None, None), - "Geno": set_geno_riset_fields, - "Publish": set_publish_riset_fields, - "ProbeSet": set_probeset_riset_fields +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 not trait_info.get("haveinfo", None): + if trait_inf["name"] not in qtl_info_functions.keys(): return trait_info - riset, riid = riset_functions_map[trait_info["type"]]( - trait_info["name"], conn) - return { - **trait_info, "risetid": riid, - "riset": "BXD" if riset == "BXD300" else riset} + 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 { - "trait_db": name_parts[0], + "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_full_name: str, trait_dataset_id: int, - trait_dataset_name: str, conn: Any, qtl=None): + 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.""" - # pylint: disable=[R0913] trait = build_trait_name(trait_full_name) trait_info_function_table = { "Publish": retrieve_publish_trait_info, @@ -370,15 +335,19 @@ def retrieve_trait_info( } common_post_processing_fn = compose( - lambda ti: set_riset_fields(ti, conn), - lambda ti: set_homologene_id_field(ti, conn), - lambda ti: {"type": trait_type, **ti}, - lambda ti: {**ti, **trait}, + 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(set_confidential_field, common_post_processing_fn), - "ProbeSet": compose(common_post_processing_fn), + "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 } @@ -387,10 +356,16 @@ def retrieve_trait_info( trait_post_processing_functions_table[trait_type], trait_info_function_table[trait_type]) - return retrieve_info( + trait_dataset = retrieve_trait_dataset(trait_type, trait, threshold, conn) + trait_info = retrieve_info( { "trait_name": trait["trait_name"], - "trait_dataset_id": trait_dataset_id, - "trait_dataset_name":trait_dataset_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"] + } |