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get_spongEffects_run_ID now can return a list #30

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merged 2 commits into from
Dec 14, 2024
Merged

get_spongEffects_run_ID now can return a list #30

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e680482
get_spongEffects_run_ID now can return a list
strasserle Dec 14, 2024
e8e4f98
Merge branch 'SPONGEdb_v2' of github.com:daisybio/SPONGE-web-backend …
strasserle Dec 14, 2024
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151 changes: 99 additions & 52 deletions app/controllers/spongEffects.py
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Original file line number Diff line number Diff line change
Expand Up @@ -35,27 +35,39 @@ def get_spongEffects_run_ID(dataset_ID: int = None, disease_name: str = None, le
# Build the query
query = db.select(models.SpongeRun.sponge_run_ID)

# join with dataset if necessary
if dataset_ID is not None or disease_name is not None:
query = query.join(models.Dataset, models.SpongeRun.dataset_ID == models.Dataset.dataset_ID)

# filter for sponge_db_version
query = query.where(models.Dataset.sponge_db_version == sponge_db_version)

if dataset_ID is not None:
query = query.where(models.SpongeRun.dataset_ID == dataset_ID)
if disease_name is not None:
query = query.join(models.Dataset, models.SpongeRun.dataset_ID == models.Dataset.dataset_ID).where(models.Dataset.disease_name.like(f"%{disease_name}%"))
query = query.where(models.Dataset.disease_name.like(f"%{disease_name}%"))

# Execute the query and fetch the sponge_run_ID
sponge_run_ID = db.session.execute(query).scalar()
sponge_run_IDs = db.session.execute(query).scalars().all()

if not sponge_run_ID:
if len(sponge_run_IDs) == 0:
abort(404, f"No sponge run found for disease_name: {disease_name} and dataset_ID: {dataset_ID}")

# Build the query to get spong_effects_run_ID
query = db.select(models.SpongEffectsRun.spong_effects_run_ID).where(models.SpongEffectsRun.sponge_run_ID == sponge_run_ID)
query = db.select(models.SpongEffectsRun.spongEffects_run_ID).where(models.SpongEffectsRun.sponge_run_ID.in_(sponge_run_IDs))

# filter for level
if level is not None:
query = query.where(models.SpongEffectsRun.level == level)

# Execute the query and fetch the result
spong_effects_run_ID = db.session.execute(query).scalar()
spong_effects_run_IDs = db.session.execute(query).scalars().all()

if len(spong_effects_run_IDs) == 0:
abort(404, f"No spongEffects run found for sponge_run_ID: {sponge_run_IDs}")

if spong_effects_run_ID:
return spong_effects_run_ID
else:
abort(404, f"No spongEffects run found for sponge_run_ID: {sponge_run_ID}")
return spong_effects_run_IDs


def get_run_performance(dataset_ID: int = None, disease_name: str = None, level: str = 'gene', sponge_db_version: int = LATEST):
Expand All @@ -67,10 +79,10 @@ def get_run_performance(dataset_ID: int = None, disease_name: str = None, level:
:param sponge_db_version: Database version (defaults to most recent version)
:return: Best spongEffects model performances for given disease and level
"""
spongEffects_run_ID = get_spongEffects_run_ID(dataset_ID, disease_name, level, sponge_db_version)
spongEffects_run_IDs = get_spongEffects_run_ID(dataset_ID, disease_name, level, sponge_db_version)
query = models.SpongEffectsRunPerformance.query \
.join(models.SpongEffectsRun, models.SpongEffectsRun.spongEffects_run_ID == models.SpongEffectsRunPerformance.spongEffects_run_ID) \
.filter(models.SpongEffectsRun.spongEffects_run_ID == spongEffects_run_ID) \
.filter(models.SpongEffectsRun.spongEffects_run_ID.in_(spongEffects_run_IDs)) \
.all()

if len(query) > 0:
Expand All @@ -88,11 +100,11 @@ def get_run_class_performance(dataset_ID: int = None, disease_name: str = None,
:param sponge_db_version: Database version (defaults to most recent version)
:return: Best spongEffects model class performances for given disease and level
"""
spongEffects_run_ID = get_spongEffects_run_ID(dataset_ID, disease_name, level, sponge_db_version)
spongEffects_run_IDs = get_spongEffects_run_ID(dataset_ID, disease_name, level, sponge_db_version)
query = models.SpongEffectsRunClassPerformance.query \
.join(models.SpongEffectsRunPerformance,
models.SpongEffectsRunPerformance.spongEffects_run_performance_ID == models.SpongEffectsRunClassPerformance.spongEffects_run_performance_ID) \
.filter(models.SpongEffectsRunPerformance.spongEffects_run_ID == spongEffects_run_ID) \
.filter(models.SpongEffectsRunPerformance.spongEffects_run_ID.in_(spongEffects_run_IDs)) \
.all()
if len(query) > 0:
return models.SpongEffectsRunClassPerformanceSchema(many=True).dump(query)
Expand All @@ -114,10 +126,10 @@ def get_enrichment_score_class_distributions(dataset_ID: int = None, disease_nam
if level not in ['gene', 'transcript']:
abort(404, 'Provided level not recognised, please use one of gene/transcript')
# extract spongEffects_run_ID
spongEffects_run_ID = get_spongEffects_run_ID(dataset_ID, disease_name, level, sponge_db_version)
spongEffects_run_IDs = get_spongEffects_run_ID(dataset_ID, disease_name, level, sponge_db_version)
# extract density data for spongEffects run
query = models.SpongEffectsEnrichmentClassDensity.query \
.filter(models.SpongEffectsEnrichmentClassDensity.spongEffects_run_ID == spongEffects_run_ID) \
.filter(models.SpongEffectsEnrichmentClassDensity.spongEffects_run_ID.in_(spongEffects_run_IDs)) \
.all()
if len(query) > 0:
return models.SpongEffectsEnrichmentClassDensitySchema(many=True).dump(query)
Expand All @@ -134,14 +146,21 @@ def get_gene_modules(dataset_ID: int = None, disease_name: str = None, sponge_db
:return: Best spongEffects gene modules for given disease
"""
# get spongEffects_run_ID
spongEffects_run_ID = get_spongEffects_run_ID(dataset_ID, disease_name, "gene", sponge_db_version)
spongEffects_run_IDs = get_spongEffects_run_ID(dataset_ID, disease_name, "gene", sponge_db_version)
# get modules
query = db.session.execute(
"SELECT * FROM spongEffects_gene_module as A"
" JOIN gene g ON A.gene_ID = g.gene_ID"
f" WHERE spongEffects_run_ID = {spongEffects_run_ID}"
" ORDER BY mean_accuracy_decrease DESC, mean_accuracy_decrease DESC;"
).fetchall()
# query = db.session.execute(
# "SELECT * FROM spongEffects_gene_module as A"
# " JOIN gene g ON A.gene_ID = g.gene_ID"
# f" WHERE spongEffects_run_ID = {spongEffects_run_ID}"
# " ORDER BY mean_accuracy_decrease DESC, mean_accuracy_decrease DESC;"
# ).fetchall()

query = db.select(models.SpongEffectsGeneModule) \
.where(models.SpongEffectsGeneModule.spongEffects_run_ID.in_(spongEffects_run_IDs)) \
.order_by(models.SpongEffectsGeneModule.mean_accuracy_decrease.desc(), models.SpongEffectsGeneModule.mean_accuracy_decrease.desc())

query = db.session.execute(query).scalars().all()

if len(query) > 0:
return models.SpongEffectsGeneModuleSchema(many=True).dump(query)
else:
Expand All @@ -159,7 +178,7 @@ def get_gene_module_members(dataset_ID: int = None, disease_name: str = None, en
:return: spongEffects gene module members for given disease and gene identifier
"""
# get spongEffects_run_ID
spongEffects_run_ID = get_spongEffects_run_ID(dataset_ID, disease_name, "gene", sponge_db_version)
spongEffects_run_IDs = get_spongEffects_run_ID(dataset_ID, disease_name, "gene", sponge_db_version)
# test if any of the two identification possibilities is given
if ensg_number is None and gene_symbol is None:
abort(404, "One of the two possible identification numbers must be provided")
Expand All @@ -183,16 +202,25 @@ def get_gene_module_members(dataset_ID: int = None, disease_name: str = None, en
else:
search_val = "'"+search_val+"'"
# search DB
query = db.session.execute(
"SELECT gA.ensg_number AS hub_ensg_number, gA.gene_symbol AS hub_gene_symbol,"
" g.ensg_number AS member_ensg_number, g.gene_symbol as member_gene_symbol"
" FROM spongEffects_gene_module_members as A"
" JOIN spongEffects_gene_module sEgm on A.spongEffects_gene_module_ID = sEgm.spongEffects_gene_module_ID"
" JOIN gene g on g.gene_ID = A.gene_ID"
" JOIN gene gA on gA.gene_ID = sEgm.gene_ID"
f" WHERE gA.{search_key} IN ({search_val}) AND spongEffects_run_ID = {spongEffects_run_ID};"
).fetchall()
# query = db.session.execute(
# "SELECT gA.ensg_number AS hub_ensg_number, gA.gene_symbol AS hub_gene_symbol,"
# " g.ensg_number AS member_ensg_number, g.gene_symbol as member_gene_symbol"
# " FROM spongEffects_gene_module_members as A"
# " JOIN spongEffects_gene_module sEgm on A.spongEffects_gene_module_ID = sEgm.spongEffects_gene_module_ID"
# " JOIN gene g on g.gene_ID = A.gene_ID"
# " JOIN gene gA on gA.gene_ID = sEgm.gene_ID"
# f" WHERE gA.{search_key} IN ({search_val}) AND spongEffects_run_ID = {spongEffects_run_ID};"
# ).fetchall()

query = db.select(models.SpongEffectsGeneModuleMembers) \
.join(models.SpongEffectsGeneModule, models.SpongEffectsGeneModuleMembers.spongEffects_gene_module_ID == models.SpongEffectsGeneModule.spongEffects_gene_module_ID) \
.join(models.Gene, models.SpongEffectsGeneModuleMembers.gene_ID == models.Gene.gene_ID) \
.join(models.Gene, models.SpongEffectsGeneModule.gene_ID == models.Gene.gene_ID) \
.where(models.SpongEffectsGeneModule.spongEffects_run_ID.in_(spongEffects_run_IDs)) \
.where(getattr(models.Gene, search_key).in_(search_val))

query = db.session.execute(query).scalars().all()

if len(query) > 0:
return models.SpongEffectsGeneModuleMembersSchema(many=True).dump(query)
else:
Expand All @@ -209,16 +237,24 @@ def get_transcript_modules(dataset_ID: int = None, disease_name: str = None, spo
"""

# get spongEffects_run_ID
spongEffects_run_ID = get_spongEffects_run_ID(dataset_ID, disease_name, "transcript", sponge_db_version)
spongEffects_run_IDs = get_spongEffects_run_ID(dataset_ID, disease_name, "transcript", sponge_db_version)

# get modules
query = db.session.execute(
"SELECT * FROM spongEffects_transcript_module as A"
" JOIN transcript t ON A.transcript_ID = t.transcript_ID"
" JOIN gene g ON t.gene_ID = g.gene_ID"
f" WHERE spongEffects_run_ID = {spongEffects_run_ID}"
" ORDER BY mean_accuracy_decrease DESC, mean_accuracy_decrease DESC;"
).fetchall()
# query = db.session.execute(
# "SELECT * FROM spongEffects_transcript_module as A"
# " JOIN transcript t ON A.transcript_ID = t.transcript_ID"
# " JOIN gene g ON t.gene_ID = g.gene_ID"
# f" WHERE spongEffects_run_ID = {spongEffects_run_ID}"
# " ORDER BY mean_accuracy_decrease DESC, mean_accuracy_decrease DESC;"
# ).fetchall()

query = db.select(models.SpongEffectsTranscriptModule) \
.join(models.Transcript, models.SpongEffectsTranscriptModule.transcript_ID == models.Transcript.transcript_ID) \
.join(models.Gene, models.Transcript.gene_ID == models.Gene.gene_ID) \
.where(models.SpongEffectsTranscriptModule.spongEffects_run_ID.in_(spongEffects_run_IDs)) \
.order_by(models.SpongEffectsTranscriptModule.mean_accuracy_decrease.desc(), models.SpongEffectsTranscriptModule.mean_accuracy_decrease.desc())

query = db.session.execute(query).scalars().all()

if len(query) > 0:
return models.SpongEffectsTranscriptModuleSchema(many=True).dump(query)
Expand All @@ -238,7 +274,7 @@ def get_transcript_module_members(dataset_ID: int = None, disease_name: str = No
:return: spongEffects transcript module members for given disease and gene identifier
"""
# get spongEffects_run_ID
spongEffects_run_ID = get_spongEffects_run_ID(dataset_ID, disease_name, "gene", sponge_db_version)
spongEffects_run_IDs = get_spongEffects_run_ID(dataset_ID, disease_name, "gene", sponge_db_version)
# test if any of the two identification possibilities is given
tests: list = [enst_number is not None, ensg_number is not None, gene_symbol is not None]
if sum(tests) == 0:
Expand All @@ -264,18 +300,29 @@ def get_transcript_module_members(dataset_ID: int = None, disease_name: str = No
else:
search_val = "'"+search_val+"'"
# search DB
query = db.session.execute(
"SELECT tA.enst_number as hub_enst_number, t.enst_number as member_enst_number"
" gA.ensg_number AS hub_ensg_number, gA.gene_symbol AS hub_gene_symbol,"
" g.ensg_number AS member_ensg_number, g.gene_symbol as member_gene_symbol"
" FROM spongEffects_transcript_module_members as A"
" JOIN spongEffects_transcript_module sEtm on A.spongEffects_transcript_module_ID = sEtm.spongEffects_transcript_module_ID"
" JOIN transcript t on t.transcript_ID = A.transcript_ID"
" JOIN transcript tA on tA.transcript_ID = sEtm.transcript_ID"
" JOIN gene g on g.gene_ID = t.gene_ID"
" JOIN gene gA on gA.gene_ID = tA.gene_ID"
f" WHERE tA.{search_key} IN ({search_val}) AND spongEffects_run_ID = {spongEffects_run_ID};"
).fetchall()
# query = db.session.execute(
# "SELECT tA.enst_number as hub_enst_number, t.enst_number as member_enst_number"
# " gA.ensg_number AS hub_ensg_number, gA.gene_symbol AS hub_gene_symbol,"
# " g.ensg_number AS member_ensg_number, g.gene_symbol as member_gene_symbol"
# " FROM spongEffects_transcript_module_members as A"
# " JOIN spongEffects_transcript_module sEtm on A.spongEffects_transcript_module_ID = sEtm.spongEffects_transcript_module_ID"
# " JOIN transcript t on t.transcript_ID = A.transcript_ID"
# " JOIN transcript tA on tA.transcript_ID = sEtm.transcript_ID"
# " JOIN gene g on g.gene_ID = t.gene_ID"
# " JOIN gene gA on gA.gene_ID = tA.gene_ID"
# f" WHERE tA.{search_key} IN ({search_val}) AND spongEffects_run_ID = {spongEffects_run_ID};"
# ).fetchall()

query = db.select(models.SpongEffectsTranscriptModuleMembers) \
.join(models.SpongEffectsTranscriptModule, models.SpongEffectsTranscriptModuleMembers.spongEffects_transcript_module_ID == models.SpongEffectsTranscriptModule.spongEffects_transcript_module_ID) \
.join(models.Transcript, models.SpongEffectsTranscriptModuleMembers.transcript_ID == models.Transcript.transcript_ID) \
.join(models.Transcript, models.SpongEffectsTranscriptModule.transcript_ID == models.Transcript.transcript_ID) \
.join(models.Gene, models.Transcript.gene_ID == models.Gene.gene_ID) \
.join(models.Gene, models.SpongEffectsTranscriptModule.gene_ID == models.Gene.gene_ID) \
.where(models.SpongEffectsTranscriptModule.spongEffects_run_ID.in_(spongEffects_run_IDs)) \
.where(getattr(models.Gene, search_key).in_(search_val))

query = db.session.execute(query).scalars().all()

if len(query) > 0:
return models.SpongEffectsGeneModuleMembersSchema(many=True).dump(query)
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