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-rw-r--r--wqflask/base/data_set/dataset.py2
-rw-r--r--wqflask/base/species.py71
-rw-r--r--wqflask/tests/unit/base/test_species.py20
-rw-r--r--wqflask/wqflask/heatmap/heatmap.py7
-rw-r--r--wqflask/wqflask/show_trait/show_trait.py6
-rw-r--r--wqflask/wqflask/snp_browser/snp_browser.py10
-rw-r--r--wqflask/wqflask/views.py104
7 files changed, 110 insertions, 110 deletions
diff --git a/wqflask/base/data_set/dataset.py b/wqflask/base/data_set/dataset.py
index f035e028..69c842ad 100644
--- a/wqflask/base/data_set/dataset.py
+++ b/wqflask/base/data_set/dataset.py
@@ -45,7 +45,7 @@ class DataSet:
self.accession_id = self.get_accession_id()
if get_samplelist == True:
self.group.get_samplelist(redis_conn)
- self.species = species.TheSpecies(self)
+ self.species = species.TheSpecies(dataset=self)
def as_dict(self):
return {
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 0ee04630..68b00c70 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -1,23 +1,19 @@
-from collections import OrderedDict
from dataclasses import dataclass
-from dataclasses import InitVar
-from typing import Optional, Dict, Any, Union
+from typing import Optional, Union
+from collections import OrderedDict
+
from wqflask.database import database_connection
-@dataclass
class TheSpecies:
"""Data related to species."""
- dataset: Optional[Dict] = None
- species_name: Optional[str] = None
- def __post_init__(self) -> None:
- # Just an alias of species_name. It's safe for this to be None.
- self.name = self.species_name
- with database_connection() as conn:
- self.chromosomes = Chromosomes(conn=conn,
- species=self.species_name,
- dataset=self.dataset)
+ def __init__(self, dataset=None, species_name=None) -> None:
+ "Initialise the Species object"
+ self.dataset = dataset
+ self.name = self.species_name = species_name
+ self.chromosomes = Chromosomes(species=species_name,
+ dataset=dataset)
@dataclass
@@ -35,34 +31,31 @@ class IndChromosome:
@dataclass
class Chromosomes:
"""Data related to a chromosome"""
- conn: Any
- dataset: InitVar[Dict] = None
- species: Optional[str] = None
- def __post_init__(self, dataset) -> None:
- if self.species is None:
+ def __init__(self, dataset, species: Optional[str]) -> None:
+ "initialise the Chromosome object"
+ self.species = species
+ if species is None:
self.dataset = dataset
- @property
- def chromosomes(self) -> OrderedDict:
+ def chromosomes(self, db_cursor) -> OrderedDict:
"""Lazily fetch the chromosomes"""
chromosomes = OrderedDict()
- with database_connection() as conn, conn.cursor() as cursor:
- if self.species is not None:
- cursor.execute(
- "SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
- "FROM Chr_Length, Species WHERE "
- "Chr_Length.SpeciesId = Species.SpeciesId AND "
- "Species.Name = %s "
- "ORDER BY OrderId", (self.species.capitalize(),))
- else:
- cursor.execute(
- "SELECT Chr_Length.Name, Chr_Length.OrderId, "
- "Length FROM Chr_Length, InbredSet WHERE "
- "Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
- "InbredSet.Name = "
- "%s ORDER BY OrderId", (self.dataset.group.name,))
- for name, _, length in cursor.fetchall():
- chromosomes[name] = IndChromosome(
- name=name, length=length)
- return chromosomes
+ if self.species is not None:
+ db_cursor.execute(
+ "SELECT Chr_Length.Name, Chr_Length.OrderId, Length "
+ "FROM Chr_Length, Species WHERE "
+ "Chr_Length.SpeciesId = Species.SpeciesId AND "
+ "Species.Name = %s "
+ "ORDER BY OrderId", (self.species.capitalize(),))
+ else:
+ db_cursor.execute(
+ "SELECT Chr_Length.Name, Chr_Length.OrderId, "
+ "Length FROM Chr_Length, InbredSet WHERE "
+ "Chr_Length.SpeciesId = InbredSet.SpeciesId AND "
+ "InbredSet.Name = "
+ "%s ORDER BY OrderId", (self.dataset.group.name,))
+ for name, _, length in db_cursor.fetchall():
+ chromosomes[name] = IndChromosome(
+ name=name, length=length)
+ return chromosomes
diff --git a/wqflask/tests/unit/base/test_species.py b/wqflask/tests/unit/base/test_species.py
index d7ba30a3..f12bde6d 100644
--- a/wqflask/tests/unit/base/test_species.py
+++ b/wqflask/tests/unit/base/test_species.py
@@ -30,17 +30,14 @@ class MockDataset:
(None, "Random Dataset", None, 1)))
def test_species(mocker, species_name, dataset,
expected_name, chromosome_param):
- mock_conn = mocker.patch("base.species.database_connection")
- mock_conn.return_value.__enter__.return_value = mocker.MagicMock()
_c = mocker.patch("base.species.Chromosomes",
return_value=chromosome_param)
- with mock_conn() as conn:
- test_species = TheSpecies(dataset=dataset,
- species_name=species_name)
- _c.assert_called_with(conn=conn, species=species_name,
- dataset=dataset)
- assert test_species.name == expected_name
- assert test_species.chromosomes == chromosome_param
+ test_species = TheSpecies(dataset=dataset,
+ species_name=species_name)
+ _c.assert_called_with(species=species_name,
+ dataset=dataset)
+ assert test_species.name == expected_name
+ assert test_species.chromosomes == chromosome_param
@pytest.mark.parametrize(
@@ -74,9 +71,8 @@ def test_create_chromosomes(mocker, species, dataset, expected_call):
cursor.fetchall.return_value = (("1", 2, 10,),
("2", 3, 11,),
("4", 5, 15,),)
- _c = Chromosomes(conn=mock_conn,
- dataset=dataset, species=species)
- assert _c.chromosomes == OrderedDict([
+ _c = Chromosomes(dataset=dataset, species=species)
+ assert _c.chromosomes(cursor) == OrderedDict([
("1", IndChromosome("1", 10)),
("2", IndChromosome("2", 11)),
("4", IndChromosome("4", 15)),
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 1c8a4ff6..8d9c9e7f 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -9,12 +9,14 @@ from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
from redis import Redis
from flask import Flask, g
+from wqflask.database import database_connection
+
Redis = Redis()
class Heatmap:
- def __init__(self, start_vars, temp_uuid):
+ def __init__(self, db_cursor, start_vars, temp_uuid):
trait_db_list = [trait.strip()
for trait in start_vars['trait_list'].split(',')]
helper_functions.get_trait_db_obs(self, trait_db_list)
@@ -30,7 +32,8 @@ class Heatmap:
chrnames = []
self.species = species.TheSpecies(dataset=self.trait_list[0][1])
- for key in list(self.species.chromosomes.chromosomes.keys()):
+
+ for key in list(self.species.chromosomes(db_cursor).chromosomes.keys()):
chrnames.append([self.species.chromosomes.chromosomes[key].name,
self.species.chromosomes.chromosomes[key].mb_length])
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index ae6cf0cf..8cea271d 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -36,7 +36,7 @@ ONE_YEAR = 60 * 60 * 24 * 365
class ShowTrait:
- def __init__(self, user_id, kw):
+ def __init__(self, db_cursor, user_id, kw):
self.admin_status = None
if 'trait_id' in kw and kw['dataset'] != "Temp":
self.temp_trait = False
@@ -197,9 +197,9 @@ class ShowTrait:
# ZS: Get list of chromosomes to select for mapping
self.chr_list = [["All", -1]]
- for i, this_chr in enumerate(self.dataset.species.chromosomes.chromosomes):
+ for i, this_chr in enumerate(self.dataset.species.chromosomes.chromosomes(db_cursor)):
self.chr_list.append(
- [self.dataset.species.chromosomes.chromosomes[this_chr].name, i])
+ [self.dataset.species.chromosomes.chromosomes(db_cursor)[this_chr].name, i])
self.genofiles = self.dataset.group.get_genofiles()
study_samplelist_json = self.dataset.group.get_study_samplelists()
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 0dfa3e64..d5c4e946 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -9,7 +9,7 @@ from wqflask.database import database_connection
class SnpBrowser:
- def __init__(self, start_vars):
+ def __init__(self, db_cursor, start_vars):
self.strain_lists = get_browser_sample_lists()
self.initialize_parameters(start_vars)
@@ -30,7 +30,7 @@ class SnpBrowser:
self.header_fields, self.empty_field_count, self.header_data_names = get_header_list(
variant_type=self.variant_type, strains=self.strain_lists, species=self.species_name, empty_columns=self.empty_columns)
- def initialize_parameters(self, start_vars):
+ def initialize_parameters(self, db_cursor, start_vars):
if 'first_run' in start_vars:
self.first_run = "false"
else:
@@ -51,13 +51,13 @@ class SnpBrowser:
self.mouse_chr_list = []
self.rat_chr_list = []
mouse_species_ob = species.TheSpecies(species_name="Mouse")
- for key in mouse_species_ob.chromosomes.chromosomes:
+ for key in mouse_species_ob.chromosomes.chromosomes(db_cursor):
self.mouse_chr_list.append(
mouse_species_ob.chromosomes.chromosomes[key].name)
rat_species_ob = species.TheSpecies(species_name="Rat")
- for key in rat_species_ob.chromosomes.chromosomes:
+ for key in rat_species_ob.chromosomes.chromosomes(db_cursor):
self.rat_chr_list.append(
- rat_species_ob.chromosomes.chromosomes[key].name)
+ rat_species_ob.chromosomes.chromosomes(db_cursor)[key].name)
if self.species_id == 1:
self.this_chr_list = self.mouse_chr_list
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 11482469..4ea2d529 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -80,6 +80,8 @@ from utility.redis_tools import get_redis_conn
from base.webqtlConfig import GENERATED_IMAGE_DIR
+from wqflask.database import database_connection
+
Redis = get_redis_conn()
@@ -452,26 +454,30 @@ def export_perm_data():
@app.route("/show_temp_trait", methods=('POST',))
def show_temp_trait_page():
- user_id = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8")
- or g.user_session.record.get("user_id") or "")
- template_vars = show_trait.ShowTrait(user_id=user_id,
- kw=request.form)
- template_vars.js_data = json.dumps(template_vars.js_data,
- default=json_default_handler,
- indent=" ")
- return render_template("show_trait.html", **template_vars.__dict__)
+ with database_connection() as conn, conn.cursor() as cursor:
+ user_id = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8")
+ or g.user_session.record.get("user_id") or "")
+ template_vars = show_trait.ShowTrait(cursor,
+ user_id=user_id,
+ kw=request.form)
+ template_vars.js_data = json.dumps(template_vars.js_data,
+ default=json_default_handler,
+ indent=" ")
+ return render_template("show_trait.html", **template_vars.__dict__)
@app.route("/show_trait")
def show_trait_page():
- user_id = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8")
- or g.user_session.record.get("user_id") or "")
- template_vars = show_trait.ShowTrait(user_id=user_id,
- kw=request.args)
- template_vars.js_data = json.dumps(template_vars.js_data,
- default=json_default_handler,
- indent=" ")
- return render_template("show_trait.html", **template_vars.__dict__)
+ with database_connection() as conn, conn.cursor() as cursor:
+ user_id = ((g.user_session.record.get(b"user_id") or b"").decode("utf-8")
+ or g.user_session.record.get("user_id") or "")
+ template_vars = show_trait.ShowTrait(cursor,
+ user_id=user_id,
+ kw=request.args)
+ template_vars.js_data = json.dumps(template_vars.js_data,
+ default=json_default_handler,
+ indent=" ")
+ return render_template("show_trait.html", **template_vars.__dict__)
@app.route("/heatmap", methods=('POST',))
@@ -480,31 +486,32 @@ def heatmap_page():
temp_uuid = uuid.uuid4()
traits = [trait.strip() for trait in start_vars['trait_list'].split(',')]
- if traits[0] != "":
- version = "v5"
- key = "heatmap:{}:".format(
- version) + json.dumps(start_vars, sort_keys=True)
- result = Redis.get(key)
+ with database_connection() as conn, conn.cursor() as cursor:
+ if traits[0] != "":
+ version = "v5"
+ key = "heatmap:{}:".format(
+ version) + json.dumps(start_vars, sort_keys=True)
+ result = Redis.get(key)
- if result:
- result = pickle.loads(result)
+ if result:
+ result = pickle.loads(result)
- else:
- template_vars = heatmap.Heatmap(request.form, temp_uuid)
- template_vars.js_data = json.dumps(template_vars.js_data,
- default=json_default_handler,
- indent=" ")
+ else:
+ template_vars = heatmap.Heatmap(cursor, request.form, temp_uuid)
+ template_vars.js_data = json.dumps(template_vars.js_data,
+ default=json_default_handler,
+ indent=" ")
- result = template_vars.__dict__
+ result = template_vars.__dict__
- pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
- Redis.set(key, pickled_result)
- Redis.expire(key, 60 * 60)
- rendered_template = render_template("heatmap.html", **result)
+ pickled_result = pickle.dumps(result, pickle.HIGHEST_PROTOCOL)
+ Redis.set(key, pickled_result)
+ Redis.expire(key, 60 * 60)
+ rendered_template = render_template("heatmap.html", **result)
- else:
- rendered_template = render_template(
- "empty_collection.html", **{'tool': 'Heatmap'})
+ else:
+ rendered_template = render_template(
+ "empty_collection.html", **{'tool': 'Heatmap'})
return rendered_template
@@ -856,9 +863,9 @@ def corr_scatter_plot_page():
@app.route("/snp_browser", methods=('GET',))
def snp_browser_page():
- template_vars = snp_browser.SnpBrowser(request.args)
-
- return render_template("snp_browser.html", **template_vars.__dict__)
+ with database_connection() as conn, conn.cursor() as cursor:
+ template_vars = snp_browser.SnpBrowser(cursor, request.args)
+ return render_template("snp_browser.html", **template_vars.__dict__)
@app.route("/db_info", methods=('GET',))
@@ -870,15 +877,16 @@ def db_info_page():
@app.route("/snp_browser_table", methods=('GET',))
def snp_browser_table():
- snp_table_data = snp_browser.SnpBrowser(request.args)
- current_page = server_side.ServerSideTable(
- snp_table_data.rows_count,
- snp_table_data.table_rows,
- snp_table_data.header_data_names,
- request.args,
- ).get_page()
-
- return flask.jsonify(current_page)
+ with database_connection() as conn, conn.cursor() as cursor:
+ snp_table_data = snp_browser.SnpBrowser(cursor, request.args)
+ current_page = server_side.ServerSideTable(
+ snp_table_data.rows_count,
+ snp_table_data.table_rows,
+ snp_table_data.header_data_names,
+ request.args,
+ ).get_page()
+
+ return flask.jsonify(current_page)
@app.route("/tutorial/WebQTLTour", methods=('GET',))
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-19 15:49:02 +0000