aboutsummaryrefslogtreecommitdiff
path: root/wqflask
diff options
context:
space:
mode:
authorFrederick Muriuki Muriithi2021-12-06 17:58:28 +0300
committerzsloan2022-01-29 00:42:44 -0600
commita01033438a85e3097e4ade30e9a208fd5109d4e1 (patch)
tree256aeec8bb4cdaa9101581709568b5506838f791 /wqflask
parentb9f16a3b28c4d996ac91befa5a919a9e0a7ac981 (diff)
downloadgenenetwork2-a01033438a85e3097e4ade30e9a208fd5109d4e1.tar.gz
Add "Partial Correlations" UI elements on collections page
Issue: https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/partial-correlations.gmi * Add UI elements to trigger the partial correlations feature * Connect partial correlation view to the application * Point to correct application element for gunicorn
Diffstat (limited to 'wqflask')
-rw-r--r--wqflask/wqflask/__init__.py1
-rw-r--r--wqflask/wqflask/partial_correlations_views.py263
-rw-r--r--wqflask/wqflask/templates/collections/view.html17
-rw-r--r--wqflask/wqflask/templates/partial_correlations.html199
4 files changed, 480 insertions, 0 deletions
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index 05e040ed..ab8b9e66 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -98,3 +98,4 @@ from wqflask import user_login
from wqflask import user_session
import wqflask.views
+import wqflask.partial_correlations_views
diff --git a/wqflask/wqflask/partial_correlations_views.py b/wqflask/wqflask/partial_correlations_views.py
new file mode 100644
index 00000000..bee0a033
--- /dev/null
+++ b/wqflask/wqflask/partial_correlations_views.py
@@ -0,0 +1,263 @@
+from typing import Union, Tuple
+
+import MySQLdb
+from gn3.db.traits import retrieve_trait_info
+from flask import flash, request, current_app, render_template
+from gn3.computations.partial_correlations import partial_correlations_entry
+
+from wqflask import app
+
+def parse_trait(trait_str: str) -> Union[dict, None]:
+ keys = ("name", "dataset", "symbol", "description", "data_hmac")
+ parts = tuple(part.strip() for part in trait_str.split(":::"))
+ if len(parts) == len(keys):
+ return dict(zip(keys, parts))
+ return None
+
+def process_step_select_primary(
+ primary_trait: dict, control_traits: Tuple[dict, ...],
+ target_traits: Tuple[dict, ...],
+ traits_list: Tuple[dict, ...], corr_method: str) -> Tuple[
+ str, dict, Tuple[dict, ...], Tuple[dict, ...], Tuple[dict, ...],
+ str]:
+ if primary_trait is None:
+ flash("You must select a primary trait", "alert-danger")
+ return (
+ "select-primary", primary_trait, control_traits, target_traits,
+ traits_list, corr_method)
+
+ return (
+ "select-controls", primary_trait, control_traits, target_traits,
+ tuple(
+ trait for trait in traits_list
+ if trait["data_hmac"] != primary_trait["data_hmac"]),
+ corr_method)
+
+def process_step_select_controls(
+ primary_trait: dict, control_traits: Tuple[dict, ...],
+ target_traits: Tuple[dict, ...],
+ traits_list: Tuple[dict, ...], corr_method: str) -> Tuple[
+ str, dict, Tuple[dict, ...], Tuple[dict, ...], Tuple[dict, ...],
+ str]:
+ if len(control_traits) == 0 or len(control_traits) > 3:
+ flash(
+ ("You must select a minimum of one control trait, up to a maximum "
+ "of three control traits."),
+ "alert-danger")
+ return (
+ "select-controls", primary_trait, control_traits, target_traits,
+ traits_list, corr_method)
+
+ hmacs =(primary_trait["data_hmac"],) + tuple(
+ trait["data_hmac"] for trait in control_traits)
+ return (
+ "select-targets", primary_trait, control_traits, target_traits,
+ tuple(
+ trait for trait in traits_list if trait["data_hmac"] not in hmacs),
+ corr_method)
+
+def process_step_select_targets(
+ primary_trait: dict, control_traits: Tuple[dict, ...],
+ target_traits: Tuple[dict, ...],
+ traits_list: Tuple[dict, ...], corr_method: str) -> Tuple[
+ str, dict, Tuple[dict, ...], Tuple[dict, ...], Tuple[dict, ...],
+ str]:
+ if len(target_traits) == 0:
+ flash(
+ "You must select at least one target trait.", "alert-danger")
+ return (
+ "select-targets", primary_trait, control_traits, target_traits,
+ traits_list, corr_method)
+
+ hmacs =(primary_trait["data_hmac"],) + tuple(
+ trait["data_hmac"] for trait in (control_traits + target_traits))
+ return (
+ "select-corr-method", primary_trait, control_traits, target_traits,
+ tuple(
+ trait for trait in traits_list if trait["data_hmac"] not in hmacs),
+ corr_method)
+
+def process_step_select_corr_method(
+ primary_trait: dict, control_traits: Tuple[dict, ...],
+ target_traits: Tuple[dict, ...],
+ traits_list: Tuple[dict, ...], corr_method: str) -> Tuple[
+ str, dict, Tuple[dict, ...], Tuple[dict, ...], Tuple[dict, ...],
+ str]:
+ methods = (
+ "genetic correlation, pearson's r",
+ "genetic correlation, spearman's rho",
+ "sgo literature correlation",
+ "tissue correlation, pearson's r",
+ "tissue correlation, spearman's rho")
+ if corr_method.lower() not in methods:
+ flash(
+ "Selected method is unknown.", "alert-danger")
+ return (
+ "select-corr-method", primary_trait, control_traits, target_traits,
+ traits_list, corr_method)
+
+ hmacs =(primary_trait["data_hmac"],) + tuple(
+ trait["data_hmac"] for trait in (control_traits + target_traits))
+ return (
+ "run-correlation", primary_trait, control_traits, target_traits,
+ tuple(
+ trait for trait in traits_list if trait["data_hmac"] not in hmacs),
+ corr_method)
+
+def process_step(
+ step: str, primary_trait: dict, control_traits: Tuple[dict, ...],
+ target_traits: Tuple[dict, ...], traits_list: Tuple[dict, ...],
+ corr_method: str) -> Tuple[
+ str, dict, Tuple[dict, ...], Tuple[dict, ...], Tuple[dict, ...],
+ str]:
+ processor_functions = {
+ # "select-traits": lambda arg: arg,
+ "select-primary": process_step_select_primary,
+ "select-controls": process_step_select_controls,
+ "select-targets": process_step_select_targets,
+ "select-corr-method": process_step_select_corr_method
+ }
+ return processor_functions[(step or "select-primary")](
+ primary_trait, control_traits, target_traits, traits_list, corr_method)
+
+def sequence_of_traits(trait_strs) -> Tuple[dict, ...]:
+ return tuple(filter(
+ lambda trt: trt is not None,
+ (parse_trait(tstr.strip()) for tstr in trait_strs)))
+
+def publish_target_dabases(conn, group, threshold):
+ query = (
+ "SELECT PublishFreeze.FullName,PublishFreeze.Name "
+ "FROM PublishFreeze, InbredSet "
+ "WHERE PublishFreeze.InbredSetId = InbredSet.Id "
+ "AND InbredSet.Name = %(group)s "
+ "AND PublishFreeze.public > %(threshold)s")
+ with conn.cursor() as cursor:
+ cursor.execute(query, {"group": group, "threshold": threshold})
+ res = cursor.fetchall()
+ if res:
+ return tuple(
+ dict(zip(("description", "value"), row)) for row in res)
+
+ return tuple()
+
+def geno_target_databases(conn, group, threshold):
+ query = (
+ "SELECT GenoFreeze.FullName,GenoFreeze.Name "
+ "FROM GenoFreeze, InbredSet "
+ "WHERE GenoFreeze.InbredSetId = InbredSet.Id "
+ "AND InbredSet.Name = %(group)s "
+ "AND GenoFreeze.public > %(threshold)s")
+ with conn.cursor() as cursor:
+ cursor.execute(query, {"group": group, "threshold": threshold})
+ res = cursor.fetchall()
+ if res:
+ return tuple(
+ dict(zip(("description", "value"), row)) for row in res)
+
+ return tuple()
+
+def probeset_target_databases(conn, group, threshold):
+ query1 = "SELECT Id, Name FROM Tissue order by Name"
+ query2 = (
+ "SELECT ProbeFreeze.TissueId, ProbeSetFreeze.FullName, ProbeSetFreeze.Name "
+ "FROM ProbeSetFreeze, ProbeFreeze, InbredSet "
+ "WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id "
+ "AND ProbeFreeze.TissueId IN %(tissue_ids)s "
+ "AND ProbeSetFreeze.public > %(threshold)s "
+ "AND ProbeFreeze.InbredSetId = InbredSet.Id "
+ "AND InbredSet.Name like %(group)s "
+ "ORDER BY ProbeSetFreeze.CreateTime desc, ProbeSetFreeze.AvgId")
+ with conn.cursor() as cursor:
+ cursor.execute(query1)
+ tissue_res = cursor.fetchall()
+ if tissue_res:
+ tissue_ids = tuple(row[0] for row in tissue_res)
+ cursor.execute(
+ query2,{
+ "tissue_ids": tissue_ids, "group": f"{group}%%",
+ "threshold": threshold
+ })
+ db_res = cursor.fetchall()
+ if db_res:
+ databases = tuple(
+ dict(zip(("tissue_id", "description", "value"), row))
+ for row in db_res)
+ return tuple(
+ {tissue_name: tuple(
+ {
+ "value": item["value"],
+ "description": item["description"]
+ } for item in databases
+ if item["tissue_id"] == tissue_id)}
+ for tissue_id, tissue_name in tissue_res)
+
+ return tuple()
+
+def target_databases(conn, step, trait, threshold):
+ """
+ Retrieves the names of possible target databases from the database.
+ """
+ if step != "select-corr-method":
+ return None
+
+ trait_info = retrieve_trait_info(
+ threshold, f"{trait['dataset']}::{trait['name']}", conn)
+ group = trait_info["group"]
+ return (
+ publish_target_dabases(conn, group, threshold) +
+ geno_target_databases(conn, group, threshold) +
+ probeset_target_databases(conn, group, threshold))
+
+def pcorrelations(conn, values):
+ if values["step"] != "run-correlation":
+ return None
+
+ def trait_fullname(trait):
+ return f"{trait['dataset']}::{trait['name']}"
+
+ return partial_correlations_entry(
+ conn, trait_fullname(values["primary_trait"]),
+ tuple(trait_fullname(trait) for trait in values["control_traits"]),
+ values["method"], values["criteria"], values["target_db"])
+
+@app.route("/partial_correlations", methods=("POST",))
+def partial_correlations():
+ form = request.form
+ traits_list = tuple(filter(
+ lambda trt: trt is not None,
+ (parse_trait(tstr) for tstr in form.get("traits_list", "").split("|||"))))
+
+ args_dict = dict(zip(
+ ("step", "primary_trait", "control_traits", "target_traits",
+ "traits_list", "method"),
+ process_step(
+ form.get("step", None),
+ parse_trait(form.get("primary_trait", "")),
+ sequence_of_traits(
+ form.getlist("control_traits[]") or
+ form.get("control_traits", "").split("|||")),
+ sequence_of_traits(
+ form.getlist("target_traits[]") or
+ form.get("target_traits", "").split("|||")),
+ sequence_of_traits(form.get("traits_list", "").split("|||")),
+ form.get("method"))))
+
+ conn = MySQLdb.Connect(
+ db=current_app.config.get("DB_NAME"),
+ user=current_app.config.get("DB_USER"),
+ passwd=current_app.config.get("DB_PASS"),
+ host=current_app.config.get("DB_HOST"))
+ target_dbs = target_databases(
+ conn, args_dict["step"], args_dict["primary_trait"], 0)
+
+ if args_dict["step"] == "run-correlation":
+ args_dict = {
+ **args_dict, "target_db": form.get("target_db"),
+ "criteria": int(form.get("criteria", 500))}
+
+ corr_results = pcorrelations(conn, args_dict)
+
+ return render_template(
+ "partial_correlations.html", **args_dict, target_dbs=target_dbs,
+ corr_results=corr_results)
diff --git a/wqflask/wqflask/templates/collections/view.html b/wqflask/wqflask/templates/collections/view.html
index 0ded66a6..f4270b67 100644
--- a/wqflask/wqflask/templates/collections/view.html
+++ b/wqflask/wqflask/templates/collections/view.html
@@ -34,6 +34,23 @@
</form>
</div>
+ <form id="partial-correlations-form"
+ method="POST"
+ action="{{url_for('partial_correlations')}}">
+ <input type="hidden"
+ id="collection_uuid"
+ value="{{uc.uc_id}}" />
+ <input type="hidden"
+ name="traits_list"
+ value="{% for this_trait in trait_obs %}{{ this_trait.name }}:::{{ this_trait.dataset.name }}:::{{this_trait.symbol}}:::{{this_trait.description_display}}:::{{data_hmac('{}:{}'.format(this_trait.name, this_trait.dataset.name))}}|||{% endfor %}" />
+ <button id="run-partial-correlations"
+ class="btn btn-primary"
+ title="Run partial correlations"
+ type="submit">
+ Partial Correlations
+ </button>
+ </form>
+
<div>
<br />
<form id="heatmaps_form">
diff --git a/wqflask/wqflask/templates/partial_correlations.html b/wqflask/wqflask/templates/partial_correlations.html
new file mode 100644
index 00000000..b61f7fc4
--- /dev/null
+++ b/wqflask/wqflask/templates/partial_correlations.html
@@ -0,0 +1,199 @@
+{%extends "base.html"%}
+
+{%block content%}
+<div class="container">
+ <form id="partial-correlations-form"
+ method="POST"
+ action="{{url_for('partial_correlations')}}">
+ {%with messages = get_flashed_messages(with_categories=true)%}
+ {%if messages:%}
+ <ul class=flashes>
+ {%for category, message in messages:%}
+ <li class="{{category}}">{{message}}</li>
+ {%endfor%}
+ </ul>
+ {%endif%}
+ {%endwith%}
+
+ <input type="hidden" name="step" id="step-indicator" value="{{step}}" />
+ <input type="hidden"
+ name="traits_list"
+ value="{% for trait in traits_list %}{{trait['name']}}:::{{trait['dataset']}}:::{{trait['symbol']}}:::{{trait['description']}}:::{{trait['data_hmac']}}|||{% endfor %}">
+
+ {%if primary_trait:%}
+ <input type="hidden"
+ name="primary_trait"
+ value="{{primary_trait['name']}}:::{{primary_trait['dataset']}}:::{{primary_trait['symbol']}}:::{{primary_trait['description']}}:::{{primary_trait['data_hmac']}}"
+ id="trait_{{primary_trait['data_hmac']}}" />
+ <p>
+ Primary Trait: {{primary_trait["name"]}}&nbsp;-&nbsp;
+ {{primary_trait["symbol"]}}&nbsp;-&nbsp;{{primary_trait["description"]}}
+ </p>
+ {%endif%}
+
+ {%if control_traits:%}
+ <input type="hidden"
+ name="control_traits"
+ value="{%for trait in control_traits:%}{{trait['name']}}:::{{trait['dataset']}}:::{{trait['symbol']}}:::{{trait['description']}}:::{{trait['data_hmac']}}|||{%endfor%}" />
+ <p>
+ Control Traits:
+ <ul>
+ {%for trait in control_traits:%}
+ <li>
+ {{trait["name"]}}&nbsp;-&nbsp;{{trait["symbol"]}}&nbsp;-&nbsp;
+ {{trait["description"]}}</li>
+ {%endfor%}
+ </ul>
+ </p>
+ {%endif%}
+
+ {%if target_traits:%}
+ <input type="hidden"
+ name="target_traits"
+ value="{%for trait in target_traits:%}{{trait['name']}}:::{{trait['dataset']}}:::{{trait['symbol']}}:::{{trait['description']}}:::{{trait['data_hmac']}},{%endfor%}" />
+ <p>
+ Target Traits:
+ <ul>
+ {%for trait in target_traits:%}
+ <li>
+ {{trait["name"]}}&nbsp;-&nbsp;{{trait["symbol"]}}&nbsp;-&nbsp;
+ {{trait["description"]}}</li>
+ {%endfor%}
+ </ul>
+ </p>
+ {%endif%}
+
+
+
+ {%if step == "select-primary":%}
+ <p>Please select the primary trait (X)</p>
+ {%for trait in traits_list:%}
+ <div class="form-group">
+ <input type="radio"
+ name="primary_trait"
+ value="{{trait['name']}}:::{{trait['dataset']}}:::{{trait['symbol']}}:::{{trait['description']}}:::{{trait['data_hmac']}}"
+ id="trait_{{trait['data_hmac']}}" />
+ <label for="trait_{{trait['data_hmac']}}">
+ {{trait["name"]}} - {{trait["symbol"]}} - {{trait["description"]}}
+ </label>
+ </div>
+ {%endfor%}
+ <button type="submit" class="btn btn-primary">
+ Next: Select Control Traits
+ </button>
+ {%endif%}
+
+
+
+ {%if step == "select-controls":%}
+
+ <p>Select a maximum of three (3) control traits (Z)</p>
+ {%for trait in traits_list:%}
+ <div class="form-group">
+ <input type="checkbox"
+ name="control_traits[]"
+ value="{{trait['name']}}:::{{trait['dataset']}}:::{{trait['symbol']}}:::{{trait['description']}}:::{{trait['data_hmac']}}"
+ id="trait_{{trait['data_hmac']}}" />
+ <label for="trait_{{trait['data_hmac']}}">
+ {{trait["name"]}} - {{trait["symbol"]}} - {{trait["description"]}}
+ </label>
+ </div>
+ {%endfor%}
+ <button type="submit" class="btn btn-primary">
+ Next: Select Target Traits
+ </button>
+ {%endif%}
+
+
+
+ {%if step == "select-targets":%}
+ <p>Select at least one target trait (Y)</p>
+ {%for trait in traits_list:%}
+ <div class="form-group">
+ <input type="checkbox"
+ name="target_traits[]"
+ value="{{trait['name']}}:::{{trait['dataset']}}:::{{trait['symbol']}}:::{{trait['description']}}:::{{trait['data_hmac']}}"
+ checked="checked"
+ id="trait_{{trait['data_hmac']}}" />
+ <label for="trait_{{trait['data_hmac']}}">
+ {{trait["name"]}} - {{trait["symbol"]}} - {{trait["description"]}}
+ </label>
+ </div>
+ {%endfor%}
+ <button type="submit" class="btn btn-primary">
+ Next: Select Correlation Method
+ </button>
+ {%endif%}
+
+
+
+ {%if step == "select-corr-method":%}
+ <div class="form-group">
+ <label for="target-db-input">Choose Database</label>
+ <select id="target-db-input" required="required" name="target_db">
+ {%if target_dbs:%}
+ {%for item in target_dbs:%}
+ {%if "description" in item.keys():%}
+ <option value="{{item['value']}}">{{item['description']}}</option>
+ {%else:%}
+ {%for group, opts in item.items()%}
+ {%if opts | length > 0:%}
+ <optgroup label="{{group}} ------">
+ {%for item2 in opts:%}
+ <option value="{{item2['value']}}">{{item2['description']}}</option>
+ {%endfor%}
+ </optgroup>
+ {%endif%}
+ {%endfor%}
+ {%endif%}
+ {%endfor%}
+ {%endif%}
+ </select>
+ </div>
+
+ <div class="form-group">
+ <label for="corr-method-input">Compute</label>
+ <select id="corr-method-input" required="required" name="method">
+ <option value="Genetic Correlation, Pearson's r">
+ Genetic Correlation, Pearson's r</option>
+ <option value="Genetic Correlation, Spearman's rho">
+ Genetic Correlation, Spearman's rho</option>
+ <option value="SGO Literature Correlation">
+ SGO Literature Correlation</option>
+ <option value="Tissue Correlation, Pearson's r">
+ Tissue Correlation, Pearson's r</option>
+ <option value="Tissue Correlation, Spearman's rho">
+ Tissue Correlation, Spearman's rho</option>
+ </select>
+ </div>
+
+ <div class="form-group">
+ <label for="criteria-input">Return</label>
+ <select id="criteria-input" required="required" name="criteria" size="1">
+ <option value="100">top 100</option>
+ <option value="200">top 200</option>
+ <option value="500" selected="selected">top 500</option>
+ <option value="1000">top 1000</option>
+ <option value="2000">top 2000</option>
+ <option value="5000">top 5000</option>
+ <option value="10000">top 10000</option>
+ <option value="15000">top 15000</option>
+ <option value="20000">top 20000</option>
+ </select>
+ </div>
+
+ <button type="submit" class="btn btn-primary">
+ Run Partial Correlation
+ </button>
+ {%endif%}
+
+ {%if step == "run-correlation":%}
+ <input type="hidden" name="selected_method" value="{{method}}" />
+ <input type="hidden" name="selected_target_db" value="{{target_db}}" />
+ <input type="hidden" name="selected_criteria" value="{{criteria}}" />
+
+ {{corr_results}}
+ {%endif%}
+ </form>
+</div>
+{%endblock%}