diff options
| -rwxr-xr-x | bin/genenetwork2 | 2 | ||||
| -rw-r--r-- | wqflask/wqflask/__init__.py | 1 | ||||
| -rw-r--r-- | wqflask/wqflask/partial_correlations_views.py | 263 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/collections/view.html | 17 | ||||
| -rw-r--r-- | wqflask/wqflask/templates/partial_correlations.html | 199 |
5 files changed, 481 insertions, 1 deletions
diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 7669a89a..024f34d2 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -139,7 +139,7 @@ fi if [ "$1" = '-gunicorn-dev' ] ; then cd $GN2_BASE_DIR/wqflask if [ -z $SERVER_PORT ]; then echo "ERROR: Provide a SERVER_PORT" ; exit 1 ; fi - cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload wsgi" + cmd="--bind 0.0.0.0:$SERVER_PORT --workers=1 --timeout 180 --reload run_gunicorn:app" echo RUNNING gunicorn $cmd gunicorn $cmd exit $? 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"]}} - + {{primary_trait["symbol"]}} - {{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"]}} - {{trait["symbol"]}} - + {{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"]}} - {{trait["symbol"]}} - + {{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%} |