diff options
| -rw-r--r-- | etc/default_config.py | 1 | ||||
| -rw-r--r-- | mypy.ini | 3 | ||||
| -rw-r--r-- | qc_app/__init__.py | 2 | ||||
| -rw-r--r-- | qc_app/dbinsert.py | 63 | ||||
| -rw-r--r-- | qc_app/parse.py | 3 | ||||
| -rw-r--r-- | qc_app/static/css/styles.css | 19 | ||||
| -rw-r--r-- | qc_app/static/js/dbinsert.js | 105 | ||||
| -rw-r--r-- | qc_app/templates/dbupdate_error.html | 12 | ||||
| -rw-r--r-- | qc_app/templates/parse_results.html | 7 | ||||
| -rw-r--r-- | qc_app/templates/select_dataset.html | 75 |
10 files changed, 289 insertions, 1 deletions
diff --git a/etc/default_config.py b/etc/default_config.py index 76b6b43..fcb17d9 100644 --- a/etc/default_config.py +++ b/etc/default_config.py @@ -10,3 +10,4 @@ SECRET_KEY = b"<Please! Please! Please! Change This!>" UPLOAD_FOLDER = "/tmp/qc_app_files" REDIS_URL = "redis://" JOBS_TTL_SECONDS = 1209600 # 14 days +GN3_URL="http://localhost:8080" @@ -19,4 +19,7 @@ ignore_missing_imports = True ignore_missing_imports = True [mypy-jsonpickle.*] +ignore_missing_imports = True + +[mypy-requests.*] ignore_missing_imports = True
\ No newline at end of file diff --git a/qc_app/__init__.py b/qc_app/__init__.py index 08b56c9..6b760b9 100644 --- a/qc_app/__init__.py +++ b/qc_app/__init__.py @@ -6,6 +6,7 @@ from flask import Flask from .entry import entrybp from .parse import parsebp +from .dbinsert import dbinsertbp def instance_path(): """Retrieve the `instance_path`. Raise an exception if not defined.""" @@ -27,4 +28,5 @@ def create_app(instance_dir): # setup blueprints app.register_blueprint(entrybp, url_prefix="/") app.register_blueprint(parsebp, url_prefix="/parse") + app.register_blueprint(dbinsertbp, url_prefix="/dbinsert") return app diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py new file mode 100644 index 0000000..0733e5f --- /dev/null +++ b/qc_app/dbinsert.py @@ -0,0 +1,63 @@ +"Handle inserting data into the database" +import os +import json +from functools import reduce + +import requests +from redis import Redis +from flask import request, Blueprint, render_template, current_app as app + +from . import jobs + +dbinsertbp = Blueprint("dbinsert", __name__) + +def render_error(error_msg): + "Render the generic error page" + return render_template("dbupdate_error.html", error_message=error_msg), 400 + +def make_menu_items_grouper(grouping_fn=lambda item: item): + "Build function to be used to group menu items." + def __grouper__(acc, row): + grouping = grouping_fn(row[2]) + row_values = (row[0].strip(), row[1].strip()) + if acc.get(grouping) is None: + return {**acc, grouping: (row_values,)} + return {**acc, grouping: (acc[grouping] + (row_values,))} + return __grouper__ + +@dbinsertbp.route("/select-dataset", methods=["POST"]) +def select_dataset(): + "Select the dataset to add the file contents against" + job_id = request.form["job_id"] + with Redis.from_url(app.config["REDIS_URL"], decode_responses=True) as rconn: + job = jobs.job(rconn, job_id) + if job: + filename = job["filename"] + filepath = f"{app.config['UPLOAD_FOLDER']}/{filename}" + if os.path.exists(filepath): + req = requests.get( + "https://genenetwork.org/api3/api/menu/generate/json") + menu_contents = req.json() + default_species = "mouse" + mouse_groups = reduce( + make_menu_items_grouper( + lambda item: item.strip()[7:].strip()), + menu_contents["groups"][default_species], {}) + default_group = "BXD" + group_types = reduce( + make_menu_items_grouper(), + menu_contents["types"][default_species][default_group], {}) + default_type = group_types[tuple(group_types)[0]][0][0] + datasets = menu_contents[ + "datasets"][default_species][default_group][ + default_type] + + return render_template( + "select_dataset.html", job_id=job_id, job_name=filename, + species=menu_contents["species"], + default_species=default_species, groups=mouse_groups, + types=group_types, datasets=datasets, + menu_contents=json.dumps(menu_contents)) + return render_error(f"File '{filename}' no longer exists.") + return render_error(f"Job '{job_id}' no longer exists.") + return render_error("Unknown error") diff --git a/qc_app/parse.py b/qc_app/parse.py index 5d75c37..2a33fd0 100644 --- a/qc_app/parse.py +++ b/qc_app/parse.py @@ -104,7 +104,8 @@ def results(job_id: str): "parse_results.html", errors=errors, job_name = f"Parsing '{filename}'", - user_aborted = job.get("user_aborted")) + user_aborted = job.get("user_aborted"), + job_id=job["job_id"]) return render_template("no_such_job.html", job_id=job_id) diff --git a/qc_app/static/css/styles.css b/qc_app/static/css/styles.css index 9e5a4ec..4d0fa8c 100644 --- a/qc_app/static/css/styles.css +++ b/qc_app/static/css/styles.css @@ -101,3 +101,22 @@ table { border: 2px solid; border-radius: 1em; } + +form { + width: 30%; +} + +fieldset { + border-style: none; + display: grid; + grid-template-columns: 5em 1fr; + column-gap: 5px; +} + +label { + grid-column: 1 / 2; +} + +input,select,button { + grid-column: 2 / 3; +} diff --git a/qc_app/static/js/dbinsert.js b/qc_app/static/js/dbinsert.js new file mode 100644 index 0000000..3c0be54 --- /dev/null +++ b/qc_app/static/js/dbinsert.js @@ -0,0 +1,105 @@ +function remove_children(element) { + Array.from(element.children).forEach(child => { + element.removeChild(child); + }); +} + +function trigger_change_event(element) { + evt = new Event("change"); + element.dispatchEvent(evt); +} + +function setup_groups(group_data) { + elt = document.getElementById("group"); + remove_children(elt); + the_groups = group_data.reduce( + function(acc, row) { + grouping = row[2].slice(7).trim(); + if(acc[grouping] === undefined) { + acc[grouping] = []; + } + acc[grouping].push([row[0], row[1]]); + return acc; + }, + {}); + for(grouping in the_groups) { + optgrp = document.createElement("optgroup"); + optgrp.setAttribute("label", grouping); + the_groups[grouping].forEach(group => { + opt = document.createElement("option"); + opt.setAttribute("value", group[0]); + opt.appendChild(document.createTextNode(group[1])); + optgrp.appendChild(opt); + }); + elt.appendChild(optgrp); + } + trigger_change_event(elt); +} + +function setup_types(type_data) { + elt = document.getElementById("type"); + remove_children(elt); + the_types = type_data.reduce(function(acc, row) { + grp = row[2]; + if(acc[grp] === undefined) { + acc[grp] = []; + } + acc[grp].push([row[0], row[1]]); + return acc; + }, {}); + for(type_group in the_types) { + optgrp = document.createElement("optgroup"); + optgrp.setAttribute("label", type_group); + the_types[type_group].forEach(type => { + opt = document.createElement("option"); + opt.setAttribute("value", type[0]); + opt.appendChild(document.createTextNode(type[1])); + optgrp.appendChild(opt); + }); + elt.appendChild(optgrp); + } + trigger_change_event(elt); +} + +function setup_datasets(dataset_data) { + console.info("DATASET DATA:", dataset_data); + elt = document.getElementById("dataset"); + remove_children(elt); + dataset_data.forEach(dataset => { + opt = document.createElement("option"); + opt.setAttribute("value", dataset[0]); + opt.appendChild(document.createTextNode( + "[" + dataset[1] + "] " + dataset[2])); + elt.appendChild(opt); + }); + trigger_change_event(elt); +} + +function menu_contents() { + return JSON.parse( + document.getElementsByTagName("form")[0].getAttribute( + "data-menu-content")); +} + +function update_menu(event) { + menu = menu_contents(); + + species_elt = document.getElementById("species"); + group_elt = document.getElementById("group"); + type_elt = document.getElementById("type"); + dataset_elt = document.getElementById("dataset"); + + if(event.target == species_elt) { + setup_groups(menu["groups"][species_elt.value]); + } + + if(event.target == group_elt) { + setup_types(menu["types"][species_elt.value][group_elt.value]); + } + + if(event.target == type_elt) { + setup_datasets( + menu["datasets"][species_elt.value][group_elt.value][type_elt.value] + ); + } +} diff --git a/qc_app/templates/dbupdate_error.html b/qc_app/templates/dbupdate_error.html new file mode 100644 index 0000000..83e34fe --- /dev/null +++ b/qc_app/templates/dbupdate_error.html @@ -0,0 +1,12 @@ +{%extends "base.html"%} + +{%block title%}DB Update Error{%endblock%} + +{%block contents%} +<h1 class="heading">database update error</h2> + +<p class="alert-error"> + <strong>Database Update Error</strong>: {{error_message}} +</p> + +{%endblock%} diff --git a/qc_app/templates/parse_results.html b/qc_app/templates/parse_results.html index 358c5e8..1a224e8 100644 --- a/qc_app/templates/parse_results.html +++ b/qc_app/templates/parse_results.html @@ -12,4 +12,11 @@ {{errors_display(errors, "No errors found in the file", "We found the following errors")}} +{%if errors | length == 0 %} +<form method="post" action="{{url_for('dbinsert.select_dataset')}}"> + <input type="hidden" name="job_id" value="{{job_id}}" /> + <input type="submit" value="update database" class="btn btn-main" /> +</form> +{%endif%} + {%endblock%} diff --git a/qc_app/templates/select_dataset.html b/qc_app/templates/select_dataset.html new file mode 100644 index 0000000..5fefccc --- /dev/null +++ b/qc_app/templates/select_dataset.html @@ -0,0 +1,75 @@ +{%extends "base.html"%} + +{%block title%}Select Dataset{%endblock%} + +{%block contents%} +<h1 class="heading">{{job_name}}: select dataset</h2> + +<form method="POST" data-menu-content="{{menu_contents}}"> + <input type="hidden" name="job_id" value="{{job_id}}" /> + + <fieldset> + <label for="species">species:</label> + <select id="species" name="species"> + {%for row in species:%} + <option value="{{row[0]}}" + {%if row[0] == default_species:%} + selected="selected" + {%endif%}> + {{row[1]}} + </option> + {%endfor%} + </select> + </fieldset> + + <fieldset> + <label for="group">group:</label> + <select id="group" name="group"> + {%for grouping, grps in groups.items():%} + <optgroup label="{{grouping}}"> + {%for group in grps:%} + <option value="{{group[0]}}">{{group[1]}}</option> + {%endfor%} + </optgroup> + {%endfor%} + </select> + </fieldset> + + <fieldset> + <label for="type">type:</label> + <select id="type" name="type"> + {%for grouping, typs in types.items():%} + <optgroup label="{{grouping}}"> + {%for type in typs:%} + <option value="{{type[0]}}">{{type[1]}}</option> + {%endfor%} + </optgroup> + {%endfor%} + </select> + </fieldset> + + <fieldset> + <label for="dataset">dataset:</label> + <select id="dataset" name="dataset"> + {%for dataset_id, name1, name2 in datasets:%} + <option value="{{dataset_id}}">[{{name1}}] {{name2}}</option> + {%endfor%} + </select> + </fieldset> + + <fieldset> + <input type="submit" class="btn btn-main" value="update database" /> + </fieldset> + +</form> + +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/dbinsert.js"></script> +<script type="text/javascript"> + document.getElementById("species").addEventListener("change", update_menu); + document.getElementById("group").addEventListener("change", update_menu); + document.getElementById("type").addEventListener("change", update_menu); +</script> +{%endblock%} |