diff options
| -rw-r--r-- | qc_app/dbinsert.py | 49 | ||||
| -rw-r--r-- | qc_app/static/js/select_platform.js | 59 | ||||
| -rw-r--r-- | qc_app/static/js/utils.js | 10 | ||||
| -rw-r--r-- | qc_app/templates/parse_results.html | 2 | ||||
| -rw-r--r-- | qc_app/templates/select_platform.html | 72 |
5 files changed, 183 insertions, 9 deletions
diff --git a/qc_app/dbinsert.py b/qc_app/dbinsert.py index 09dd3e1..ea47806 100644 --- a/qc_app/dbinsert.py +++ b/qc_app/dbinsert.py @@ -27,24 +27,57 @@ def make_menu_items_grouper(grouping_fn=lambda item: item): return {**acc, grouping: (acc[grouping] + (row_values,))} return __grouper__ +def species() -> tuple: + "Retrieve the species from the database." + with database_connection() as conn: + with conn.cursor(cursorclass=DictCursor) as cursor: + cursor.execute( + "SELECT SpeciesId, SpeciesName, LOWER(Name) AS Name, MenuName " + "FROM Species") + return tuple(cursor.fetchall()) + + return tuple() + def genechips(): "Retrieve the genechip information from the database" def __organise_by_species__(acc, chip): - species = chip["species_name"] - if acc.get(species) is None: - return {**acc, species: (chip,)} - return {**acc, species: acc[species] + (chip,)} + speciesid = chip["SpeciesId"] + if acc.get(speciesid) is None: + return {**acc, speciesid: (chip,)} + return {**acc, species: acc[speciesid] + (chip,)} with database_connection() as conn: with conn.cursor(cursorclass=DictCursor) as cursor: - cursor.execute( - "SELECT GeneChip.*, LOWER(Species.Name) AS species_name " - "FROM GeneChip INNER JOIN Species " - "ON GeneChip.SpeciesId=Species.SpeciesId") + cursor.execute("SELECT * FROM GeneChip ORDER BY GeneChipName ASC") return reduce(__organise_by_species__, cursor.fetchall(), {}) return {} +@dbinsertbp.route("/platform", methods=["POST"]) +def select_platform(): + "Select the platform (GeneChipId) used for the data." + 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): + default_species = 1 + gchips = genechips() + return render_template( + "select_platform.html", filename=filename, + filetype=job["filetype"], default_species=default_species, + species=species(), genechips=gchips[default_species], + genechips_data=json.dumps(gchips)) + return render_error(f"File '{filename}' no longer exists.") + return render_error(f"Job '{job_id}' no longer exists.") + return render_error("Unknown error") + +@dbinsertbp.route("/study", methods=["POST"]) +def select_study(): + return "Not implemented yet" + @dbinsertbp.route("/select-dataset", methods=["POST"]) def select_dataset(): "Select the dataset to add the file contents against" diff --git a/qc_app/static/js/select_platform.js b/qc_app/static/js/select_platform.js new file mode 100644 index 0000000..d7541fa --- /dev/null +++ b/qc_app/static/js/select_platform.js @@ -0,0 +1,59 @@ +function radio_column(chip) { + col = document.createElement("td"); + radio = document.createElement("input"); + radio.setAttribute("type", "radio"); + radio.setAttribute("name", "genechipid"); + radio.setAttribute("value", chip["GeneChipId"]); + radio.setAttribute("required", "required"); + col.appendChild(radio); + return col; +} + +function setup_genechips(genechip_data) { + columns = ["GeneChipName", "Name", "GeoPlatform", "GO_tree_value"] + submit_button = document.querySelector( + "#select-platform-form input[type='submit']"); + elt = document.getElementById( + "genechips-table").getElementsByTagName("tbody")[0]; + remove_children(elt); + if((genechip_data === undefined) || genechip_data.length === 0) { + row = document.createElement("tr"); + col = document.createElement("td"); + col.setAttribute("colspan", "5"); + text = document.createTextNode("No chips found for selected species"); + col.appendChild(text); + row.appendChild(col); + elt.appendChild(row); + submit_button.setAttribute("disabled", true); + return false; + } + + submit_button.removeAttribute("disabled") + genechip_data.forEach(chip => { + row = document.createElement("tr"); + row.appendChild(radio_column(chip)); + columns.forEach(column => { + col = document.createElement("td"); + content = document.createTextNode(chip[column]); + col.appendChild(content); + row.appendChild(col); + }); + elt.appendChild(row); + }); +} + +function genechips() { + return JSON.parse( + document.getElementById("select-platform-form").getAttribute( + "data-genechips")); +} + +function update_genechips(event) { + genec = genechips(); + + species_elt = document.getElementById("species"); + + if(event.target == species_elt) { + setup_genechips(genec[species_elt.value.toLowerCase()]); + } +} diff --git a/qc_app/static/js/utils.js b/qc_app/static/js/utils.js new file mode 100644 index 0000000..045dd47 --- /dev/null +++ b/qc_app/static/js/utils.js @@ -0,0 +1,10 @@ +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); +} diff --git a/qc_app/templates/parse_results.html b/qc_app/templates/parse_results.html index 1a224e8..80d6a2d 100644 --- a/qc_app/templates/parse_results.html +++ b/qc_app/templates/parse_results.html @@ -13,7 +13,7 @@ {{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')}}"> +<form method="post" action="{{url_for('dbinsert.select_platform')}}"> <input type="hidden" name="job_id" value="{{job_id}}" /> <input type="submit" value="update database" class="btn btn-main" /> </form> diff --git a/qc_app/templates/select_platform.html b/qc_app/templates/select_platform.html new file mode 100644 index 0000000..f8db736 --- /dev/null +++ b/qc_app/templates/select_platform.html @@ -0,0 +1,72 @@ +{%extends "base.html"%} + +{%block title%}Select Dataset{%endblock%} + +{%block contents%} +<h1 class="heading">{{filename}}: select platform</h2> + +<form method="POST" action="{{url_for('dbinsert.select_study')}}" + id="select-platform-form" data-genechips="{{genechips_data}}"> + <input type="hidden" name="filename" value="{{filename}}" /> + <input type="hidden" name="filetype" value="{{filetype}}" /> + + <fieldset> + <label for="species" class="form-col-1">species</label> + <select id="species" name="species" class="form-col-2"> + {%for row in species:%} + <option value="{{row['SpeciesId']}}" + {%if row["Name"] == default_species:%} + selected="selected" + {%endif%}> + {{row["MenuName"]}} + </option> + {%endfor%} + </select> + </fieldset> + + <table id="genechips-table"> + <thead> + <tr> + <th>Select</th> + <th>GeneChip Name</th> + <th>Name</th> + <th>GeoPlatform</th> + <th>GO Tree Value</th> + </tr> + </thead> + + <tbody> + {%for chip in genechips:%} + <tr> + <td> + <input type="radio" name="genechipid" value="{{chip['GeneChipId']}}" + required="required" /> + </td> + <td>{{chip["GeneChipName"]}}</td> + <td>{{chip["Name"]}}</td> + <td>{{chip["GeoPlatform"]}}</td> + <td>{{chip["GO_tree_value"]}}</td> + </tr> + {%else%} + <tr> + <td colspan="5">No chips found for selected species</td> + </tr> + {%endfor%} + </tbody> + </table> + + <fieldset> + <input type="submit" class="btn btn-main form-col-2" + value="submit platform" /> + </fieldset> +</form> +{%endblock%} + +{%block javascript%} +<script type="text/javascript" src="/static/js/utils.js"></script> +<script type="text/javascript" src="/static/js/select_platform.js"></script> +<script type="text/javascript"> + document.getElementById( + "species").addEventListener("change", update_genechips); +</script> +{%endblock%} |