diff options
| -rw-r--r-- | wqflask/wqflask/templates/edit_probeset.html | 239 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 31 |
2 files changed, 268 insertions, 2 deletions
diff --git a/wqflask/wqflask/templates/edit_probeset.html b/wqflask/wqflask/templates/edit_probeset.html new file mode 100644 index 00000000..85d49561 --- /dev/null +++ b/wqflask/wqflask/templates/edit_probeset.html @@ -0,0 +1,239 @@ +{% extends "base.html" %} +{% block title %}Trait Submission{% endblock %} +{% block content %} +<!-- Start of body --> +Edit Trait for Probeset +Submit Trait | Reset + +{% if diff %} + +<div class="container"> + <details class="col-sm-12 col-md-10 col-lg-12"> + <summary> + <h2>Update History</h2> + </summary> + <table class="table"> + <tbody> + <tr> + <th>Timestamp</th> + <th>Editor</th> + <th>Field</th> + <th>Diff</th> + </tr> + {% set ns = namespace(display_cell=True) %} + + {% for timestamp, group in diff %} + {% set ns.display_cell = True %} + {% for i in group %} + <tr> + {% if ns.display_cell and i.timestamp == timestamp %} + + {% set author = i.author %} + {% set timestamp_ = i.timestamp %} + + {% else %} + + {% set author = "" %} + {% set timestamp_ = "" %} + + {% endif %} + <td>{{ timestamp_ }}</td> + <td>{{ author }}</td> + <td>{{ i.diff.field }}</td> + <td><pre>{{ i.diff.diff }}</pre></td> + {% set ns.display_cell = False %} + </tr> + {% endfor %} + {% endfor %} + </tbody> + </table> + </details> + +</div> + +{% endif %} + +<form id="edit-form" class="form-horizontal" method="post" action="/probeset/update"> + <h2 class="text-center">Probeset Information:</h2> + <div class="form-group"> + <label for="symbol" class="col-sm-2 control-label">Symbol:</label> + <div class="col-sm-4"> + <textarea name="symbol" class="form-control" rows="1">{{ probeset.symbol |default('', true) }}</textarea> + <input name="old_symbol" class="changed" type="hidden" value="{{ probeset.symbol |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="description" class="col-sm-2 control-label">Description:</label> + <div class="col-sm-5"> + <textarea name="description" class="form-control" rows="3">{{ probeset.description |default('', true) }}</textarea> + <input name="old_description" class="changed" type="hidden" value="{{ probeset.description |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_target_description" class="col-sm-2 control-label">Probe Target Description:</label> + <div class="col-sm-4"> + <textarea name="probe_target_description" class="form-control" rows="4">{{ probeset.probe_target_description |default('', true) }}</textarea> + <input name="old_probe_target_description" class="changed" type="hidden" value="{{ probeset.probe_target_description |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="chr" class="col-sm-2 control-label">Chr:</label> + <div class="col-sm-4"> + <textarea name="chr" class="form-control" rows="1">{{ probeset.chr_ |default('', true) }}</textarea> + <input name="old_chr_" class="changed" type="hidden" value="{{ probeset.chr_ |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="mb" class="col-sm-2 control-label">Mb:</label> + <div class="col-sm-4"> + <textarea name="mb" class="form-control" rows="1">{{ probeset.mb |default('', true) }}</textarea> + <input name="old_mb" class="changed" type="hidden" value="{{ probeset.mb |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="alias" class="col-sm-2 control-label"> + Alias: + </label> + <div class="col-sm-4"> + <textarea name="alias" class="form-control" rows="1">{{ probeset.alias |default('', true) }}</textarea> + <input name="old_alias" class="changed" type="hidden" value="{{ probeset.alias |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="geneid" class="col-sm-2 control-label"> + Gene Id: + </label> + <div class="col-sm-4"> + <textarea name="geneid" class="form-control" rows="1">{{ probeset.geneid |default('', true) }}</textarea> + <input name="old_geneid" class="changed" type="hidden" value="{{ probeset.geneid |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="homologeneid" class="col-sm-2 control-label"> + Homolegene Id: + </label> + <div class="col-sm-4"> + <textarea name="homologeneid" class="form-control" rows="1">{{ probeset.homologeneid |default('', true) }}</textarea> + <input name="old_homologeneid" class="changed" type="hidden" value="{{ probeset.homologeneid |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="unigeneid" class="col-sm-2 control-label"> + Unigene Id: + </label> + <div class="col-sm-4"> + <textarea name="unigeneid" class="form-control" rows="1">{{ probeset.unigeneid |default('', true) }}</textarea> + <input name="old_unigeneid" class="changed" type="hidden" value="{{ probeset.unigeneid |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="omim" class="col-sm-2 control-label">OMIM:</label> + <div class="col-sm-4"> + <textarea name="omim" class="form-control" rows="1">{{ probeset.omim |default('', true) }}</textarea> + <input name="old_omim" class="changed" type="hidden" value="{{ probeset.omim |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="refseq_transcriptid" class="col-sm-2 control-label"> + Refseq TranscriptId: + </label> + <div class="col-sm-4"> + <textarea name="refseq_transcriptid" class="form-control" rows="1">{{ probeset.refseq_transcriptid |default('', true) }}</textarea> + <input name="old_refseq_transcriptid" class="changed" type="hidden" value="{{ probeset.refseq_transcriptid |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="blatseq" class="col-sm-2 control-label">BlatSeq:</label> + <div class="col-sm-8"> + <textarea name="blatseq" class="form-control" rows="6">{{ probeset.blatseq |default('', true) }}</textarea> + <input name="old_blatseq" class="changed" type="hidden" value="{{ probeset.blatseq |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="targetseq" class="col-sm-2 control-label">TargetSeq:</label> + <div class="col-sm-8"> + <textarea name="targetseq" class="form-control" rows="6">{{ probeset.targetseq |default('', true) }}</textarea> + <input name="old_targetseq" class="changed" type="hidden" value="{{ probeset.targetseq |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="strand_probe" class="col-sm-2 control-label">Strand Probe:</label> + <div class="col-sm-2"> + <textarea name="strand_probe" class="form-control" rows="1">{{ probeset.strand_probe |default('', true) }}</textarea> + <input name="old_strand_probe" class="changed" type="hidden" value="{{ probeset.strand_probe |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_target_region" class="col-sm-2 control-label">Probe Set Target Region:</label> + <div class="col-sm-8"> + <textarea name="probe_set_target_region" class="form-control" rows="1">{{ probeset.probe_set_target_region |default('', true) }}</textarea> + <input name="old_probe_set_target_region" class="changed" type="hidden" value="{{ probeset.probe_set_target_region_ |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_specificity" class="col-sm-2 control-label">Probeset Specificity:</label> + <div class="col-sm-8"> + <textarea name="probe_set_specificity" class="form-control" rows="1">{{ probeset.probe_set_specificity |default('', true) }}</textarea> + <input name="old_probe_set_specificity" class="changed" type="hidden" value="{{ probeset.probe_set_specificity |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_blat_score" class="col-sm-2 control-label">Probeset Blat Score:</label> + <div class="col-sm-8"> + <textarea name="probe_set_blat_score" class="form-control" rows="1">{{ probeset.probe_set_blat_score |default('', true) }}</textarea> + <input name="old_probe_set_blat_score" class="changed" type="hidden" value="{{ probeset.probe_set_blat_score |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_blat_mb_start" class="col-sm-2 control-label"> + Probeset Blat Mb Start:</label> + <div class="col-sm-8"> + <textarea name="probe_set_blat_mb_start" class="form-control" rows="1">{{ probeset.probe_set_blat_mb_start |default('', true) }}</textarea> + <input name="old_probe_set_blat_mb_start" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_start |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_blat_mb_end" class="col-sm-2 control-label">Probeset Blat Mb End:</label> + <div class="col-sm-8"> + <textarea name="probe_set_blat_mb_end" class="form-control" rows="6">{{ probeset.probe_set_blat_mb_end |default('', true) }}</textarea> + <input name="old_probe_set_blat_mb_end" class="changed" type="hidden" value="{{ probeset.probe_set_blat_mb_end |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_strand" class="col-sm-2 control-label">Probeset Strand:</label> + <div class="col-sm-8"> + <textarea name="probe_set_strand" class="form-control" rows="6">{{ probeset.probe_set_strand |default('', true) }}</textarea> + <input name="old_probe_set_strand" class="changed" type="hidden" value="{{ probeset.probe_set_strand |default('', true) }}"/> + </div> + </div> + <div class="form-group"> + <label for="probe_set_note_by_rw" class="col-sm-2 control-label">Probeset Strand:</label> + <div class="col-sm-8"> + <textarea name="probe_set_note_by_rw" class="form-control" rows="6">{{ probeset.probe_set_note_by_rw |default('', true) }}</textarea> + <input name="old_probe_set_note_by_rw" class="changed" type="hidden" value="{{ probeset.probe_set_note_by_rw |default('', true) }}"/> + </div> + </div> + <div class="controls" style="display:block; margin-left: 40%; margin-right: 20%;"> + <input name="id" class="changed" type="hidden" value="{{ probeset.id_ }}"/> + <input name="old_id_" class="changed" type="hidden" value="{{ probeset.id_ }}"/> + <input name="probeset_name" class="changed" type="hidden" value="{{ probeset.name }}"/> + <input type="submit" style="width: 125px; margin-right: 25px;" class="btn btn-primary form-control col-xs-2 changed" value="Submit Change"> + <input type="reset" style="width: 110px;" class="btn btn-primary form-control col-xs-2 changed" onClick="window.location.reload();" value="Reset"> + </div> +</form> + +{%endblock%} + +{% block js %} +<script> + gn_server_url = "{{ gn_server_url }}"; + function MarkAsChanged(){ + $(this).addClass("changed"); + } + $(":input").blur(MarkAsChanged).change(MarkAsChanged); + + $("input[type=submit]").click(function(){ + $(":input:not(.changed)").attr("disabled", "disabled"); + }); +</script> +{% endblock %} diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index e1f6dd71..741861e6 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -498,13 +498,40 @@ def edit_probeset(dataset_name): table="ProbeSet", columns=list(probeset_mapping.values()), where=Probeset(name=dataset_name)) + json_data = fetchall( + conn, + "metadata_audit", + where=MetadataAudit(dataset_id=probeset_.id_)) + Edit = namedtuple("Edit", ["field", "old", "new", "diff"]) + Diff = namedtuple("Diff", ["author", "diff", "timestamp"]) + diff_data = [] + for data in json_data: + json_ = json.loads(data.json_data) + timestamp = json_.get("timestamp") + author = json_.get("author") + for key, value in json_.items(): + if isinstance(value, dict): + for field, data_ in value.items(): + diff_data.append( + Diff(author=author, + diff=Edit(field, + data_.get("old"), + data_.get("new"), + "\n".join(difflib.ndiff( + [data_.get("old")], + [data_.get("new")]))), + timestamp=timestamp)) + diff_data_ = None + if len(diff_data) > 0: + diff_data_ = groupby(diff_data, lambda x: x.timestamp) return render_template( "edit_probeset.html", - probeset=probeset_ - ) + diff=diff_data_, + probeset=probeset_) @app.route("/trait/update", methods=["POST"]) +@admin_login_required def update_phenotype(): conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"), user=current_app.config.get("DB_USER"), |