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-rw-r--r--bh20simplewebuploader/main.py120
-rw-r--r--bh20simplewebuploader/static/main.css18
-rw-r--r--bh20simplewebuploader/static/main.js128
-rw-r--r--bh20simplewebuploader/templates/form.html77
4 files changed, 262 insertions, 81 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py
index 126b8dd..1a441f0 100644
--- a/bh20simplewebuploader/main.py
+++ b/bh20simplewebuploader/main.py
@@ -1,4 +1,5 @@
import collections
+import itertools
import tempfile
import shutil
import subprocess
@@ -153,11 +154,19 @@ def generate_form(schema, options):
# Decide if the field is optional (type ends in ?)
optional = False
- if len(field_type) > 0 and field_type[-1] == '?':
+ if field_type.endswith('?'):
# It's optional
optional = True
# Drop the ?
field_type = field_type[:-1]
+
+ # Decide if the field is a list (type ends in [])
+ is_list = False
+ if field_type.endswith('[]'):
+ # It's a list
+ is_list = True
+ # Reduce to the normal type
+ field_type = field_type[:-2]
if field_type in by_name:
# This is a subrecord. We need to recurse
@@ -169,6 +178,7 @@ def generate_form(schema, options):
record['id'] = '.'.join(parent_keys + [field_name])
record['label'] = name_to_label(field_name)
record['required'] = not optional and not subtree_optional
+ record['list'] = is_list
if ref_iri:
record['ref_iri'] = ref_iri
if docstring:
@@ -193,18 +203,10 @@ def generate_form(schema, options):
record['type'] = 'text'
elif field_type == 'int':
record['type'] = 'number'
- elif field_type == 'float':
+ elif field_type == 'float' or field_type == 'double':
record['type'] = 'number'
# Choose a reasonable precision for the control
record['step'] = '0.0001'
-
- ### This is to fix the homepage for the moment ## needs more love though
- # implementation of the [] stuff instead of just text fields
- ## ToDo - implement lists
- elif field_type == 'string[]':
- record['type'] = 'text'
- elif field_type == 'float[]':
- record['type'] = 'text'
else:
raise NotImplementedError('Unimplemented field type {} in {} in metadata schema'.format(field_type, type_name))
yield record
@@ -248,9 +250,10 @@ def copy_with_limit(in_file, out_file, limit=1024*1024):
buf = in_file.read(buf_size)
bytes_used += len(buf)
-def parse_input(input_string, html_type):
+def parse_input(input_string, html_type, number_step=None):
"""
Parse an input from the given HTML input type into a useful Python type.
+ Also needs the step we sent to distinguish int fields and float/double fields.
Raise ValueError if something does not parse.
Raise NotImplementedError if we forgot to implement a type.
@@ -259,7 +262,15 @@ def parse_input(input_string, html_type):
if html_type == 'text':
return input_string
elif html_type == 'number':
- return int(input_string)
+ # May be an int or a float.
+ if number_step is None:
+ # TODO: Assumes we only use the step for floats
+ return int(input_string)
+ else:
+ return float(input_string)
+ elif html_type == 'date':
+ # Don't do our own date validation; pass it on as a string
+ return input_string
else:
raise NotImplementedError('Unimplemented input type: {}'.format(html_type))
@@ -299,31 +310,84 @@ def receive_files():
elif request.form.get('metadata_type', None) == 'fill':
# Build a metadata dict
metadata = {}
+
+ # When we have metadata for an item, use this to set it.
+ # If it is an item in a list, set is_list=True
+ def set_metadata(item_id, value, is_list=False):
+ # We have this thing. Make a place in the dict tree for it.
+ parts = item_id.split('.')
+ key = parts[-1]
+ # Remove leading 'metadata'
+ path = parts[1:-1]
+ dest_dict = metadata
+ for parent in path:
+ if parent not in dest_dict:
+ dest_dict[parent] = {}
+ dest_dict = dest_dict[parent]
+
+ if not is_list:
+ dest_dict[key] = value
+ else:
+ if key not in dest_dict:
+ dest_dict[key] = []
+ dest_dict[key].append(value)
for item in FORM_ITEMS:
# Pull all the field values we wanted from the form
if 'heading' in item:
continue
-
- if item['id'] in request.form and len(request.form[item['id']]) > 0:
- # We have this thing. Make a place in the dict tree for it.
- parts = item['id'].split('.')
- key = parts[-1]
- # Remove leading 'metadata'
- path = parts[1:-1]
- dest_dict = metadata
- for parent in path:
- if parent not in dest_dict:
- dest_dict[parent] = {}
- dest_dict = dest_dict[parent]
-
+
+ if item['list']:
+ # This is a list, serialized into form fields
+
+ # We count how many values we got
+ value_count = 0
+
+ for index in itertools.count():
+ # Get [0] through [n], until something isn't there.
+ entry_id = '{}[{}]'.format(item['id'], index)
+
+ if index == 1000:
+ # Don't let them provide too much stuff.
+ return (render_template('error.html',
+ error_message="You provided an extremely large number of values for the metadata item {}".format(item['id'])), 403)
+
+ if entry_id in request.form:
+ if len(request.form[entry_id]) > 0:
+ # Put an entry in the list
+ try:
+ # Parse the item
+ parsed = parse_input(request.form[entry_id], item['type'], item.get('step', None))
+ except ValueError:
+ # We don't like that input
+ return (render_template('error.html',
+ error_message="You provided an unacceptable value for the metadata item {}".format(entry_id)), 403)
+ # Save it
+ set_metadata(item['id'], parsed, is_list=True)
+ value_count += 1
+ else:
+ # Empty items are silently skipped.
+ pass
+ else:
+ # We have run out of form fields for this list.
+ break
+
+ if item['required'] and value_count == 0:
+ # They forgot a required item. Maybe all entries were empty.
+ return (render_template('error.html',
+ error_message="You omitted any values for the required metadata item {}".format(item['id'])), 403)
+
+ elif item['id'] in request.form and len(request.form[item['id']]) > 0:
+ # Not a list, but a single item which is present.
try:
- # Now finally add the item
- dest_dict[key] = parse_input(request.form[item['id']], item['type'])
+ # Parse the item
+ parsed = parse_input(request.form[item['id']], item['type'], item.get('step', None))
except ValueError:
# We don't like that input
return (render_template('error.html',
error_message="You provided an unacceptable value for the metadata item {}".format(item['id'])), 403)
+ # Save it
+ set_metadata(item['id'], parsed)
elif item['required']:
return (render_template('error.html',
error_message="You omitted the required metadata item {}".format(item['id'])), 403)
@@ -526,4 +590,4 @@ def getSEQbyLocationAndSpecimenSource():
payload = {'query': query, 'format': 'json'}
r = requests.get(baseURL, params=payload)
result = r.json()['results']['bindings']
- return str(result) \ No newline at end of file
+ return str(result)
diff --git a/bh20simplewebuploader/static/main.css b/bh20simplewebuploader/static/main.css
index 57e29ef..c881253 100644
--- a/bh20simplewebuploader/static/main.css
+++ b/bh20simplewebuploader/static/main.css
@@ -167,16 +167,19 @@ pre code {
border: solid 1px black;
}
-.record {
+.record, .record .field-group, .record .field-group .field {
display: flex;
flex-direction: column;
+ -webkit-column-break-inside: avoid; /* Chrome, Safari, Opera */
+ page-break-inside: avoid; /* Firefox */
+ break-inside: avoid;
+}
+
+.record {
border: solid 1px #808080;
padding: 1em;
background: #F8F8F8;
margin-bottom: 1em;
- -webkit-column-break-inside: avoid; /* Chrome, Safari, Opera */
- page-break-inside: avoid; /* Firefox */
- break-inside: avoid;
}
.record label {
@@ -232,13 +235,6 @@ footer {
.sponsors img {
width: 100%;
}
-.metadata input#metadata_upload:checked ~ #metadata_upload_form_spot {
- display: block;
-}
-
-.metadata input#metadata_upload ~ #metadata_upload_form_spot {
- display: none;
-}
.loader {
display: block;
diff --git a/bh20simplewebuploader/static/main.js b/bh20simplewebuploader/static/main.js
index 96199a0..56213fa 100644
--- a/bh20simplewebuploader/static/main.js
+++ b/bh20simplewebuploader/static/main.js
@@ -34,14 +34,128 @@ let fetchAllaccessions = () => {
fetchAPI("/api/getAllaccessions");
};
+/*
+ * Make sure that only one of the manual metadata entry and metadata upload
+ * form components is *actually* a child of the form element in the DOM.
+ *
+ * Because both make use of the "required" attribute, we can't get away with
+ * just hiding the one we don't want the user to fill in. The hidden part will
+ * still have possibly empty required fields and (some) browsers will
+ * blocksubmission because of it. Moreover, the data (including file uploads)
+ * from the hidden elements will still be sent to the server, which the user
+ * may not expect.
+ */
+
+let uploadForm = document.getElementById('metadata_upload_form')
+let uploadFormSpot = document.getElementById('metadata_upload_form_spot')
+let fillForm = document.getElementById('metadata_fill_form')
+let fillFormSpot = document.getElementById('metadata_fill_form_spot')
+
+function setUploadMode() {
+ // Make the upload form the one in use.
+ uploadFormSpot.appendChild(uploadForm)
+ // Remove the upload form from the DOM so its required-ness does not block submission.
+ fillFormSpot.removeChild(fillForm)
+}
+
+function setFillMode() {
+ // Make the fillable form the one in use
+ uploadFormSpot.removeChild(uploadForm)
+ // Remove the fillable form from the DOM so its required-ness does not block submission.
+ fillFormSpot.appendChild(fillForm)
+}
+
+function setMode() {
+ // Pick mode based on radio
+ if (document.getElementById('metadata_upload').checked) {
+ setUploadMode()
+ } else {
+ setFillMode()
+ }
+}
+
+/*
+ * Machinery for variable-length lists of input items.
+ */
+
+// Start in mode appropriate to selected form item.
+// It is important that we run this code when the page starts! The browser may
+// have set the radio button to whatever the state was on last page load,
+// instead of the default state, without raising an event, and we have to
+// handle that.
+setMode()
+
+/**
+ * Add another form field to the group this button is part of.
+ */
+function addField(e) {
+ // Find our parent field-group div
+ let fieldGroup = this.parentElement
+
+ // Get its keypath
+ let keypath = fieldGroup.dataset.keypath
+
+ // Find its last field child
+ let existingFields = fieldGroup.getElementsByClassName('field')
+ let templateField = existingFields[existingFields.length - 1]
+
+ // Get its number
+ let fieldNumber = templateField.dataset.number
+
+ // Duplicate it
+ let newField = templateField.cloneNode(true)
+
+ // Increment the number and use the keypath and number to set IDs and cross
+ // references.
+ // TODO: Heavily dependent on the form field HTML. Maybe we want custom
+ // elements for the labeled controlsd that know how to be list items?
+ fieldNumber++
+ newField.dataset.number = fieldNumber
+ let newID = keypath + '[' + fieldNumber + ']'
+ let newControl = newField.getElementsByClassName('control')[0]
+ newControl.id = newID
+ newControl.setAttribute('name', newID)
+ let newLabel = newField.getElementsByTagName('label')[0]
+ newLabel.setAttribute('for', newID)
+
+ // Find the minus button
+ let minusButton = fieldGroup.getElementsByClassName('remove-field')[0]
+
+ // Put new field as a child before the minus button
+ fieldGroup.insertBefore(newField, minusButton)
+
+ // Enable the minus button
+ minusButton.classList.remove('invisible')
+}
+
/**
- * Show form if checked
+ * Remove the last form field from the group button is part of.
*/
-let fillFormSpot = document.getElementById('metadata_fill_form_spot');
-function displayForm() {
- if (document.getElementById('metadata_form').checked) {
- fillFormSpot.classList.remove("invisible");
- return;
+function removeField(e) {
+ // Find our parent field-group div
+ let fieldGroup = this.parentElement
+
+ // Find its field children
+ let existingFields = fieldGroup.getElementsByClassName('field')
+
+ if (existingFields.length > 1) {
+ // There is a last field we can safely remove.
+ let lastField = existingFields[existingFields.length - 1]
+ fieldGroup.removeChild(lastField)
}
- fillFormSpot.classList.add("invisible");
+
+ if (existingFields.length <= 1) {
+ // Collection auto-updates. Now there's only one element. Don't let the
+ // user remove it. If they don't want it, they can leave it empty.
+ this.classList.add('invisible')
+ }
+}
+
+// Find all the add and remove field buttons and hook up the listeners.
+for (let button of document.getElementsByClassName('add-field')) {
+ button.addEventListener('click', addField)
}
+for (let button of document.getElementsByClassName('remove-field')) {
+ button.addEventListener('click', removeField)
+}
+
diff --git a/bh20simplewebuploader/templates/form.html b/bh20simplewebuploader/templates/form.html
index ffd4158..1bbf515 100644
--- a/bh20simplewebuploader/templates/form.html
+++ b/bh20simplewebuploader/templates/form.html
@@ -32,10 +32,10 @@
<div class="search">
<input id="search-input" id="global-search" type="search" placeholder="FASTA uri" required>
<button class="button search-button" type="submit" onclick="search()">
- <span class="icon ion-search">
- <span class="sr-only">Search</span>
- </span>
- </button>
+ <span class="icon ion-search">
+ <span class="sr-only">Search</span>
+ </span>
+ </button>
</div>
</section>
@@ -87,21 +87,21 @@
<div class="metadata">
<label>Select metadata submission method:</label>
<br>
- <input type="radio" id="metadata_form" name="metadata_type" value="fill" checked onchange="displayForm()" required>
+ <input type="radio" id="metadata_form" name="metadata_type" value="fill" checked onchange="setMode()" required>
<label for="metadata_form">Fill in metadata manually</label>
- <input type="radio" id="metadata_upload" name="metadata_type" value="upload" onchange="displayForm()" required>
+ <input type="radio" id="metadata_upload" name="metadata_type" value="upload" onchange="setMode()" required>
<label for="metadata_upload">Upload metadata file</label>
<br>
<small>Make sure the metadata has submitter attribution details.</small>
<div id="metadata_upload_form_spot">
- <div id="metadata_upload_form">
- <br>
- <label for="metadata">Select JSON or YAML metadata file following <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml" target="_blank">this schema</a> and <a href="https://github.com/arvados/bh20-seq-resource/blob/master/example/metadata.yaml" target="_blank">example</a> (max 50K):</label>
- <br>
- <input type="file" id="metadata" name="metadata" accept=".json,.yml,.yaml" required>
- <br>
- </div>
+ <div id="metadata_upload_form">
+ <br>
+ <label for="metadata">Select JSON or YAML metadata file following <a href="https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml" target="_blank">this schema</a> and <a href="https://github.com/arvados/bh20-seq-resource/blob/master/example/metadata.yaml" target="_blank">example</a> (max 50K):</label>
+ <br>
+ <input type="file" id="metadata" name="metadata" accept=".json,.yml,.yaml" required>
+ <br>
+ </div>
</div>
</div>
@@ -116,26 +116,34 @@
<div class="record">
<h4>{{ record['heading'] }}</h4>
{% else %}
- <label for="{{ record['id'] }}" title="{{ record.get('docstring', '') }}">
- {{ record['label'] }}
- {{ "*" if record['required'] else "" }}
- {% if 'docstring' in record %}
- <a href='javascript:alert({{ record['docstring'] | tojson }})'>❓</a>
- {% endif %}
- {% if 'ref_iri' in record %}
- <a href="{{ record['ref_iri'] }}" target="_blank" title="Ontology Link">🔗</a>
+ <div class="field-group" data-keypath="{{ record['id'] }}">
+ <div class="field" data-number="0">
+ <label for="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}" title="{{ record.get('docstring', '') }}">
+ {{ record['label'] }}
+ {{ "*" if record['required'] else "" }}
+ {% if 'docstring' in record %}
+ <a href='javascript:alert({{ record['docstring'] | tojson }})'>❓</a>
+ {% endif %}
+ {% if 'ref_iri' in record %}
+ <a href="{{ record['ref_iri'] }}" target="_blank" title="Ontology Link">🔗</a>
+ {% endif %}
+ </label>
+ {% if record['type'] == 'select' %}
+ <select class="control" id="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}" name="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}" {{ "required" if record['required'] else "" }}>
+ <option value="" selected>Choose one...</option>
+ {% for option in record['options'] %}
+ <option value="{{ option[1] }}">{{ option[0] }}</option>
+ {% endfor %}
+ </select>
+ {% else %}
+ <input class="control" type="{{ record['type'] }}" id="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}" name="{{ record['id'] }}{{ '[0]' if record['list'] else ''}}" {{ "required" if record['required'] else "" }} {{ ("step=" + record['step']) if 'step' in record else ""}}>
+ {% endif %}
+ </div>
+ {% if record['list'] %}
+ <button type="button" title="Remove field" class="remove-field invisible">➖</button>
+ <button type="button" title="Add field" class="add-field">➕</button>
{% endif %}
- </label>
- {% if record['type'] == 'select' %}
- <select id="{{ record['id'] }}" name="{{ record['id'] }}" {{ "required" if record['required'] else "" }}>
- <option value="" selected>Choose one...</option>
- {% for option in record['options'] %}
- <option value="{{ option[1] }}">{{ option[0] }}</option>
- {% endfor %}
- </select>
- {% else %}
- <input type="{{ record['type'] }}" id="{{ record['id'] }}" name="{{ record['id'] }}" {{ "required" if record['required'] else "" }} {{ ("step=" + record['step']) if 'step' in record else ""}}>
- {% endif %}
+ </div>
{% endif %}
{% if loop.index == loop.length %}
</div>
@@ -145,8 +153,7 @@
</div>
-
-<input class="submit" type="submit" value="Add to Pangenome">
+ <input class="submit" type="submit" value="Add to Pangenome">
</form>
</section>
<br>
@@ -190,7 +197,7 @@
</div>
<script type="text/javascript">
- let scriptRoot = {{ request.script_root|tojson|safe }};
+ let scriptRoot = {{ request.script_root|tojson|safe }};
</script>
<script type="text/javascript" src="/static/main.js"></script>
generated by cgit v1.2.3 (git 2.45.2) at 2024-11-26 12:10:38 +0000