diff options
Diffstat (limited to 'bh20simplewebuploader/main.py')
| -rw-r--r-- | bh20simplewebuploader/main.py | 43 |
1 files changed, 22 insertions, 21 deletions
diff --git a/bh20simplewebuploader/main.py b/bh20simplewebuploader/main.py index e80713f..f4eabe6 100644 --- a/bh20simplewebuploader/main.py +++ b/bh20simplewebuploader/main.py @@ -48,10 +48,10 @@ def name_to_label(field_name): """ Turn a filed name like "host_health_status" from the metadata schema into a human-readable label. """ - + # May end in a number, which should be set off by a space set_off_number = re.sub('([0-9]+)$', r' \1', field_name) - + return string.capwords(set_off_number.replace('_', ' ')) def is_iri(string): @@ -72,13 +72,13 @@ def generate_form(schema, options): Each dict either has a 'heading' (in which case we put a heading for a form section in the template) or an 'id', 'label', 'type', and 'required' (in which case we make a form field in the template). - + Non-heading dicts with type 'select' will have an 'options' field, with a list of (name, value) tuples, and represent a form dropdown element. - + Non-heading dicts with type 'number' may have a 'step', which, if <1 or 'any', allows the number to be a float. - + Non-heading dicts may have a human-readable 'docstring' field describing them. @@ -125,7 +125,7 @@ def generate_form(schema, options): docstring = None if not isinstance(field_type, str): # If the type isn't a string - + # It may have documentation docstring = field_type.get('doc', None) @@ -159,7 +159,7 @@ def generate_form(schema, options): 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('[]'): @@ -280,6 +280,7 @@ def receive_files(): Receive the uploaded files. """ + return 0 # We're going to work in one directory per request dest_dir = tempfile.mkdtemp() # The uploader will happily accept a FASTQ with this name @@ -310,7 +311,7 @@ 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): @@ -324,7 +325,7 @@ def receive_files(): if parent not in dest_dict: dest_dict[parent] = {} dest_dict = dest_dict[parent] - + if not is_list: dest_dict[key] = value else: @@ -336,22 +337,22 @@ def receive_files(): # Pull all the field values we wanted from the form if 'heading' in item: continue - + 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 @@ -371,7 +372,7 @@ def receive_files(): 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', @@ -450,7 +451,7 @@ def getDetailsForSeq(): @app.route('/api/getSEQCountbytech', methods=['GET']) def getSEQCountbytech(): - query="""SELECT ?tech ?tech_label (count(?fasta) as ?fastaCount) WHERE + query="""SELECT ?tech ?tech_label (count(?fasta) as ?fastaCount) WHERE {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech] . OPTIONAL {?tech <http://www.w3.org/2000/01/rdf-schema#label> ?tech_tmp_label } . BIND(IF(BOUND(?tech_tmp_label), ?tech_tmp_label,?tech) as ?tech_label)} @@ -466,8 +467,8 @@ def getSEQCountbytech(): ## Is this one really necessary or should we just use getSEQCountbytech instead? @app.route('/api/getAvailableTech', methods=['GET']) def getAvailableTech(): - query="""SELECT distinct ?tech ?tech_label WHERE - {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech] + query="""SELECT distinct ?tech ?tech_label WHERE + {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> ?tech] BIND (concat(?tech,"_label") as ?tech_label) } """ payload = {'query': query, 'format': 'json'} @@ -479,7 +480,7 @@ def getAvailableTech(): ## Has to be encoded again so should be --> http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000759 @app.route('/api/getSEQbytech', methods=['GET']) def getSEQbytech(): - query="""SELECT ?fasta WHERE + query="""SELECT ?fasta WHERE {?fasta ?x [<http://purl.obolibrary.org/obo/OBI_0600047> <placeholder>] } """ tech = request.args.get('tech') @@ -565,7 +566,7 @@ def getSEQCountbyHostHealthStatus(): @app.route('/api/getSEQbyLocationAndTech', methods=['GET']) def getSEQbyLocationAndTech(): - query="""SELECT ?fasta WHERE { ?fasta ?x [ + query="""SELECT ?fasta WHERE { ?fasta ?x [ <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholderLoc>; <http://purl.obolibrary.org/obo/OBI_0600047> <placeholderTech> ]}""" location=request.args.get('location') tech=request.args.get('tech') @@ -582,7 +583,7 @@ def getSEQbyLocationAndTech(): # Example specimen http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C155831 @app.route('/api/getSEQbyLocationAndSpecimenSource', methods=['GET']) def getSEQbyLocationAndSpecimenSource(): - query="""SELECT ?fasta WHERE { ?fasta ?x [ + query="""SELECT ?fasta WHERE { ?fasta ?x [ <http://purl.obolibrary.org/obo/GAZ_00000448> <placeholderLoc>; <http://purl.obolibrary.org/obo/OBI_0001479> <placeholderSpecimen> ]} """ location = request.args.get('location') |