Example #1
0
def creg_index(request):
    if request.method == 'POST':
        smiles = request.POST.get("smiles", None)
        inchi = request.POST.get("inchi", False)
        inchi_check = True if inchi == 'on' else False
        if not smiles:
            return render(request, 'cmpd_reg/cmpd-reg.html', {})
        try:
            result_compound, is_new = get_or_create_compound(
                smiles, clean=True, inchi_standard=inchi_check)
        except Exception, e:
            print str(e)
            return render(
                request, 'cmpd_reg/cmpd-reg.html', {
                    'smiles_error':
                    "Error! Could not convert SMILES '{}' to molecule object".
                    format(smiles),
                })
        searched_image = create_compound_image(smiles, smiles=True)
        if searched_image:
            img_tag = create_image_tag(searched_image)
            return render(
                request, 'cmpd_reg/cmpd-reg.html', {
                    'searched_smiles': smiles,
                    'searched_compound_image': img_tag,
                    'returned_compound': str(result_compound.id),
                    'is_new': str(is_new),
                })
        else:
            return render(
                request, 'cmpd_reg/cmpd-reg.html', {
                    'smiles_error':
                    "Error! Could not convert SMILES '{}' to image".format(
                        smiles),
                })
Example #2
0
def creg_index(request):
	if request.method == 'POST':
		smiles = request.POST.get("smiles", None)
		inchi = request.POST.get("inchi", False)
		inchi_check = True if inchi == 'on' else False
		if not smiles:
			return render(request, 'cmpd_reg/cmpd-reg.html', {})
		try:
			result_compound, is_new = get_or_create_compound(smiles, clean=True, inchi_standard=inchi_check)
		except Exception, e:
			print str(e)
			return render(request, 'cmpd_reg/cmpd-reg.html', {
				'smiles_error': "Error! Could not convert SMILES '{}' to molecule object".format(smiles),
			})
		searched_image = create_compound_image(smiles, smiles=True)
		if searched_image:
			img_tag = create_image_tag(searched_image)
			return render(request, 'cmpd_reg/cmpd-reg.html', {
				'searched_smiles': smiles,
				'searched_compound_image': img_tag,
				'returned_compound': str(result_compound.id),
				'is_new': str(is_new),
			})
		else:
			return render(request, 'cmpd_reg/cmpd-reg.html', {
				'smiles_error': "Error! Could not convert SMILES '{}' to image".format(smiles),
			})
Example #3
0
def bulk_loader(request):
	if request.method == "POST":
		inchi = request.POST.get("inchi", False)
		inchi_check = True if inchi == 'on' else False
		output_stats = {'new':0,'existing':0,'errors':{'count':0,'report':[]}}
		reader = csv.DictReader(request.FILES['file'])
		row_count = 1
		for row in reader:
			row_count += 1
			if 'SMILES' not in row.keys():
				return render(request, 'cmpd_reg/bulk_loader.html', {
					'load_error': "Error! CSV must contain a column header named 'SMILES'"
				})
			try:
				_, is_new = get_or_create_compound(row['SMILES'], clean=True, inchi_standard=inchi_check)
				if is_new:
					output_stats['new'] += 1
				else:
					output_stats['existing'] += 1
			except Exception, e:
				print str(e)
				output_stats['errors']['count'] += 1
				output_stats['errors']['report'].append({'smiles':row['SMILES'],'msg':str(e),'row':str(row_count)})
		return render(request, 'cmpd_reg/bulk_loader.html', {
			'load_results': output_stats
		})
Example #4
0
def bulk_loader(request):
    if request.method == "POST":
        inchi = request.POST.get("inchi", False)
        inchi_check = True if inchi == 'on' else False
        output_stats = {
            'new': 0,
            'existing': 0,
            'errors': {
                'count': 0,
                'report': []
            }
        }
        reader = csv.DictReader(request.FILES['file'])
        row_count = 1
        for row in reader:
            row_count += 1
            if 'SMILES' not in row.keys():
                return render(
                    request, 'cmpd_reg/bulk_loader.html', {
                        'load_error':
                        "Error! CSV must contain a column header named 'SMILES'"
                    })
            try:
                _, is_new = get_or_create_compound(row['SMILES'],
                                                   clean=True,
                                                   inchi_standard=inchi_check)
                if is_new:
                    output_stats['new'] += 1
                else:
                    output_stats['existing'] += 1
            except Exception, e:
                print str(e)
                output_stats['errors']['count'] += 1
                output_stats['errors']['report'].append({
                    'smiles': row['SMILES'],
                    'msg': str(e),
                    'row': str(row_count)
                })
        return render(request, 'cmpd_reg/bulk_loader.html',
                      {'load_results': output_stats})