Add instrument metler toledo dl55

CHANGES.rst

@@ -6,6 +6,7 @@ Changelog
 
 **Added**
 
+- #737 Added Instrument: Metler Toledo DL55
 - #730 Added Instrument: LaChat QuickChem FIA
 - #729 Added Instrument: Varian Vista-PRO ICP
 - #694 Added "Warn Min" and "Warn Max" subfields in Analysis Specifications

bika/lims/exportimport/instruments/__init__.py

@@ -22,6 +22,7 @@
 from alere.pima import beads, cd4
 from lachat import quickchem
 from lifetechnologies.qubit import qubit
+from metler.toledo import dl55
 from biodrop.ulite import ulite
 from tescan.tima import tima
 from sysmex.xs import i500, i1000
@@ -43,6 +44,7 @@
 from genexpert import genexpert
 from varian.vistapro import icp
 
+
 __all__ = ['abaxis.vetscan.vs2',
            'abbott.m2000rt.m2000rt',
            'agilent.masshunter.masshunter',
@@ -61,6 +63,7 @@
            'horiba.jobinyvon.icp',
            'lachat.quickchem',
            'lifetechnologies.qubit.qubit',
+           'metler.toledo.dl55',
            'myself.myinstrument',
            'nuclisens.easyq',
            'panalytical.omnia.axios_xrf',
@@ -103,6 +106,7 @@
            ['generic.two_dimension', 'TwoDimensionCSVParser'],
            # ['generic.xml', ''],
            ['horiba.jobinyvon.icp', 'HoribaJobinYvonCSVParser'],
+           ['metler.toledo.dl55', 'MetlerToledoDL55Parser'],
            ['rigaku.supermini.wxrf', 'RigakuSuperminiWXRFCSVParser'],
            ['rochecobas.taqman.model48', 'RocheCobasTaqmanRSFParser'],
            ['rochecobas.taqman.model96', 'RocheCobasTaqmanRSFParser'],

bika/lims/exportimport/instruments/metler/toledo/__init__.py

@@ -0,0 +1 @@
+# -*- coding: utf-8 -*-

bika/lims/exportimport/instruments/metler/toledo/dl55.py

@@ -0,0 +1,152 @@
+# -*- coding: utf-8 -*-
+""" Metler Toledo DL55
+"""
+import json
+import re
+import traceback
+
+from bika.lims import api
+from bika.lims import bikaMessageFactory as _
+from bika.lims.exportimport.instruments.utils import \
+    (get_instrument_import_search_criteria,
+     get_instrument_import_override,
+     get_instrument_import_ar_allowed_states)
+from bika.lims.exportimport.instruments.resultsimport import \
+    AnalysisResultsImporter, InstrumentResultsFileParser
+from openpyxl import load_workbook
+
+title = "Metler Toledo DL55"
+
+
+class MetlerToledoDL55Parser(InstrumentResultsFileParser):
+    def __init__(self, rsf):
+        InstrumentResultsFileParser.__init__(self, rsf, 'XLSX')
+
+    def parse(self):
+        """ parse the data
+        """
+
+        wb = load_workbook(self.getInputFile())
+        sheet = wb.worksheets[0]
+
+        sample_id = None
+        cnt = 0
+        for row in sheet.rows:
+
+            # sampleid is only present in first row of each sample.
+            # any rows above the first sample id are ignored.
+            if row[1].value:
+                sample_id = row[1].value
+            if not sample_id:
+                continue
+
+            # If no keyword is present, this row is skipped.
+            if len(row) < 7 or not isinstance(row[6].value, basestring):
+                continue
+            # keyword is stripped of non-word characters
+            keyword = re.sub(r"\W", "", row[6].value)
+
+            # result is floatable or error
+            result = row[4].value
+            try:
+                float(result)
+            except ValueError:
+                self.log(
+                    "Error in sample '" + sample_id + "': " + "Result for '" +
+                    keyword + "' is not a number " + "(" + result + ").")
+                continue
+
+            # Compose dict for importer.  No interim values, just a result.
+            rawdict = {
+                'DefaultResult': 'Result',
+                'Result': result,
+            }
+            result = rawdict[rawdict['DefaultResult']]
+            column_name = rawdict['DefaultResult']
+            cnt += 1
+            result = self.get_result(column_name, result, cnt)
+            rawdict[rawdict['DefaultResult']] = result
+            self._addRawResult(sample_id,
+                               values={keyword: rawdict},
+                               override=False)
+        return True
+
+    def get_result(self, column_name, result, line):
+        result = str(result)
+        if result.startswith('--') or result == '' or result == 'ND':
+            return 0.0
+
+        if api.is_floatable(result):
+            result = api.to_float(result)
+            return result > 0.0 and result or 0.0
+        self.err("No valid number ${result} in column (${column_name})",
+                 mapping={"result": result,
+                          "column_name": column_name},
+                 numline=self._numline, line=line)
+        return
+
+
+class Importer(AnalysisResultsImporter):
+    """ Importer
+    """
+
+    def __init__(self, parser, context, idsearchcriteria, override,
+                 allowed_ar_states=None, allowed_analysis_states=None,
+                 instrument_uid=None):
+        AnalysisResultsImporter.__init__(self,
+                                         parser,
+                                         context,
+                                         idsearchcriteria,
+                                         override,
+                                         allowed_ar_states,
+                                         allowed_analysis_states,
+                                         instrument_uid)
+
+
+def Import(context, request):
+    """ Import Form
+    """
+    form = request.form
+    # form['file'] sometimes returns a list
+    infile = form['instrument_results_file'][0] if \
+        isinstance(form['instrument_results_file'], list) \
+        else form['instrument_results_file']
+    override = form['results_override']
+    artoapply = form['artoapply']
+    sample = form.get('sample', 'requestid')
+    instrument = form.get('instrument', None)
+    errors = []
+    logs = []
+    warns = []
+
+    # Load the most suitable parser according to file extension/options/etc...
+    parser = None
+    if not hasattr(infile, 'filename'):
+        errors.append(_("No file selected"))
+
+    parser = MetlerToledoDL55Parser(infile)
+    status = get_instrument_import_ar_allowed_states(artoapply)
+    over = get_instrument_import_override(override)
+    sam = get_instrument_import_search_criteria(sample)
+
+    importer = Importer(parser=parser,
+                        context=context,
+                        idsearchcriteria=sam,
+                        allowed_ar_states=status,
+                        allowed_analysis_states=None,
+                        override=over,
+                        instrument_uid=instrument)
+    tbex = ''
+    try:
+        importer.process()
+    except:
+        tbex = traceback.format_exc()
+    errors = importer.errors
+    logs = importer.logs
+    warns = importer.warns
+    if tbex:
+        errors.append(tbex)
+
+    results = {'errors': errors, 'log': logs, 'warns': warns}
+
+    return json.dumps(results)