Python Selection.exporter方法代码示例

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def SelectionAnnotation(request):
    """Updates the selected level of annotation"""
    protein_source = request.GET['protein_source']
    
    if protein_source == 'All':
        pss = ProteinSource.objects.all()
    else:
        pss = ProteinSource.objects.filter(name=protein_source)

    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    # reset the annotation selection
    selection.clear('annotation')

    # add the selected items to the selection
    for ps in pss:
        selection_object = SelectionItem('annotation', ps)
        selection.add('annotation', 'annotation', selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection
    return render(request, 'common/selection_filters_annotation.html', selection.dict('annotation'))

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def site_upload(request):
    
    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    selection_type = 'segments'
    selection_subtype = 'site_residue'

    if request.FILES == {}:
        return render(request, 'common/selection_lists_sitesearch.html', '')

    #Overwriting the existing selection
    selection.clear(selection_type)

    print(type(request.FILES['xml_file'].file))

    wb=load_workbook(filename=request.FILES['xml_file'].file)
    ws=wb.active


    for row in ws.rows:
        if len(row) < 5:
            continue
        group_id = int(row[0].value)
        min_match = int(row[1].value)
        try:
            position = ResidueGenericNumberEquivalent.objects.get(label=row[2].value, scheme__slug=row[3].value)
        except e:
            print(e)
            continue
        feature = row[4].value

        # update the selected group
        selection.active_site_residue_group = group_id
        print(selection.site_residue_groups)
        if not selection.site_residue_groups:
            selection.site_residue_groups = [[]]
        selection.site_residue_groups[selection.active_site_residue_group - 1].append(1)
        if len(selection.site_residue_groups) < group_id:
            for x in group_id - len(selection.site_residue_groups):
                selection.site_residue_groups.append([])
        selection.site_residue_groups[group_id - 1][0] = min_match
        selection_object = SelectionItem(selection_subtype, position)
        selection_object.properties['feature'] = feature
        selection_object.properties['site_residue_group'] = selection.active_site_residue_group
        selection_object.properties['amino_acids'] = ','.join(definitions.AMINO_ACID_GROUPS[feature])
        selection.add(selection_type, selection_subtype, selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection
    
    return render(request, 'common/selection_lists_sitesearch.html', selection.dict(selection_type))

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def SelectResidueGroup(request):
    """Receives a selection request, updates the active residue group, and returns the updated selection"""
    selection_type = request.GET['selection_type']
    group_id = int(request.GET['group_id'])
    
    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    # update the selected group
    selection.active_site_residue_group = group_id

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection

    # context 
    context = selection.dict(selection_type)
    
    # amino acid groups
    amino_acid_groups = {
        'amino_acid_groups': definitions.AMINO_ACID_GROUPS,
        'amino_acid_group_names': definitions.AMINO_ACID_GROUP_NAMES }
    context.update(amino_acid_groups)

    # template to load
    template = 'common/selection_lists_sitesearch.html'

    return render(request, template, context)

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def SelectionSpeciesToggle(request):
    """Updates the selected species arbitrary selections"""
    species_id = request.GET['species_id']

    all_sps = Species.objects.all()
    sps = Species.objects.filter(pk=species_id)

    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    # add the selected items to the selection
    for sp in sps:
        exists = selection.remove('species', 'species', species_id)
        if not exists:
            selection_object = SelectionItem('species', sp)
            selection.add('species', 'species', selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection

    # add all species objects to context (for comparison to selected species)
    context = selection.dict('species')
    context['sps'] = Species.objects.all()
    
    return render(request, 'common/selection_filters_species_selector.html', context)

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def SelectionSchemesToggle(request):
    """Updates the selected numbering schemes arbitrary selections"""
    numbering_scheme_id = request.GET['numbering_scheme_id']
    gns = ResidueNumberingScheme.objects.filter(pk=numbering_scheme_id)

    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    # add the selected items to the selection
    for gn in gns:
        exists = selection.remove('numbering_schemes', 'numbering_schemes', numbering_scheme_id)
        if not exists:
            selection_object = SelectionItem('numbering_schemes', gn)
            selection.add('numbering_schemes', 'numbering_schemes', selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection

    # add all species objects to context (for comparison to selected species)
    context = selection.dict('numbering_schemes')
    context['gns'] = ResidueNumberingScheme.objects.exclude(slug=settings.DEFAULT_NUMBERING_SCHEME)
    
    return render(request, 'common/selection_filters_numbering_schemes.html', context)

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def SelectAlignableSegments(request):
    """Adds all alignable segments to the selection"""
    selection_type = request.GET['selection_type']

    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    # get all segments
        # get all segments
    if "protein_type" in request.GET:
        gsegments = definitions.G_PROTEIN_SEGMENTS

        preserved = Case(*[When(slug=pk, then=pos) for pos, pk in enumerate(gsegments['Structured'])])
        segments = ProteinSegment.objects.filter(slug__in = gsegments['Structured'], partial=False).order_by(preserved)
    else:
        segments = ProteinSegment.objects.filter(partial=False, slug__startswith='TM')

    for segment in segments:
        selection_object = SelectionItem(segment.category, segment)
        # add the selected item to the selection
        selection.add(selection_type, segment.category, selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection
    
    return render(request, 'common/selection_lists.html', selection.dict(selection_type))

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def SelectAlignableSegments(request):
    """Adds all alignable segments to the selection"""
    selection_type = request.GET['selection_type']

    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    # get all segments
    segments = ProteinSegment.objects.filter(partial=False, slug__startswith='TM')
    for segment in segments:
        selection_object = SelectionItem(segment.category, segment)
        # add the selected item to the selection
        selection.add(selection_type, segment.category, selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection
    
    return render(request, 'common/selection_lists.html', selection.dict(selection_type))

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def SelectionGproteinPredefined(request):
    """Updates the selected g proteins to predefined sets (Gi/Go and all)"""
    g_protein = request.GET['g_protein']
    preferred = request.GET['preferred']

    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)
    
    all_gprots = ProteinGProtein.objects.all()
    gprots = False
    if g_protein == 'All':
        gprots = []
    if g_protein != 'All' and g_protein:
        gprots = ProteinGProtein.objects.filter(name=g_protein)

    if gprots != False:
        # reset the g proteins selection
        if preferred == 'true':
            selection.clear('pref_g_proteins')
        else:
            selection.clear('g_proteins')

        # add the selected items to the selection
        for gprot in gprots:
            selection_object = SelectionItem('g_protein', gprot)
            if preferred == 'true':
                selection.add('pref_g_proteins', 'g_protein', selection_object)
            else:
                selection.add('g_proteins', 'g_protein', selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection

    # add all species objects to context (for comparison to selected species)
    if preferred == 'true':
        context = selection.dict('pref_g_proteins')
    else:
        context = selection.dict('g_proteins')
    context['gprots'] = ProteinGProtein.objects.all()
    
    if preferred == 'true':
        return render(request, 'common/selection_filters_pref_gproteins.html', context)
    else:
        return render(request, 'common/selection_filters_gproteins.html', context)

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def ResiduesUpload(request):
    """Receives a file containing generic residue positions along with numbering scheme and adds those to the selection."""

    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    selection_type = 'segments'
    if request.FILES == {}:
        return render(request, 'common/selection_lists.html', '')

    #Overwriting the existing selection
    selection.clear(selection_type)

    #The excel file
    o = []
    workbook = xlrd.open_workbook(file_contents=request.FILES['xml_file'].read())
    worksheets = workbook.sheet_names()
    for worksheet_name in worksheets:
        worksheet = workbook.sheet_by_name(worksheet_name)
        for row in worksheet.get_rows():
            if len(row) < 2:
                continue
            try:
                if row[0].value == 'residue':
                    position = ResidueGenericNumberEquivalent.objects.get(label=row[2].value, scheme__slug=row[1].value)
                    o.append(position)
                elif row[0].value == 'helix':
                    o.append(ProteinSegment.objects.get(slug=row[2].value))
            except Exception as msg:
                print(msg)
                continue
    for obj in o:
        # add the selected item to the selection
        if obj.__class__.__name__ == 'ResidueGenericNumberEquivalent':
            selection_subtype = 'residue'
        else: 
            selection_subtype = 'helix'
        selection_object = SelectionItem(selection_subtype, obj)
        selection.add(selection_type, selection_subtype, selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection

    return render(request, 'common/selection_lists.html', selection.dict(selection_type))

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
    def post(self, request, *args, **kwargs):

        context = super(PDBClean, self).get_context_data(**kwargs)

        self.posted = True
        pref = True
        water = False
        hets = False
        
        if 'pref_chain' not in request.POST.keys():
            pref = False
        if 'water' in request.POST.keys():
            water = True
        if 'hets' in request.POST.keys():
            hets = True

        # get simple selection from session
        simple_selection = request.session.get('selection', False)
        selection = Selection()
        if simple_selection:
            selection.importer(simple_selection)
        out_stream = BytesIO()
        io = PDBIO()
        zipf = zipfile.ZipFile(out_stream, 'w', zipfile.ZIP_DEFLATED)
        if selection.targets != []:
            for selected_struct in [x for x in selection.targets if x.type == 'structure']:
                struct_name = '{}_{}.pdb'.format(selected_struct.item.protein_conformation.protein.parent.entry_name, selected_struct.item.pdb_code.index)
                if hets:
                    lig_names = [x.pdb_reference for x in StructureLigandInteraction.objects.filter(structure=selected_struct.item, annotated=True)]
                else:
                    lig_names = None
                gn_assigner = GenericNumbering(structure=PDBParser(QUIET=True).get_structure(struct_name, StringIO(selected_struct.item.get_cleaned_pdb(pref, water, lig_names)))[0])
                tmp = StringIO()
                io.set_structure(gn_assigner.assign_generic_numbers())
                request.session['substructure_mapping'] = gn_assigner.get_substructure_mapping_dict()
                io.save(tmp)
                zipf.writestr(struct_name, tmp.getvalue())
                del gn_assigner, tmp
            for struct in selection.targets:
                selection.remove('targets', 'structure', struct.item.id)
            # export simple selection that can be serialized
            simple_selection = selection.exporter()

            request.session['selection'] = simple_selection
            request.session['cleaned_structures'] = out_stream

        attributes = inspect.getmembers(self, lambda a:not(inspect.isroutine(a)))
        for a in attributes:
            if not(a[0].startswith('__') and a[0].endswith('__')):
                context[a[0]] = a[1]
        return render(request, self.template_name, context)

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def SelectionGproteinToggle(request):
    """Updates the selected g proteins arbitrary selections"""
    g_protein_id = request.GET['g_protein_id']
    preferred = request.GET['preferred']

    all_gprots = ProteinGProtein.objects.all()
    gprots = ProteinGProtein.objects.filter(pk=g_protein_id)
    print("'{}'".format(ProteinGProtein.objects.get(pk=g_protein_id).name))

    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    # add the selected items to the selection
    for gprot in gprots:
        if preferred == 'true':
            exists = selection.remove('pref_g_proteins', 'g_protein', g_protein_id)
        else:
            exists = selection.remove('g_proteins', 'g_protein', g_protein_id)
        if not exists:
            selection_object = SelectionItem('g_protein', gprot)
            if preferred == 'true':
                selection.add('pref_g_proteins', 'g_protein', selection_object)
            else:
                selection.add('g_proteins', 'g_protein', selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection

    # add all species objects to context (for comparison to selected species)
    if preferred == 'true':
        context = selection.dict('pref_g_proteins')
    else:
        context = selection.dict('g_proteins')

    context['gprots'] = ProteinGProtein.objects.all()
    
    if preferred == 'true':
        print(request.session['selection'])
        return render(request, 'common/selection_filters_pref_gproteins_selector.html', context)
    else:
        return render(request, 'common/selection_filters_gproteins_selector.html', context)

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def UpdateSiteResidueFeatures(request):
    """Updates the selected features of a site residue"""
    selection_type = request.GET['selection_type']
    selection_subtype = request.GET['selection_subtype']
    selection_id = request.GET['selection_id']
    
    o = []
    if selection_type == 'reference' or selection_type == 'targets':
        if selection_subtype == 'protein':
            o.append(Protein.objects.get(pk=selection_id))
        elif selection_subtype == 'protein_set':
            selection_subtype = 'protein'
            pset = ProteinSet.objects.get(pk=selection_id)
            for protein in pset.proteins.all():
                o.append(protein)
        elif selection_subtype == 'family':
            o.append(ProteinFamily.objects.get(pk=selection_id))
        elif selection_subtype == 'set':
            o.append(ProteinSet.objects.get(pk=selection_id))
        elif selection_subtype == 'structure':
            o.append(Protein.objects.get(entry_name=selection_id.lower()))
    elif selection_type == 'segments':
        if selection_subtype == 'residue':
            o.append(ResidueGenericNumberEquivalent.objects.get(pk=selection_id))
        elif selection_subtype == 'residue_with_properties': # used in site search
            o.append(ResidueGenericNumberEquivalent.objects.get(pk=selection_id))
        else:
            o.append(ProteinSegment.objects.get(pk=selection_id))

    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)

    for obj in o:
        # add the selected item to the selection
        selection_object = SelectionItem(selection_subtype, obj)
        selection.add(selection_type, selection_subtype, selection_object)

    # export simple selection that can be serialized
    simple_selection = selection.exporter()

    # add simple selection to session
    request.session['selection'] = simple_selection
    
    return render(request, 'common/selection_lists.html', selection.dict(selection_type))

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def SetTreeSelection(request):
    """Adds all alignable segments to the selection"""
    option_no = request.GET['option_no']
    option_id = request.GET['option_id']
    # get simple selection from session
    simple_selection = request.session.get('selection', False)
    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)
    selection.tree_settings[int(option_no)]=option_id
    simple_selection = selection.exporter()
    # add simple selection to session
    request.session['selection'] = simple_selection
    return render(request, 'common/tree_options.html', selection.dict('tree_settings'))

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
def preserve_targets(request):

    request.session['targets_pos'] = deepcopy(request.session.get('selection', False))
    # get simple selection from session
    simple_selection = request.session.get('selection', False)

    # create full selection and import simple selection (if it exists)
    selection = Selection()
    if simple_selection:
        selection.importer(simple_selection)
        selection.clear('targets')
        # export simple selection that can be serialized
        simple_selection = selection.exporter()
        # add simple selection to session
        request.session['selection'] = simple_selection

    return redirect('/seqsign/negativegroupselection',)

# 需要导入模块: from common.selection import Selection [as 别名]
# 或者: from common.selection.Selection import exporter [as 别名]
    def get_context_data(self, **kwargs):
        """get context from parent class (really only relevant for children of this class, as TemplateView does
        not have any context variables)"""
        context = super().get_context_data(**kwargs)

        # get selection from session and add to context
        # get simple selection from session
        simple_selection = self.request.session.get('selection', False)
        
        # create full selection and import simple selection (if it exists)
        selection = Selection()

        # on the first page of a workflow, clear the selection (or dont' import from the session)
        if self.step is not 1:
            if simple_selection:
                selection.importer(simple_selection)

        # default species selection
        if self.default_species:
            sp = Species.objects.get(common_name=self.default_species)
            o = SelectionItem('species', sp)
            selection.species = [o]

        # update session
        simple_selection = selection.exporter()
        self.request.session['selection'] = simple_selection

        context['selection'] = {}
        for selection_box, include in self.selection_boxes.items():
            if include:
                context['selection'][selection_box] = selection.dict(selection_box)['selection'][selection_box]

        if self.filters:
            context['selection']['species'] = selection.species
            context['selection']['annotation'] = selection.annotation
            context['selection']['g_proteins'] = selection.g_proteins
            context['selection']['pref_g_proteins'] = selection.pref_g_proteins

        # get attributes of this class and add them to the context
        attributes = inspect.getmembers(self, lambda a:not(inspect.isroutine(a)))
        for a in attributes:
            if not(a[0].startswith('__') and a[0].endswith('__')):
                context[a[0]] = a[1]
        return context