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How to use update_mapping method in tempest

Best Python code snippet using tempest_python

build_index.py

Source:build_index.py

1#!/usr/bin/env python2# -*- coding: utf-8 -*-3'''4TODO:5       score-tuning:   1. Symbol6                    2. any ID7                    3. name8                    4. summary9                    5. other text (uniprot name, interpro desc, go term)10       case to consider:11                q=hypoxia inducible factor12                 if matching from the beginning, rank higher?13           appear first     # name: "hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)"14           appear latter    # name: "similar to egl nine homolog 1 (hypoxia-inducible factor prolyl hydroxylase 2) (hif-prolyl hydroxylase 2) (hif-ph2) (hph-2) (sm-20)"15    auto-correction:  1. multiple terms use default AND first, if no hit, do the OR automatically (with a note on UI)16'''17from functools import partial18from django.conf import settings19from django.db.models.signals import post_save, post_delete20from pyes.exceptions import (NotFoundException, IndexMissingException,21                             ElasticSearchException, TypeMissingException)22from biogps.utils import ask23from biogps.utils.models import queryset_iterator24from es_lib import get_es_conn25import logging26log = logging.getLogger('pyes')27if settings.DEBUG:28    log.setLevel(logging.DEBUG)29    if len(log.handlers) == 0:30        log_handler = logging.StreamHandler()31        log.addHandler(log_handler)32class BiogpsESIndexerBase(object):33    ES_HOST = settings.ES_HOST34    ES_INDEX_NAME = settings.ES_INDEXES['default']35    step = 10036    def __init__(self):37        self.conn = get_es_conn(self.ES_HOST, default_idx=[self.ES_INDEX_NAME])38    def check(self):39        '''print out ES server info for verification.'''40        print "Servers:", self.conn.servers41        print "Default indices:", self.conn.default_indices42        print "ES_INDEX_TYPE:", self.ES_INDEX_TYPE43    def create_index(self):44        try:45            print self.conn.open_index(self.ES_INDEX_NAME)46        #except NotFoundException:47        except IndexMissingException:48            print self.conn.create_index(self.ES_INDEX_NAME)49    def delete_index_type(self, index_type):50        '''Delete all indexes for a given index_type.'''51        index_name = self.ES_INDEX_NAME52        #Check if index_type exists53        try:54            mapping = self.conn.get_mapping(index_type, index_name)55        except TypeMissingException:56            print 'Error: index type "%s" does not exist in index "%s".' % (index_type, index_name)57            return58        path = '/%s/%s' % (index_name, index_type)59        if ask('Confirm to delete all data under "%s":' % path) == 'Y':60            return self.conn.delete_mapping(index_name, index_type)61    def verify_mapping(self, update_mapping=False):62        '''Verify if index and mapping exist, update mapping if mapping does not exist,63           or "update_mapping=True" explicitly64        '''65        conn = self.conn66        index_name = self.ES_INDEX_NAME67        index_type = self.ES_INDEX_TYPE68        #Test if index exists69        try:70            print "Opening index...", conn.open_index(index_name)71        except NotFoundException:72            print 'Error: index "%s" does not exist. Create it first.' % index_name73            return -174        try:75            cur_mapping = conn.get_mapping(index_type, index_name)76            empty_mapping = False77        except ElasticSearchException:78            #if no existing mapping available for index_type79            #force update_mapping to True80            empty_mapping = True81            update_mapping = True82#        empty_mapping = not cur_mapping[index_name].get(index_type, {})83#        if empty_mapping:84#            #if no existing mapping available for index_type85#            #force update_mapping to True86#            update_mapping = True87        if update_mapping:88            print "Updating mapping...",89            if not empty_mapping:90                print "\n\tRemoving existing mapping...",91                print conn.delete_mapping(index_name, index_type)92            _mapping = self.get_field_mapping()93            print conn.put_mapping(index_type,94                                   _mapping,95                                   [index_name])96    def index(self, doc, index_type, id=None):97        '''add a doc to the index. If id is not None, the existing doc will be98           updated.99        '''100        return self.conn.index(doc, self.ES_INDEX_NAME, index_type, id=id)101    def delete_index(self, index_type, id):102        '''delete a doc from the index based on passed id.'''103        return self.conn.delete(self.ES_INDEX_NAME, index_type, id)104    def optimize(self):105        return self.conn.optimize(self.ES_INDEX_NAME, wait_for_merge=True)106class BiogpsModelESIndexer(BiogpsESIndexerBase):107    '''The base class for indexing objects from BioGPSModel derived models,108       e.g., BioGPSPlugin, BiogpsGenereportLayout, etc.109    '''110    _model = None           # need to specify in each subclass111    ES_INDEX_TYPE = None    # need to specify in each subclass112    step = 100              # how many objects to retrieve in one queryset query113    def _get_field_mapping(self, extra_attrs={}):114        #field mapping templates115        id_type = {'store': "yes",116                   'index': 'not_analyzed',117                   'type': 'string',118                   'term_vector': 'with_positions_offsets'}119        text_type = {'store': "no",120              'index': 'analyzed',121              'type': 'string',122              'term_vector': 'with_positions_offsets'}123        date_type = {'store': "no",124              'index': 'not_analyzed',125              'type': 'date',126              'format': 'YYYY-MM-dd HH:mm:ss'}127        integer_type = {'type': 'integer'}128        float_type = {'type': 'float'}129        object_type = {'type': 'object'}130        boolean_type = {'type': 'boolean'}131        store_only = {'store': "yes",132                      'index': 'no',133                      'type': 'string'}134        disabled_object = {'type': 'object',135                           'enabled': False}136        disabled_string = {'type': 'string',137                           'index': 'no'}138        disabled_double = {'type': 'double',139                           'index': 'no'}140        disabled_integer = {'type': 'integer',141                             'index': 'no'}142        td = {'id_type': id_type,143              'text_type': text_type,144              'date_type': date_type,145              'integer_type': integer_type,146              'float_type': float_type,147              'boolean_type': boolean_type,148              'object_type': object_type,149              'store_only': store_only,150              'disabled_object':  disabled_object,151              'disabled_string':  disabled_string,152              'disabled_double':  disabled_double,153              'disabled_integer': disabled_integer}154        properties = {'in': id_type,155                      'id': id_type,156                      'created': date_type,157                      'lastmodified': date_type,158                      'role_permission': id_type,159                      'tags': id_type}160        for t_id in td.keys():161            for attr in extra_attrs.pop(t_id, []):162                properties[attr] = td[t_id]163        properties.update(extra_attrs)164        for f in properties:165            properties[f] = properties[f].copy()166        #some special settings167        #for tag field168        properties['tags']['index_name'] = 'tag'169        #for name field170        properties['name'] = {171             "type" : "multi_field",172             "store": "yes",173             "fields" : {174                "name" : {175                          'index': 'analyzed',176                          'type': 'string',177                          'boost': 2.0,178                          'term_vector': 'with_positions_offsets'179                         },180                "for_sort" : {181                              "type" : "string",182                              "index" : "not_analyzed"183                             }184              }185        }186        #for owner field187        properties['owner'] = {188            "store": "yes",189            "type": "object",190            "path": 'just_name',  #! This is important to make query "username:cwudemo" work, instead of using "owner.username:cwudemo"191            "properties" : {192                "username" : {193                              "type" : "string",194                              "index_name": "username",195                              "index": "not_analyzed",196                             },197                "name" : {198                           "type" : "string",199                          "index_name": "owner",200                          "index": "analyzed",201                         },202                "url" : {203                          "type" : "string",204                          "index": "no",205                         }206            }207        }208        #for rating_data field209        properties['rating_data'] = {210            "store": "yes",211            "type": "object",212            "properties": {213                "avg_stars": {"type": "short"},214                "total": {"type": "short"},215                "avg": {"type": "short"},216            }217        }218        mapping = {'properties': properties}219        # enable _source compression220        mapping["_source"] = {"enabled" : True,221                              "compress": True,222                              "compression_threshold": "1kb"}223#        #store "_all" for highlighting.224#        mapping["_all"] = {"store": "yes",225#                           "type": "string",226#                           "term_vector": "with_positions_offsets"}227        return mapping228    def get_field_mapping(self):229        raise NotImplementedError230    def build_index(self, update_mapping=False, bulk=True, verbose=False):231        conn = self.conn232        index_name = self.ES_INDEX_NAME233        index_type = self.ES_INDEX_TYPE234        self.verify_mapping(update_mapping=update_mapping)235        print "Building index..."236        cnt = 0237        for p in queryset_iterator(self._model, batch_size=self.step):238            doc = p.object_cvt(mode='es')239            conn.index(doc, index_name, index_type, doc['id'], bulk=bulk)240            cnt += 1241            if verbose:242                print cnt, ':', doc['id']243        print conn.flush()244        print conn.refresh()245        print 'Done! - {} docs indexed.'.format(cnt)246    def index_object(self, object_id):247        obj = self._model.objects.get(id=object_id)248        doc = obj.object_cvt(mode='es')249        print self.index(doc, self.ES_INDEX_TYPE, id=doc['id'])250class BiogpsPluginESIndexer(BiogpsModelESIndexer):251    '''A class for indexing all BiogpsPlugin objects.'''252    def __init__(self):253        from biogps.plugin.models import BiogpsPlugin254        self._model = BiogpsPlugin255        self.ES_INDEX_TYPE = self._model.short_name256        super(BiogpsModelESIndexer, self).__init__()257    def get_field_mapping(self):258        m_usage_data = {259            "store": "yes",260            "type": "object",261            "properties": {262                "users": {"type": "short"},263                "layouts": {"type": "short"},264            }265        }266        m = self._get_field_mapping(extra_attrs={'id_type': ['type', 'species'],267                                                 'text_type': ['name', 'description', 'short_description', 'url'],268                                                 "float_type": ['popularity'],269                                                 'disabled_object': ['options'],270                                                 'disabled_string': ['shortUrl', 'permission_style'],271                                                 'usage_data': m_usage_data272                                                 })273        return m274class BiogpsLayoutESIndexer(BiogpsModelESIndexer):275    '''A class for indexing all BiogpsGenereportLayout objects.'''276    def __init__(self):277        from biogps.layout.models import BiogpsGenereportLayout278        self._model = BiogpsGenereportLayout279        self.ES_INDEX_TYPE = self._model.short_name280        super(BiogpsModelESIndexer, self).__init__()281    def get_field_mapping(self):282        m = self._get_field_mapping(extra_attrs={'text_type': ['name', 'description'],283                                                 'disabled_string': ['permission_style'],284                                                 })285        #some special settings286#        m['name']['boost'] = 2.0287        return m288class BiogpsGenelistESIndexer(BiogpsModelESIndexer):289    '''A class for indexing all BiogpsGeneList objects.'''290    def __init__(self):291        from biogps.genelist.models import BiogpsGeneList292        self._model = BiogpsGeneList293        self.ES_INDEX_TYPE = self._model.short_name294        super(BiogpsModelESIndexer, self).__init__()295    def get_field_mapping(self):296        m = self._get_field_mapping(extra_attrs={'text_type': ['name', 'description'],297                                                 'disabled_string': ['permission_style'],298                                                 })299        #some special settings300#        m['name']['boost'] = 2.0301        return m302def _rebuild_x(delete_old=False, update_mapping=False, indexer=None):303    '''A convenient function for re-building indexes.304    '''305    es_indexer = indexer()306    if delete_old:307        es_indexer.delete_index_type(es_indexer.ES_INDEX_TYPE)308        update_mapping = True   # if delete_old is True, update_mapping should be True anyway309    es_indexer.build_index(update_mapping=update_mapping, bulk=True)310rebuild_plugin = partial(_rebuild_x, indexer=BiogpsPluginESIndexer)311rebuild_plugin.__doc__ = 'A convenient function for re-building all plugins.'312rebuild_layout = partial(_rebuild_x, indexer=BiogpsLayoutESIndexer)313rebuild_layout.__doc__ = 'A convenient function for re-building all layouts.'314rebuild_genelist = partial(_rebuild_x, indexer=BiogpsGenelistESIndexer)315rebuild_genelist.__doc__ = 'A convenient function for re-building all genelists.'316def rebuild_all(delete_old=False):317    '''A convenient function for re-building all biogpsmodel objects,318       not including genes and datasets.319    '''320    rebuild_plugin(delete_old)321    rebuild_layout(delete_old)322    rebuild_genelist(delete_old)323def on_the_fly_es_update_handler(sender, **kwargs):324    '''A post_save signal handler to update ES indexes whenever a BiogpsModel object325       is created/updated.326       To connect to a signal:327           post_save.connect(on_the_fly_es_update_handler, sender=BioGPSModel,328                             dispatch_uid="some_unique_id")329    '''330    if not getattr(settings, "SUSPEND_ES_UPDATE", None):331        object = kwargs['instance']332        es_indexer = BiogpsModelESIndexer()333        doc = object.object_cvt(mode='es')334        res = es_indexer.index(doc, object.short_name, object.id)335        return True336def on_the_fly_es_delete_handler(sender, **kwargs):337    '''A post_delete signal handler to delete ES indexes whenever a BiogpsModel object338       is deleted.339       To connect to a signal:340           post_delete.connect(on_the_fly_es_delete_handler, sender=BioGPSModel,341                               dispatch_uid="some_unique_id")342    '''343    if not getattr(settings, "SUSPEND_ES_UPDATE", None):344        object = kwargs['instance']345        es_indexer = BiogpsModelESIndexer()346        res = es_indexer.delete_index(object.short_name, object.id)347        return True348def set_on_the_fly_indexing(biogpsmodel):349    '''set input biogpsmodel for on the fly indexing:350          * add to index when a new object is created351          * update index when an object is updated352          * delete from index when an object is deleted353    '''354    post_save.connect(on_the_fly_es_update_handler, sender=biogpsmodel,355                      dispatch_uid=biogpsmodel.__name__ + 'update_indexer')356    post_delete.connect(on_the_fly_es_delete_handler, sender=biogpsmodel,...

feature_base.py

Source:feature_base.py

...28    A set of features that generates a pattern for the features it contains.29    This set will act like a mapping in that we map names to patterns.30    """31    mapping = {}32    def update_mapping(self):33        u"""34        Called every time we care about the mapping of names to features.35        """36        self.mapping = dict([(f.name, f) for f in iter(self)])37    @property38    def PATTERN(self):39        u"""40        Uses the mapping of names to features to return a PATTERN suitable41        for using the lib2to3 patcomp.42        """43        self.update_mapping()44        return u" |\n".join([pattern_unformatted % (f.name, f._pattern) for f in iter(self)])45    def __getitem__(self, key):46        u"""47        Implement a simple mapping to get patterns from names.48        """...

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