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How to use update_columns method in pandera

Best Python code snippet using pandera_python

db_connection.py

Source:db_connection.py

1import os2import json3from collections import defaultdict, OrderedDict4class BaseDBConnection(object):5    """ Base KG connection for database6    """7    def __init__(self, db_path, chunksize):8        """ Create an connection to database9        :param db_path: database path10        :type db_path: str11        :param chunksize: the chunksize to load/write database12        :type chunksize: int13        """14        self._conn = None15        self.chunksize = chunksize16    def close(self):17        """ Close the connection safely18        """19        raise NotImplementedError20    def __del__(self):21        self.close()22    def create_table(self, table_name, columns, column_types):23        """ Create a table with given columns and types24        :param table_name: the table name to create25        :type table_name: str26        :param columns: the columns to create27        :type columns: List[str]28        :param column_types: the corresponding column types29        :type column_types: List[str]30        """31        raise NotImplementedError32    def get_columns(self, table_name, columns):33        """ Get column information from a table34        :param table_name: the table name to retrieve35        :type table_name: str36        :param columns: the columns to retrieve37        :type columns: List[str]38        :return: a list of retrieved rows39        :rtype: List[Dict[str, object]]40        """41        raise NotImplementedError42    def select_row(self, table_name, _id, columns):43        """ Select a row from a table44        :param table_name: the table name to retrieve45        :type table_name: str46        :param _id: the row id47        :type _id: str48        :param columns: the columns to retrieve49        :type columns: List[str]50        :return: a retrieved row51        :rtype: Dict[str, object]52        """53        raise NotImplementedError54    def select_rows(self, table_name, _ids, columns):55        """ Select rows from a table56        :param table_name: the table name to retrieve57        :type table_name: str58        :param _ids: the row ids59        :type _ids: List[str]60        :param columns: the columns to retrieve61        :type columns: List[str]62        :return: retrieved rows63        :rtype: List[Dict[str, object]]64        """65        raise NotImplementedError66    def insert_row(self, table_name, row):67        """ Insert a row into a table68        :param table_name: the table name to insert69        :type table_name: str70        :param row: the row to insert71        :type row: Dict[str, object]72        """73        raise NotImplementedError74    def insert_rows(self, table_name, rows):75        """ Insert several rows into a table76        :param table_name: the table name to insert77        :type table_name: str78        :param rows: the rows to insert79        :type rows: List[Dict[str, object]]80        """81        raise NotImplementedError82    def get_update_op(self, update_columns, operator):83        """ Get an update operator based on columns and a operator84        :param update_columns: a list of columns to update85        :type update_columns: List[str]86        :param operator: an operator that applies to the columns, including "+", "-", "*", "/", "="87        :type operator: str88        :return: an operator that suits the backend database89        :rtype: object90        """91        raise NotImplementedError92    def update_row(self, table_name, row, update_op, update_columns):93        """ Update a row that exists in a table94        :param table_name: the table name to update95        :type table_name: str96        :param row: a new row97        :type row: Dict[str, object]98        :param update_op: an operator that returned by `get_update_op`99        :type update_op: object100        :param update_columns: the columns to update101        :type update_columns: List[str]102        """103        raise NotImplementedError104    def update_rows(self, table_name, rows, update_ops, update_columns):105        """ Update rows that exist in a table106        :param table_name: the table name to update107        :type table_name: str108        :param rows: new rows109        :type rows: List[Dict[str, object]]110        :param update_ops: operator(s) that returned by `get_update_op`111        :type update_ops: Union[List[object], object]112        :param update_columns: the columns to update113        :type update_columns: List[str]114        """115        raise NotImplementedError116    def get_rows_by_keys(self, table_name, bys, keys, columns, order_bys=None, reverse=False, top_n=None):117        """ Retrieve rows by specific keys in some order118        :param table_name: the table name to retrieve119        :type table_name: str120        :param bys: the given columns to match121        :type bys: List[str]122        :param keys: the given values to match123        :type keys: List[str]124        :param columns: the given columns to retrieve125        :type columns: List[str]126        :param order_bys: the columns whose value are used to sort rows127        :type order_bys: List[str]128        :param reverse: whether to sort in a reversed order129        :type reverse: bool130        :param top_n: how many rows to return, default `None` for all rows131        :type top_n: int132        :return: retrieved rows133        :rtype: List[Dict[str, object]]134        """135        raise NotImplementedError136class SqliteDBConnection(BaseDBConnection):137    """ KG connection for SQLite database138    """139    def __init__(self, db_path, chunksize):140        """ Create an connection to SQLite database141        :param db_path: database path, e.g., /home/xliucr/ASER/KG.db142        :type db_path: str143        :param chunksize: the chunksize to load/write database144        :type chunksize: int145        """146        import sqlite3147        super(SqliteDBConnection, self).__init__(db_path, chunksize)148        self._conn = sqlite3.connect(db_path)149    def close(self):150        """ Close the connection safely151        """152        if self._conn:153            self._conn.close()154    def create_table(self, table_name, columns, column_types):155        """ Create a table with given columns and types156        :param table_name: the table name to create157        :type table_name: str158        :param columns: the columns to create159        :type columns: List[str]160        :param column_types: the corresponding column types, please refer to https://www.sqlite.org/datatype3.html161        :type column_types: List[str]162        """163        create_table = "CREATE TABLE %s (%s);" % (164            table_name, ",".join([' '.join(x) for x in zip(columns, column_types)])165        )166        self._conn.execute(create_table)167        self._conn.commit()168    def get_columns(self, table_name, columns):169        """ Get column information from a table170        :param table_name: the table name to retrieve171        :type table_name: str172        :param columns: the columns to retrieve173        :type columns: List[str]174        :return: a list of retrieved rows175        :rtype: List[Dict[str, object]]176        """177        select_table = "SELECT %s FROM %s;" % (",".join(columns), table_name)178        result = list(map(lambda x: OrderedDict(zip(columns, x)), self._conn.execute(select_table)))179        return result180    def select_row(self, table_name, _id, columns):181        """ Select a row from a table182        (suggestion: consider to use `select_rows` if you want to retrieve multiple rows)183        :param table_name: the table name to retrieve184        :type table_name: str185        :param _id: the row id186        :type _id: str187        :param columns: the columns to retrieve188        :type columns: List[str]189        :return: a retrieved row190        :rtype: Dict[str, object]191        """192        select_table = "SELECT %s FROM %s WHERE _id=?;" % (",".join(columns), table_name)193        result = list(self._conn.execute(select_table, [_id]))194        if len(result) == 0:195            return None196        else:197            return OrderedDict(zip(columns, result[0]))198    def select_rows(self, table_name, _ids, columns):199        """ Select rows from a table200        :param table_name: the table name to retrieve201        :type table_name: str202        :param _ids: the row ids203        :type _ids: List[str]204        :param columns: the columns to retrieve205        :type columns: List[str]206        :return: retrieved rows207        :rtype: List[Dict[str, object]]208        """209        if len(_ids) > 0:210            row_cache = dict()211            result = []212            for idx in range(0, len(_ids), self.chunksize):213                select_table = "SELECT %s FROM %s WHERE _id IN ('%s');" % (214                    ",".join(columns), table_name, "','".join(_ids[idx:idx + self.chunksize])215                )216                result.extend(list(self._conn.execute(select_table)))217            for x in result:218                exact_match_row = OrderedDict(zip(columns, x))219                row_cache[exact_match_row["_id"]] = exact_match_row220            exact_match_rows = []221            for _id in _ids:222                exact_match_rows.append(row_cache.get(_id, None))223            return exact_match_rows224        else:225            return []226    def insert_row(self, table_name, row):227        """ Insert a row into a table228        (suggestion: consider to use `insert_rows` if you want to insert multiple rows)229        :param table_name: the table name to insert230        :type table_name: str231        :param row: the row to insert232        :type row: Dict[str, object]233        """234        insert_table = "INSERT INTO %s VALUES (%s)" % (table_name, ",".join(['?'] * (len(row))))235        self._conn.execute(insert_table, list(row.values()))236        self._conn.commit()237    def insert_rows(self, table_name, rows):238        """ Insert several rows into a table239        :param table_name: the table name to insert240        :type table_name: str241        :param rows: the rows to insert242        :type rows: List[Dict[str, object]]243        """244        if len(rows) > 0:245            insert_table = "INSERT INTO %s VALUES (%s)" % (table_name, ",".join(['?'] * (len(next(iter(rows))))))246            self._conn.executemany(insert_table, [list(row.values()) for row in rows])247            self._conn.commit()248    def get_update_op(self, update_columns, operator):249        """ Get an update operator based on columns and a operator250        :param update_columns: a list of columns to update251        :type update_columns: List[str]252        :param operator: an operator that applies to the columns, including "+", "-", "*", "/", "="253        :type operator: str254        :return: an operator that suits the backend database255        :rtype: str256        """257        if operator in "+-*/":258            update_ops = []259            for update_column in update_columns:260                update_ops.append(update_column + "=" + update_column + operator + "?")261            return ",".join(update_ops)262        elif operator == "=":263            update_ops = []264            for update_column in update_columns:265                update_ops.append(update_column + "=?")266            return ",".join(update_ops)267        else:268            raise NotImplementedError269    def _update_update_op(self, row, update_op, update_columns):270        update_op_sp = update_op.split('?')271        while len(update_op_sp) >= 0 and update_op_sp[-1] == '':272            update_op_sp.pop()273        assert len(update_op_sp) == len(update_columns)274        new_update_op = []275        for i in range(len(update_op_sp)):276            new_update_op.append(update_op_sp[i])277            if isinstance(row[update_columns[i]], str):278                new_update_op.append("'" + row[update_columns[i]].replace("'", "''") + "'")279            else:280                new_update_op.append(str(row[update_columns[i]]))281        return ''.join(new_update_op)282    def update_row(self, table_name, row, update_op, update_columns):283        """ Update a row that exists in a table284        (suggestion: consider to use `update_rows` if you want to update multiple rows)285        :param table_name: the table name to update286        :type table_name: str287        :param row: a new row288        :type row: Dict[str, object]289        :param update_op: an operator that returned by `get_update_op`290        :type update_op: str291        :param update_columns: the columns to update292        :type update_columns: List[str]293        """294        update_table = "UPDATE %s SET %s WHERE _id=?" % (table_name, update_op)295        self._conn.execute(update_table, [row[k] for k in update_columns] + [row["_id"]])296        self._conn.commit()297    def update_rows(self, table_name, rows, update_ops, update_columns):298        """ Update rows that exist in a table299        :param table_name: the table name to update300        :type table_name: str301        :param rows: new rows302        :type rows: List[Dict[str, object]]303        :param update_ops: operator(s) that returned by `get_update_op`304        :type update_ops: Union[List[str], str]305        :param update_columns: the columns to update306        :type update_columns: List[str]307        """308        if len(rows) > 0:309            if isinstance(update_ops, (tuple, list)):  # +-*/310                assert len(rows) == len(update_ops)311                # group rows by op to speed up312                update_op_collections = defaultdict(list)  # key: _update_update_op313                for i, row in enumerate(rows):314                    # self.update_row(row, table_name, update_ops[i], update_columns)315                    new_update_op = self._update_update_op(row, update_ops[i], update_columns)316                    update_op_collections[new_update_op].append(row)317                for new_update_op, op_rows in update_op_collections.items():318                    _ids = [row["_id"] for row in op_rows]319                    for idx in range(0, len(_ids), self.chunksize):320                        update_table = "UPDATE %s SET %s WHERE _id IN ('%s');" % (321                            table_name, new_update_op, "','".join(_ids[idx:idx + self.chunksize])322                        )323                        self._conn.execute(update_table)324            else:  # =325                update_op = update_ops326                # group rows by new values to speed up327                value_collections = defaultdict(list)  # key: values of new values328                for row in rows:329                    # self.update_row(row, table_name, update_op, update_columns)330                    value_collections[json.dumps([row[k] for k in update_columns])].append(row)331                for new_update_op, op_rows in value_collections.items():332                    new_update_op = self._update_update_op(op_rows[0], update_op, update_columns)333                    _ids = [row["_id"] for row in op_rows]334                    for idx in range(0, len(_ids), self.chunksize):335                        update_table = "UPDATE %s SET %s WHERE _id IN ('%s');" % (336                            table_name, new_update_op, "','".join(_ids[idx:idx + self.chunksize])337                        )338                        self._conn.execute(update_table)339            self._conn.commit()340    def get_rows_by_keys(self, table_name, bys, keys, columns, order_bys=None, reverse=False, top_n=None):341        """ Retrieve rows by specific keys in some order342        :param table_name: the table name to retrieve343        :type table_name: str344        :param bys: the given columns to match345        :type bys: List[str]346        :param keys: the given values to match347        :type keys: List[str]348        :param columns: the given columns to retrieve349        :type columns: List[str]350        :param order_bys: the columns whose value are used to sort rows351        :type order_bys: List[str]352        :param reverse: whether to sort in a reversed order353        :type reverse: bool354        :param top_n: how many rows to return, default `None` for all rows355        :type top_n: int356        :return: retrieved rows357        :rtype: List[Dict[str, object]]358        """359        key_match_events = []360        select_table = "SELECT %s FROM %s WHERE %s" % (361            ",".join(columns), table_name, " AND ".join(["%s=?" % (by) for by in bys])362        )363        if order_bys:364            select_table += " ORDER BY %s %s" % (",".join(order_bys), "DESC" if reverse else "ASC")365        if top_n:366            select_table += " LIMIT %d" % (top_n)367        select_table += ";"368        for x in self._conn.execute(select_table, keys):369            key_match_event = OrderedDict(zip(columns, x))370            key_match_events.append(key_match_event)371        return key_match_events372class MongoDBConnection(BaseDBConnection):373    """ KG connection for MongoDB374    """375    def __init__(self, db_path, chunksize):376        """ Create an connection to SQLite database377        :param db_path: database path, e.g., mongodb://localhost:27017/ASER378        :type db_path: str379        :param chunksize: the chunksize to load/write database380        :type chunksize: int381        """382        import pymongo383        super(MongoDBConnection, self).__init__(db_path, chunksize)384        host_port, db_name = os.path.split(db_path)385        self._client = pymongo.MongoClient(host_port, document_class=OrderedDict)386        self._conn = self._client[db_name]387    def close(self):388        """ Close the connection safely389        """390        self._client.close()391    def create_table(self, table_name):392        """ Create a table without the necessary to provide column information393        :param table_name: the table name to create394        :type table_name: str395        """396        self._conn[table_name]397    def __get_projection(self, columns):398        projection = {"_id": 0}399        for k in columns:400            projection[k] = 1401        return projection402    def get_columns(self, table_name, columns):403        """ Get column information from a table404        :param table_name: the table name to retrieve405        :type table_name: str406        :param columns: the columns to retrieve407        :type columns: List[str]408        :return: a list of retrieved rows409        :rtype: List[Dict[str, object]]410        """411        projection = self.__get_projection(columns)412        results = list(self._conn[table_name].find({}, projection))413        return results414    def select_row(self, table_name, _id, columns):415        """ Select a row from a table416        (suggestion: consider to use `select_rows` if you want to retrieve multiple rows)417        :param table_name: the table name to retrieve418        :type table_name: str419        :param _id: the row id420        :type _id: str421        :param columns: the columns to retrieve422        :type columns: List[str]423        :return: a retrieved row424        :rtype: Dict[str, object]425        """426        projection = self.__get_projection(columns)427        return self._conn[table_name].find_one({"_id": _id}, projection)428    def select_rows(self, table_name, _ids, columns):429        """ Select rows from a table430        :param table_name: the table name to retrieve431        :type table_name: str432        :param _ids: the row ids433        :type _ids: List[str]434        :param columns: the columns to retrieve435        :type columns: List[str]436        :return: retrieved rows437        :rtype: List[Dict[str, object]]438        """439        table = self._conn[table_name]440        exact_match_rows = []441        projection = self.__get_projection(columns)442        for idx in range(0, len(_ids), self.chunksize):443            query = {"_id": {'$in': _ids[idx:idx + self.chunksize]}}444            exact_match_rows.extend(table.find(query, projection))445        row_cache = {x["_id"]: x for x in exact_match_rows}446        exact_match_rows = [row_cache.get(_id, None) for _id in _ids]447        return exact_match_rows448    def insert_row(self, table_name, row):449        """ Insert a row into a table450        (suggestion: consider to use `insert_rows` if you want to insert multiple rows)451        :param table_name: the table name to insert452        :type table_name: str453        :param row: the row to insert454        :type row: Dict[str, object]455        """456        self._conn[table_name].insert_one(row)457    def insert_rows(self, table_name, rows):458        """ Insert several rows into a table459        :param table_name: the table name to insert460        :type table_name: str461        :param rows: the rows to insert462        :type rows: List[Dict[str, object]]463        """464        self._conn[table_name].insert_many(rows)465    def get_update_op(self, update_columns, operator):466        """ Get an update operator based on columns and a operator467        :param update_columns: a list of columns to update468        :type update_columns: List[str]469        :param operator: an operator that applies to the columns, including "+", "-", "*", "/", "="470        :type operator: str471        :return: an operator that suits the backend database472        :rtype: Dict[str, Dict[str, float]]473        """474        if operator == "+":475            update_ops = {}476            for update_column in update_columns:477                update_ops[update_column] = 1  # placeholder478            return {"$inc": update_ops}479        elif operator == "-":480            update_ops = {}481            for update_column in update_columns:482                update_ops[update_column] = -1  # placeholder483            return {"$inc": update_ops}484        elif operator == "*":485            update_ops = {}486            for update_column in update_columns:487                update_ops[update_column] = 2  # placeholder488            return {"$mul": update_ops}489        elif operator == "/":490            update_ops = {}491            for update_column in update_columns:492                update_ops[update_column] = 0.5  # placeholder493            return {"$mul": update_ops}494        elif operator == "=":495            update_ops = {}496            for update_column in update_columns:497                update_ops[update_column] = 1  # placeholder498            return {"$set": update_ops}499        else:500            raise NotImplementedError501    def _update_update_op(self, row, update_op, update_columns):502        """ Update the operator for a single row503        :param row: a new row504        :type row: Dict[str, object]505        :param update_op: an operator that returned by `get_update_op`506        :type update_op: Dict[str, Dict[str, float]]507        :param update_columns: the columns to update508        :type update_columns: List[str]509        :return: Dict[str, Dict[str, float]]510        :rtype: Dict[str, Dict[str, float]]511        """512        new_update_op = update_op.copy()513        for k, v in new_update_op.items():514            if k == "$inc":515                for update_column in update_columns:516                    if v[update_column] == 1:517                        v[update_column] = row[update_column]518                    else:519                        v[update_column] = -row[update_column]520            elif k == "$mul":521                for update_column in update_columns:522                    if v[update_column] == 2:523                        v[update_column] = row[update_column]524                    else:525                        v[update_column] = 1.0 / row[update_column]526            elif k == "$set":527                for update_column in update_columns:528                    v[update_column] = row[update_column]529        return new_update_op530    def update_row(self, table_name, row, update_op, update_columns):531        """ Update a row that exists in a table532        (suggestion: consider to use `update_rows` if you want to update multiple rows)533        :param table_name: the table name to update534        :type table_name: str535        :param row: a new row536        :type row: Dict[str, object]537        :param update_op: an operator that returned by `get_update_op`538        :type update_op: Dict[str, Dict[str, float]]539        :param update_columns: the columns to update540        :type update_columns: List[str]541        """542        self._conn[table_name].update_one({"_id": row["_id"]}, self._update_update_op(row, update_op, update_columns))543    def update_rows(self, table_name, rows, update_ops, update_columns):544        """ Update rows that exist in a table545        :param table_name: the table name to update546        :type table_name: str547        :param rows: new rows548        :type rows: List[Dict[str, object]]549        :param update_ops: operator(s) that returned by `get_update_op`550        :type update_ops: Union[List[Dict[str, Dict[str, float]]], Dict[str, Dict[str, float]]]551        :param update_columns: the columns to update552        :type update_columns: List[str]553        """554        if len(rows) > 0:555            if isinstance(update_ops, (tuple, list)):  # +-*/556                assert len(rows) == len(update_ops)557                update_op_collections = defaultdict(list)558                for i, row in enumerate(rows):559                    # self.update_row(row, table_name, update_ops[i], update_columns)560                    new_update_op = self._update_update_op(row, update_ops[i], update_columns)561                    update_op_collections[json.dumps(new_update_op)].append(row)562                for new_update_op, op_rows in update_op_collections.items():563                    new_update_op = json.loads(new_update_op)564                    _ids = [row["_id"] for row in op_rows]565                    for idx in range(0, len(_ids), self.chunksize):566                        query = {"_id": {'$in': _ids[idx:idx + self.chunksize]}}567                        self._conn[table_name].update_many(query, new_update_op)568            else:  # =569                update_op = update_ops570                value_collections = defaultdict(list)571                for row in rows:572                    value_collections[json.dumps([row[k] for k in update_columns])].append(row)573                for new_update_op, op_rows in value_collections.items():574                    new_update_op = self._update_update_op(op_rows[0], update_op, update_columns)575                    _ids = [row["_id"] for row in op_rows]576                    for idx in range(0, len(_ids), self.chunksize):577                        query = {"_id": {'$in': _ids[idx:idx + self.chunksize]}}578                        self._conn[table_name].update_many(query, new_update_op)579    def get_rows_by_keys(self, table_name, bys, keys, columns, order_bys=None, reverse=False, top_n=None):580        """ Retrieve rows by specific keys in some order581        :param table_name: the table name to retrieve582        :type table_name: str583        :param bys: the given columns to match584        :type bys: List[str]585        :param keys: the given values to match586        :type keys: List[str]587        :param columns: the given columns to retrieve588        :type columns: List[str]589        :param order_bys: the columns whose value are used to sort rows590        :type order_bys: List[str]591        :param reverse: whether to sort in a reversed order592        :type reverse: bool593        :param top_n: how many rows to return, default `None` for all rows594        :type top_n: int595        :return: retrieved rows596        :rtype: List[Dict[str, object]]597        """598        query = OrderedDict(zip(bys, keys))599        projection = self.__get_projection(columns)600        cursor = self._conn[table_name].find(query, projection)601        if order_bys:602            direction = -1 if reverse else 1603            cursor = cursor.sort([(k, direction) for k in order_bys])604        if top_n:605            result = []606            for x in cursor:607                result.append(x)608                if len(result) >= top_n:609                    break610            return result611        else:...

base.py

Source:base.py

1try:2    import ujson as json3except:4    import json5from collections import defaultdict, OrderedDict6class BaseConnection(object):7    def __init__(self, db_path, chunksize):8        self._conn = None9        self.chunksize = chunksize10    def close(self):11        if self._conn:12            self._conn.close()13    def __del__(self):14        self.close()15    def create_table(self, table_name, columns):16        raise NotImplementedError17    def get_columns(self, table_name, columns):18        raise NotImplementedError19    def select_row(self, table_name, _id, columns):20        raise NotImplementedError21    def select_rows(self, table_name, _ids, columns):22        raise NotImplementedError23    def insert_row(self, table_name, row):24        raise NotImplementedError25    def insert_rows(self, table_name, rows):26        raise NotImplementedError27    def update_row(self, table_name, row, update_op, update_columns):28        raise NotImplementedError29    def update_rows(self, table_name, rows, update_ops, update_columns):30        raise NotImplementedError31    def get_update_op(self, update_columns, operator):32        raise NotImplementedError33    def get_rows_by_keys(self, table_name, bys, keys, columns, order_bys=None, reverse=False, top_n=None):34        raise NotImplementedError35class SqliteConnection(BaseConnection):36    def __init__(self, db_path, chunksize):37        import sqlite338        super(SqliteConnection, self).__init__(db_path, chunksize)39        self._conn = sqlite3.connect(db_path)40    def create_table(self, table_name, columns, columns_types):41        create_table = "CREATE TABLE %s (%s);" % (table_name, ",".join(42            [' '.join(x) for x in zip(columns, columns_types)]))43        self._conn.execute(create_table)44        self._conn.commit()45    def get_columns(self, table_name, columns):46        select_table = "SELECT %s FROM %s;" % (",".join(columns), table_name)47        result = list(map(lambda x: OrderedDict(zip(columns, x)), self._conn.execute(select_table)))48        return result49    def select_row(self, table_name, _id, columns):50        select_table = "SELECT %s FROM %s WHERE _id=?;" % (",".join(columns), table_name)51        result = list(self._conn.execute(select_table, [_id]))52        if len(result) == 0:53            return None54        else:55            return OrderedDict(zip(columns, result[0]))56    def select_rows(self, table_name, _ids, columns):57        if len(_ids) > 0:58            row_cache = dict()59            result = []60            for idx in range(0, len(_ids), self.chunksize):61                select_table = "SELECT %s FROM %s WHERE _id IN ('%s');" % (62                    ",".join(columns), table_name, "','".join(_ids[idx:idx+self.chunksize]))63                result.extend(list(self._conn.execute(select_table)))64            for x in result:65                exact_match_row = OrderedDict(zip(columns, x))66                row_cache[exact_match_row["_id"]] = exact_match_row67            exact_match_rows = []68            for _id in _ids:69                exact_match_rows.append(row_cache.get(_id, None))70            return exact_match_rows71        else:72            return []73    def insert_row(self, table_name, row):74        insert_table = "INSERT INTO %s VALUES (%s)" % (table_name, ",".join(['?'] * (len(row))))75        self._conn.execute(insert_table, list(row.values()))76        self._conn.commit()77    def insert_rows(self, table_name, rows):78        if len(rows) > 0:79            insert_table = "INSERT INTO %s VALUES (%s)" % (table_name, ",".join(['?'] * (len(next(iter(rows))))))80            self._conn.executemany(insert_table, [list(row.values()) for row in rows])81            self._conn.commit()82    def _update_update_op(self, row, update_op, update_columns):83        update_op_sp = update_op.split('?')84        while len(update_op_sp) >= 0 and update_op_sp[-1] == '':85            update_op_sp.pop()86        assert len(update_op_sp) == len(update_columns)87        new_update_op = []88        for i in range(len(update_op_sp)):89            new_update_op.append(update_op_sp[i])90            if isinstance(row[update_columns[i]], str):91                new_update_op.append("'" + row[update_columns[i]].replace("'", "''") + "'")92            else:93                new_update_op.append(str(row[update_columns[i]]))94        return ''.join(new_update_op)95    def update_row(self, table_name, row, update_op, update_columns):96        update_table = "UPDATE %s SET %s WHERE _id=?" % (table_name, update_op)97        self._conn.execute(update_table, [row[k] for k in update_columns] + [row["_id"]])98        self._conn.commit()99    def update_rows(self, table_name, rows, update_ops, update_columns):100        if len(rows) > 0:101            if isinstance(update_ops, (tuple, list)): # +-*/102                assert len(rows) == len(update_ops)103                # group rows by op to speed up104                update_op_collections = defaultdict(list)  # key: _update_update_op105                for i, row in enumerate(rows):106                    # self.update_row(row, table_name, update_ops[i], update_columns)107                    new_update_op = self._update_update_op(row, update_ops[i], update_columns)108                    update_op_collections[new_update_op].append(row)109                for new_update_op, op_rows in update_op_collections.items():110                    _ids = [row["_id"] for row in op_rows]111                    for idx in range(0, len(_ids), self.chunksize):112                        update_table = "UPDATE %s SET %s WHERE _id IN ('%s');" % (113                            table_name, new_update_op, "','".join(_ids[idx:idx+self.chunksize]))114                        self._conn.execute(update_table)115            else: # =116                update_op = update_ops117                # group rows by new values to speed up118                value_collections = defaultdict(list) # key: values of new values119                for row in rows:120                    # self.update_row(row, table_name, update_op, update_columns)121                    value_collections[json.dumps([row[k] for k in update_columns])].append(row)122                for new_update_op, op_rows in value_collections.items():123                    new_update_op = self._update_update_op(op_rows[0], update_op, update_columns)124                    _ids = [row["_id"] for row in op_rows]125                    for idx in range(0, len(_ids), self.chunksize):126                        update_table = "UPDATE %s SET %s WHERE _id IN ('%s');" % (127                            table_name, new_update_op, "','".join(_ids[idx:idx+self.chunksize]))128                        self._conn.execute(update_table)129            self._conn.commit()130            """131            if isinstance(update_ops, list) or isinstance(update_ops, tuple):132                assert len(rows) == len(update_ops)133                for i, row in enumerate(rows):134                    self.update_row(row, table_name, update_ops[i], update_columns)135            else:136                update_op = update_ops137                update_table = "UPDATE %s SET %s WHERE _id=?" % (138                    table_name, update_op)139                self._conn.executemany(140                    update_table, [[row[k] for k in update_columns] + [row["_id"]] for row in rows])141            self._conn.commit()142            """143    def get_update_op(self, update_columns, operator):144        if operator in "+-*/":145            update_ops = []146            for update_column in update_columns:147                update_ops.append(update_column + "=" + update_column + operator + "?")148            return ",".join(update_ops)149        elif operator == "=":150            update_ops = []151            for update_column in update_columns:152                update_ops.append(update_column + "=?")153            return ",".join(update_ops)154        else:155            raise NotImplementedError156    def get_rows_by_keys(self, table_name, bys, keys, columns, order_bys=None, reverse=False, top_n=None):157        key_match_events = []158        select_table = "SELECT %s FROM %s WHERE %s" % (159            ",".join(columns), table_name, " AND ".join(["%s=?" % (by) for by in bys]))160        if order_bys:161            select_table += " ORDER BY %s %s" % (",".join(order_bys), "DESC" if reverse else "ASC")162        if top_n:163            select_table += " LIMIT %d" % (top_n)164        select_table += ";"165        for x in self._conn.execute(select_table, keys):166            key_match_event = OrderedDict(zip(columns, x))167            key_match_events.append(key_match_event)168        return key_match_events169class MongoDBConnection(BaseConnection):170    def __init__(self, db_path, chunksize):171        import pymongo172        super(MongoDBConnection, self).__init__(db_path, chunksize)173        self._client = pymongo.MongoClient("mongodb://localhost:27017/", document_class=OrderedDict)174        self._conn = self._client[os.path.splitext(os.path.basename(db_path))[0]]175    def close(self):176        self._client.close()177    def create_table(self, table_name, columns, columns_types):178        self._conn[table_name]179    def __get_projection(self, columns):180        projection = {"_id": 0}181        for k in columns:182            projection[k] = 1183        return projection184    def get_columns(self, table_name, columns):185        projection = self.__get_projection(columns)186        results = list(self._conn[table_name].find({}, projection))187        return results188    def select_row(self, table_name, _id, columns):189        projection = self.__get_projection(columns)190        return self._conn[table_name].find_one({"_id": _id}, projection)191    def select_rows(self, table_name, _ids, columns):192        table = self._conn[table_name]193        exact_match_rows = []194        projection = self.__get_projection(columns)195        for idx in range(0, len(_ids), self.chunksize):196            query = {"_id": {'$in': _ids[idx:idx+self.chunksize]}}197            exact_match_rows.extend(table.find(query, projection))198        row_cache = {x["_id"]: x for x in exact_match_rows}199        exact_match_rows = [row_cache.get(_id, None) for _id in _ids]200        return exact_match_rows201    def insert_row(self, table_name, row):202        self._conn[table_name].insert_one(row)203    def insert_rows(self, table_name, rows):204        self._conn[table_name].insert_many(rows)205    def _update_update_op(self, row, update_op, update_columns):206        new_update_op = update_op.copy()207        for k, v in new_update_op.items():208            if k == "$inc":209                for update_column in update_columns:210                    if v[update_column] == 1:211                        v[update_column] = row[update_column]212                    else:213                        v[update_column] = -row[update_column]214            elif k == "$mul":215                for update_column in update_columns:216                    if v[update_column] == 2:217                        v[update_column] = row[update_column]218                    else:219                        v[update_column] = 1.0 / row[update_column]220            elif k == "$set":221                for update_column in update_columns:222                    v[update_column] = row[update_column]223        return new_update_op224    def update_row(self, table_name, row, update_op, update_columns):225        self._conn[table_name].update_one(226            {"_id": row["_id"]}, self._update_update_op(row, update_op, update_columns))227    def update_rows(self, table_name, rows, update_ops, update_columns):228        if len(rows) > 0:229            if isinstance(update_ops, (tuple, list)): # +-*/230                assert len(rows) == len(update_ops)231                update_op_collections = defaultdict(list)232                for i, row in enumerate(rows):233                    # self.update_row(row, table_name, update_ops[i], update_columns)234                    new_update_op = self._update_update_op(row, update_ops[i], update_columns)235                    update_op_collections[json.dumps(new_update_op)].append(row)236                for new_update_op, op_rows in update_op_collections.items():237                    new_update_op = json.loads(new_update_op)238                    _ids = [row["_id"] for row in op_rows]239                    for idx in range(0, len(_ids), self.chunksize):240                        query = {"_id": {'$in': _ids[idx:idx+self.chunksize]}}241                        self._conn[table_name].update_many(query, new_update_op)242            else: # =243                update_op = update_ops244                value_collections = defaultdict(list)245                for row in rows:246                    # self.update_row(row, table_name, update_op, update_columns)247                    value_collections[json.dumps([row[k] for k in update_columns])].append(row)248                for new_update_op, op_rows in value_collections.items():249                    new_update_op = self._update_update_op(op_rows[0], update_op, update_columns)250                    _ids = [row["_id"] for row in op_rows]251                    for idx in range(0, len(_ids), self.chunksize):252                        query = {"_id": {'$in': _ids[idx:idx+self.chunksize]}}253                        self._conn[table_name].update_many(query, new_update_op)254    def get_update_op(self, update_columns, operator):255        if operator == "+":256            update_ops = {}257            for update_column in update_columns:258                update_ops[update_column] = 1  # placeholder259            return {"$inc": update_ops}260        elif operator == "-":261            update_ops = {}262            for update_column in update_columns:263                update_ops[update_column] = -1  # placeholder264            return {"$inc": update_ops}265        elif operator == "*":266            update_ops = {}267            for update_column in update_columns:268                update_ops[update_column] = 2  # placeholder269            return {"$mul": update_ops}270        elif operator == "/":271            update_ops = {}272            for update_column in update_columns:273                update_ops[update_column] = 0.5  # placeholder274            return {"$mul": update_ops}275        elif operator == "=":276            update_ops = {}277            for update_column in update_columns:278                update_ops[update_column] = 1  # placeholder279            return {"$set": update_ops}280        else:281            raise NotImplementedError282    def get_rows_by_keys(self, table_name, bys, keys, columns, order_bys=None, reverse=False, top_n=None):283        query = OrderedDict(zip(bys, keys))284        projection = self.__get_projection(columns)285        cursor = self._conn[table_name].find(query, projection)286        if order_bys:287            direction = -1 if reverse else 1288            cursor = cursor.sort([(k, direction) for k in order_bys])289        if top_n:290            result = []291            for x in cursor:292                result.append(x)293                if len(result) >= top_n:294                    break295            return result296        else:...

dnn_ncrt_liew_combined_latest.py

Source:dnn_ncrt_liew_combined_latest.py

...39    predicted = list(np.round(predicted))40    predicted = list(map(lambda row: list(map(int, row)), predicted))41    return predicted, classifier42def get_fingerprints(mol):43    morgan = update_columns(morgan_fingerprints(mol), 'morgan')44    maccs = update_columns(maccs_fingerprints(mol), 'maccs')45    charge_f, e = charge_features(mol)46    autocorrelation_f, e = autocorrelation_features(mol)47    harmonic_topology = pd.DataFrame(harmonic_topology_index_feature(mol))48    constitutional_f = constitutional_features(mol)49    estate_f = estate_features(mol)50    moe_f = moe_features(mol)51    bcut_f, e = bcut_features(mol)52    molproperty_f, e = molproperty_features(mol)53    cats2d_f = cats2d_features(mol)54    kappa = kappa_descriptors(mol)55    return {56        "maccs": maccs,57        "morgan": morgan,58        'charge': update_columns(charge_f, 'charge'),59        'harmonic_topology': update_columns(harmonic_topology, 'harmonic'),60        'autocorrelation': update_columns(autocorrelation_f, 'autocorrelation'),61        'constitutional': update_columns(constitutional_f, 'constitutional'),62        'estate': update_columns(estate_f, 'estate'),63        'moe': update_columns(moe_f, 'moe'),64        'bcut': update_columns(bcut_f, 'bcut'),65        'molproperty': update_columns(molproperty_f, 'molproperty'),66        'cats2d': update_columns(cats2d_f, 'cats2d'),67        'kappa': update_columns(kappa, 'kappa'),68    }69if __name__ == "__main__":70    ncrt_train = pd.read_csv('./data/raw/ncrt_liew_train.csv', index_col=0).fillna(0).reset_index(drop=True)71    ncrt_test = pd.read_csv('./data/raw/ncrt_liew_test.csv', index_col=0).fillna(0).reset_index(drop=True)72    common_comb = ['maccs', 'morgan', 'charge', 'harmonic_topology', 'autocorrelation', 'constitutional', 'estate',73                   'moe', 'bcut', 'molproperty', 'cats2d', 'kappa']74    fingerprints = get_fingerprints(convert_to_mol(ncrt_train['smiles']))75    fingerprints_test = get_fingerprints(convert_to_mol(ncrt_test['smiles']))76    all_inputs = pd.concat(list(map(lambda x: fingerprints[x], common_comb)), axis=1).fillna(0)77    all_inputs_test = pd.concat(list(map(lambda x: fingerprints_test[x], common_comb)), axis=1).fillna(0)78    X = pd.concat([all_inputs, all_inputs_test]).reset_index(drop=True)79    y = pd.concat([ncrt_train['label'], ncrt_test['label']]).reset_index(drop=True)80    # Instantiate the cross validator81    skf = StratifiedKFold(n_splits=10, random_state=1)...

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