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How to use _init_connect method in Airtest

Best Python code snippet using Airtest

read_storage.py

Source:read_storage.py

...21    cursor = None22    db_file_name = None 23    def __init__(self, file_name):24        self.db_file_name = file_name25    def _init_connect(self):26        """Initialize connection to the database,27            optimize the database.28        """29        if self.connection is None:30            try:31                self.connection = sqlite3.connect(self.db_file_name)32                #self.connection = apsw.Connection(self.db_file_name)33                self.cursor = self.connection.cursor()34                self.cursor.execute("PRAGMA synchronous = OFF;")35                self.cursor.execute("PRAGMA journal_mode = OFF;")36                self.cursor.execute("PRAGMA LOCKING_MODE = EXCLUSIVE;")37                self.cursor.execute("PRAGMA foreign_keys=off;")38            except Exception as e:39                raise DatabaseException("Error while connecting to the database.", e)40    def setup(self):41        """Create the initial table for collecting read information 42            from the BAM file.43        """44        if os.path.exists(self.db_file_name):45            os.remove(self.db_file_name)46        self._init_connect()47        try:48            self.cursor.execute("""CREATE TABLE reads ( read_id text NOT NULL, 49                                                        cell_id text NOT NULL,50                                                        sample_name text NOT NULL )51                                                         ;""")52        except Exception as e:53            raise DatabaseException("Error while initializing the database.", e)54        else:55            pass56    def create_indexes(self):57        """Try to speed up subsequent steps by creating indexes in the database."""58        self.cursor.execute("CREATE INDEX idx_reads_read_id ON reads(read_id);")59        #self.cursor.execute("CREATE INDEX idx_cell_id ON reads(cell_id);")60        #self.cursor.execute("CREATE INDEX idx_sample_name ON reads(sample_name);")61        self.cursor.execute("CREATE INDEX idx_reads_cell_sample ON reads(cell_id, sample_name);")62    def process_data(self, threshold):63        """Calculate final association table from the initial read table."""64        self._init_connect()65        print(f"{get_timestamp()}           * Calculating stats on cells")66        self._calculate_stats_on_cells()67        print(f"{get_timestamp()}           * Assigning cells to samples")68        self._assign_cells_to_samples(threshold)69        print(f"{get_timestamp()}           * Creating the association table")70        self._create_final_table()71    def get_total_cell_count(self):72        """Return total number of putative cells."""73        self.cursor.execute("SELECT COUNT(*) as count FROM cells;")74        count = self.cursor.fetchone()75        return(count[0])76    def get_cell_count_per_sample(self):77        """Return cell count per sample tag."""78        self.cursor.execute("SELECT sample, COUNT(*) as count FROM cells GROUP BY sample;")79        counts = self.cursor.fetchall()80        return(counts)81    def _calculate_stats_on_cells(self):82        """Calculate intermitten cells_stat table,83            requires: reads TABLE filled with all values (self.store() )84        """85        try:86            self.cursor.execute("""CREATE TABLE cells_stat AS 87                                SELECT cell_id, sample_name, COUNT(*) abundance 88                                FROM reads GROUP BY cell_id, sample_name;""")89            self.cursor.execute("CREATE INDEX idx_stat_cell_id ON cells_stat(cell_id);")90            self.cursor.execute("CREATE INDEX idx_stat_sample_name ON cells_stat(sample_name);")91        except Exception as e:92            raise DatabaseException("Error while calculating statistics on cell IDs.", e)93    94    def _assign_cells_to_samples(self, threshold = 0.75):95        """Create an intermitten table cells,96            requires: cells_stat TABLE (self.calculate_stats_on_cells() )97        """98        try:99            query = f"""CREATE TABLE cells AS100                          SELECT  cell_id,101                            CASE102                              WHEN max_abd >= sum_abd*{threshold} THEN sample_name103                                  ELSE 'MULTIPLE'104                              END sample FROM105                                (SELECT cell_id, sample_name,106                                     MAX(abundance) max_abd, SUM(abundance) sum_abd107                                         FROM cells_stat GROUP BY cell_id);"""108            self.cursor.execute(query)109            self.cursor.execute("CREATE INDEX idx_cells_cell_id ON cells(cell_id);")110            self.cursor.execute("CREATE INDEX idx_cells_sample_name ON cells(sample);")111        except Exception as e:112            raise DatabaseException("Error while calculating cell-sample relationships.", e)113    def cleanup(self):114        """Delete all but the final table from the database."""115        self._init_connect()116        try:117            self.cursor.execute("DROP TABLE IF EXISTS reads;")118            self.cursor.execute("DROP TABLE IF EXISTS cells;")119            self.cursor.execute("DROP TABLE IF EXISTS cells_stat;")120        except Exception as e:121            raise DatabaseException("Error while deleting the database.", e)122    def _create_final_table(self):123        """Calculate the final association table."""124        self._init_connect()125        try:126            self.cursor.execute("""CREATE TABLE read_sample_pairs AS127                                    SELECT read_id, sample FROM128                                      (SELECT read_id, reads.cell_id, sample FROM reads129                                        LEFT JOIN cells ON reads.cell_id = cells.cell_id);""")130            ## create a covering index131            self.cursor.execute("CREATE INDEX idx_pairs_cover ON read_sample_pairs(read_id, sample);")132        except Exception as e:133            raise DatabaseException("Error while assigning the dominant sample to cell IDs.", e)134    def get_multiple_read_sample_pairs(self, key_list):135        """Return sample for read IDs provided in the argument"""136        self._init_connect()137        return self.get_multiple("read_sample_pairs", ["read_id", "sample"], "read_id", key_list)138    def get_multiple(self, table, field_list, lookup_field, key_list):139        """generic method for retrieving information form the database."""140        if len(key_list) < 1:141            raise DatabaseException("No read IDs provided to look up.")142        fields_string = ",".join([ field for field in field_list ])143        keys_string = ",".join("?" * len(key_list))144        key_list = list(key_list)145        146        result = None147        try:148            self.cursor.execute(f"""SELECT {fields_string} FROM {table} 149                                    WHERE {lookup_field} IN ({keys_string});""", key_list)150            result = dict(self.cursor.fetchall())...

mysql_data_getter.py

Source:mysql_data_getter.py

...20                df.to_csv(file_name)21        finally:22            conn.close()23    @classmethod24    def _init_connect(cls, host, port, uname, pwd, db):25        """26        ç¨æ¥æå»ºmysql connect è¿æ¥å¯¹è±¡27        :param host:28        :param port: ç«¯å£å·ï¼ å¿é¡»æ¯int29        :param uname:30        :param pwd:31        :param db:32        :return: connect å¯¹è±¡33        """34        if isinstance(port, str):35            port = int(port)36        conn = pymysql.connect(host=host, port=port, user=uname,37                               password=pwd, db=db, charset="utf8",38                               cursorclass=pymysql.cursors.DictCursor)39        return conn40    @classmethod41    def download(cls, host, port, uname, pwd, db, sqls):42        conn = cls._init_connect(host=host, port=int(port), uname=uname, pwd=pwd, db=db)...

main_controller.py

Source:main_controller.py

...24        self._init_ui()25    def _init_ui(self):26        # åå§åUIï¼è§å¾ï¼27        self.setupUi(self)28        self._init_connect()29    def _init_connect(self):30        # è°ç¨èªå®ä¹ä¿¡å·åæ§½å½æ°ç±»ï¼æ¨¡åï¼...

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