Pyqi port

qiita_core/metadata_map.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+
+__author__ = "Jose Antonio Navas Molina"
+__copyright__ = "Copyright 2013, The Qiita Project"
+__credits__ = ["Jose Antonio Navas Molina"]
+__license__ = "BSD"
+__version__ = "0.1.0-dev"
+__maintainer__ = "Jose Antonio Navas Molina"
+__email__ = "josenavasmolina@gmail.edu"
+__status__ = "Development"
+
+from qiime.util import MetadataMap as QiimeMetadataMap
+
+
+class MetadataMap(QiimeMetadataMap):
+    """Extends the MetadataMap to include the id_ attribute"""
+
+    def __init__(self, **kwargs):
+        super(MetadataMap, self).__init__(kwargs)
+        self._id = None
+
+    def set_id(self, study_id, num):
+        """Set the MetadataMap id"""
+        self._id = (study_id, num)
+
+    def get_id(self):
+        """Returns the id of the MetadataMap"""
+        return self._id

qiita_db/__init__.py

@@ -9,29 +9,24 @@
 __email__ = "josenavasmolina@gmail.edu"
 __status__ = "Development"
 
-from qiita_db.backends.sql import (SQLUser, SQLAnalysis, SQLStudy, SQLSample,
-                                   SQLJob)
-from qiita_db.backends.fs import FSUser, FSAnalysis, FSStudy, FSSample, FSJob
-from qiita_db.backends.dev import (DEVUser, DEVAnalysis, DEVStudy, DEVSample,
-                                   DEVJob)
+from .backends.sql import (SQLUser, SQLAnalysis, SQLStudy, SQLSample, SQLJob,
+                           SQLMetadataMap)
+from .backends.fs import FSUser, FSAnalysis, FSStudy, FSSample, FSJob
+from qiita_db.config import qiita_db_config
 
-if BACKEND == "SQL":
+
+if qiita_db_config.backend == "SQL":
     UserStorage = SQLUser
     AnalysisStorage = SQLAnalysis
     StudyStorage = SQLStudy
     SampleStorage = SQLSample
     JobStorage = SQLJob
-elif BACKEND == "FS":
+    MetadataMapStorage = SQLMetadataMap
+elif qiita_db_config.backend == "FS":
     UserStorage = FSUser
     AnalysisStorage = FSAnalysis
     StudyStorage = FSStudy
     SampleStorage = FSSample
     JobStorage = FSJob
-elif BACKEND == "DEV":
-    UserStorage = DEVUser
-    AnalysisStorage = DEVAnalysis
-    StudyStorage = DEVStudy
-    SampleStorage = DEVSample
-    JobStorage = DEVJob
 else:
-    raise ValueError("Backend not recognized: %s" % BACKEND)
+    raise ValueError("Backend not recognized: %s" % qiita_db_config.backend)

qiita_db/backends/fs/__init__.py

@@ -9,8 +9,8 @@
 __email__ = "josenavasmolina@gmail.edu"
 __status__ = "Development"
 
-from qiita_db.backends.fs.user_storage.py import UserStorage as FSUser
-from qiita_db.backends.fs.analysis_storage.py import AnalysisStorage as FSAnalysis
-from qiita_db.backends.fs.study_storage.py import StudyStorage as FSStudy
-from qiita_db.backends.fs.sample_storage.py import SampleStorage as FSSample
-from qiita_db.backends.fs.job_storage.py import JobStorage as FSJob
+from qiita_db.backends.fs.user_storage import UserStorage as FSUser
+from qiita_db.backends.fs.analysis_storage import AnalysisStorage as FSAnalysis
+from qiita_db.backends.fs.study_storage import StudyStorage as FSStudy
+from qiita_db.backends.fs.sample_storage import SampleStorage as FSSample
+from qiita_db.backends.fs.job_storage import JobStorage as FSJob

qiita_db/backends/sql/__init__.py

@@ -9,8 +9,9 @@
 __email__ = "josenavasmolina@gmail.edu"
 __status__ = "Development"
 
-from qiita_db.backends.sql.user_storage.py import UserStorage as SQLUser
-from qiita_db.backends.sql.analysis_storage.py import AnalysisStorage as SQLAnalysis
-from qiita_db.backends.sql.study_storage.py import StudyStorage as SQLStudy
-from qiita_db.backends.sql.sample_storage.py import SampleStorage as SQLSample
-from qiita_db.backends.sql.job_storage.py import JobStorage as SQLJob
+from .user_storage import UserStorage as SQLUser
+from .analysis_storage import AnalysisStorage as SQLAnalysis
+from .study_storage import StudyStorage as SQLStudy
+from .sample_storage import SampleStorage as SQLSample
+from .job_storage import JobStorage as SQLJob
+from .metadata_map_storage import MetadataMapStorage as SQLMetadataMap

qiita_db/backends/sql/analysis_storage.py

@@ -9,9 +9,13 @@
 __email__ = ""
 __status__ = "Development"
 
-from qiita_db.core.base_api import BaseStorageAPI
+from qiita_db.backends.sql.base_sql import BaseSQLStorageAPI
 
 
-class AnalysisStorage(BaseStorageAPI):
+class AnalysisStorage(BaseSQLStorageAPI):
     """"""
-    pass
+
+    def __init__(self):
+        """"""
+        super(AnalysisStorage, self).__init__()
+

qiita_db/backends/sql/base_sql.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python
+
+__author__ = ""
+__copyright__ = "Copyright 2013, The Qiita Project"
+__credits__ = [""]
+__license__ = "BSD"
+__version__ = "0.1.0-dev"
+__maintainer__ = ""
+__email__ = ""
+__status__ = "Development"
+
+from qiita_db.core.base_api import BaseStorageAPI
+from qiita_db.backends.sql.sql_connection import SQLConnectionHandler
+
+
+class BaseSQLStorageAPI(BaseStorageAPI):
+    """"""
+    def __init__(self):
+        """"""
+        self.conn_handler = SQLConnectionHandler()

qiita_db/backends/sql/connections.py

@@ -0,0 +1,12 @@
+__author__ = "Jose Antonio Navas Molina"
+__copyright__ = "Copyright 2013, The Qiita project"
+__credits__ = ["Jose Antonio Navas Molina", "Adam Robbins-Pianka"]
+__license__ = "BSD"
+__version__ = "0.1.0-dev"
+__maintainer__ = "Jose Antonio Navas Molina"
+__email__ = "josenavasmolina@gmail.com"
+
+from psycopg2 import connect
+
+# Connect to the database
+postgres = connect(user='defaultuser', database='qiime_md', host='localhost')

qiita_db/backends/sql/exceptions.py

@@ -0,0 +1,29 @@
+__author__ = "Jose Antonio Navas Molina"
+__copyright__ = "Copyright 2013, The Qiita project"
+__credits__ = ["Jose Antonio Navas Molina"]
+__license__ = "BSD"
+__version__ = "0.1.0-dev"
+__maintainer__ = "Jose Antonio Navas Molina"
+__email__ = "josenavasmolina@gmail.com"
+
+from qiita_db.core.exceptions import QiitaDBError
+
+
+class QiitaDBSQLError(QiitaDBError):
+    """Base class for all Qiita-db SQL backend errors"""
+    pass
+
+
+class QiitaDBSQLExecutionError(QiitaDBSQLError):
+    """Exception for error when executing SQL queries"""
+    pass
+
+
+class QiitaDBSQLParseError(QiitaDBError):
+    """Exception for error when parsing files"""
+    pass
+
+
+class QiitaDBSQLConnectionError(QiitaDBError):
+    """Exception for error when connecting to the db"""
+    pass

qiita_db/backends/sql/metadata_map_storage.py

@@ -0,0 +1,88 @@
+#!/usr/bin/env python
+from __future__ import division
+
+__author__ = "Jose Antonio Navas Molina"
+__copyright__ = "Copyright 2013, The Qiita project"
+__credits__ = ["Jose Antonio Navas Molina", "Adam Robbins-Pianka"]
+__license__ = "BSD"
+__version__ = "0.1.0-dev"
+__maintainer__ = "Jose Antonio Navas Molina"
+__email__ = "josenavasmolina@gmail.com"
+
+from itertools import izip
+from string import lower
+
+from .base_sql import BaseSQLStorageAPI
+from .util import quote_column_name, quote_data_value, get_datatypes
+
+
+class MetadataMapStorage(BaseSQLStorageAPI):
+    """"""
+
+    def insert(self, metadata_map):
+        """Inserts the MetadataMap in the backend storage"""
+        # Get the table name
+        table_name = "study_%s_%s" % metadata_map.get_id()
+        headers = metadata_map.CategoryNames()
+        datatypes = get_datatypes(metadata_map)
+
+        # Get the columns names in SQL safe
+        sql_safe_column_names = [quote_column_name(h) for h in headers]
+
+        # Get the column names paired with its datatype for SQL
+        columns = []
+        for column_name, datatype in izip(sql_safe_column_names, datatypes):
+            columns.append('%s %s' % (column_name, datatype))
+        # Get the columns in a comma-separated string
+        columns = ", ".join(columns)
+        # Create a table for the study
+        self.conn_handler.execute("create table %s (sampleid varchar, %s)" %
+                                  (table_name, columns))
+
+        # Add rows to the column_tables table
+        lc_table_name = lower(table_name)
+        quoted_lc_table_name = quote_data_value(lc_table_name)
+        column_tables_sql_template = ("insert into column_tables (column_name,"
+                                      " table_name, datatype) values (%s, " +
+                                      quoted_lc_table_name + ", %s)")
+        # The column names should be lowercase and quoted
+        quoted_lc_headers = [quote_data_value(lower(h)) for h in headers]
+        # Pair up the column names with its datatype
+        sql_args_list = [(column_name, datatype) for column_name, datatype in
+                         izip(quoted_lc_headers, datatypes)]
+        self.conn_handler.executemany(column_tables_sql_template,
+                                      sql_args_list)
+
+        # Add rows into the study table
+        columns = ', '.join(sql_safe_column_names)
+        insert_sql_template = ('insert into ' + table_name + ' (sampleid, ' +
+                               columns + ') values (%s' +
+                               ', %s' * len(sql_safe_column_names) + ' )')
+
+        sql_args_list = []
+        for sample_id in metadata_map.SampleIds():
+            data = metadata_map.getSampleMetadata(sample_id)
+            values = [scrub_data(sample_id)]
+            values += [scrub_data(data[header]) for header in headers]
+            sql_args_list.append(values)
+
+        sql_executemany(insert_sql_template, sql_args_list)
+
+    def update(self, metadata_map):
+        """Updates the MetadataMap attributes in the backend storage"""
+        raise NotImplementedError("MetadataMapStorage.update not implemented")
+
+    def delete(self, md_id):
+        """Deletes the MetadataMap with id=md_id from the SQL db"""
+        table_name = "study_%s_%s" % md_id
+        # Dropping table
+        self.conn_handler.execute('drop table %s' % table_name)
+        # Deleting rows from column_tables for the study
+        # The query should never fail; even when there are no rows for this
+        # study, the query will do nothing but complete successfully
+        self.conn_handler.execute("delete from column_tables where "
+                                  "table_name = %s", (table_name,))
+
+    def search(self, searchObject):
+        """Retrieves all the objects that match searchObject queries"""
+        raise NotImplementedError("MetadataMapStorage.search not implemented")