14.1.7. Data Output

14.1.7.1. mosaic.mdio.sqlite3MDIO module

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A class that extends metaMDIO to implement SQLite support for metadata storage.

Created:

9/28/2014

Author:

Arvind Balijepalli <arvind.balijepalli@nist.gov>

License:

See LICENSE.TXT

ChangeLog:

3/25/17 AB Allow an optional argument to pass a database name.

12/6/15 AB Add sampling frequency to analysis info table

8/5/15 AB Added a function to export database tables to CSV

8/5/15 AB Misc bug fixes

4/1/15 AB Added an estimate of data length to the DB

3/23/15 AB Added a raw query function that does not automatically decode column data.

11/9/14 AB Implemented the analysis log I/O interface for sqlite3 databases.

9/28/14 AB Initial version

class mosaic.mdio.sqlite3MDIO.data_record(data_label, data, data_t)

Bases: dict

Smart data record structure that automatically encodes/decodes data for storage in a sqlite3 DB.

update([E, ]**F) → None.  Update D from dict/iterable E and F.

If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]

class mosaic.mdio.sqlite3MDIO.sqlite3MDIO

Bases: metaMDIO

closeDB()

Important

Abstract method: This method must be implemented by a sub-class.

csvString(query)

Return database records that match the specified query as a CSV formatted string.

exportToCSV(query)

Export database records that match the specified query to a CSV flat file.

queryDB(query)

Important

Abstract method: This method must be implemented by a sub-class.

Query a database. :Parameters:

• query : query string

See also

See specific implementations of metaMDIO for query syntax.

readAnalysisInfo()

Important

Abstract method: This method must be implemented by a sub-class.

Read analysis information from the database.

readAnalysisLog()

Important

Abstract method: This method must be implemented by a sub-class.

Read the analysis log from the database.

readSettings()

Important

Abstract method: This method must be implemented by a sub-class.

Read JSON settings from the database.

writeAnalysisInfo(infolist)

Important

Abstract method: This method must be implemented by a sub-class.

Write analysis information to the database. Note that subsequent calls to this method will overwrite the analysis inoformation entry in the table.

Args:

• infolistA list of strings in the following order [ datPath, dataType, partitionAlgorithm, processingAlgorithm, filteringAlgorithm].

  datPath : full path to the data directory

  dataType : type of data processed (e.g. ABF, QDF, etc.)

  partitionAlgorithm : name of partition algorithm (e.g. eventSegment)

  processingAlgorithm : name of event processing algorithm (e.g. multStateAnalysis)

  filteringAlgorithm : name of filtering algorithm (e.g. waveletDenoiseFilter) or None if no filtering was performed.

writeAnalysisLog(analysislog)

Important

Abstract method: This method must be implemented by a sub-class.

Write the analysis log string to the database. Note that subsequent calls to this method will overwrite the analysis log entry.

Args:

• analysislog : analysis log string to save

writeRecord(data, table=None)

Important

Abstract method: This method must be implemented by a sub-class.

Write data to a specified table. By default table is None. In this case sub-classes should fall back to writing data to a default table.

writeSettings(settingsstring)

Important

Abstract method: This method must be implemented by a sub-class.

Write the settings JSON object to the database.

Args:

• settingsstring : a JSON_ formatted settings string.