Source code for pwem.viewers.mdviewer.star_dao

# **************************************************************************
# *
# * Authors: Yunior C. Fonseca Reyna    (
# *          Pablo Conesa Mingo         (
# *
# * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * This program is free software; you can redistribute it and/or modify
# * it under the terms of the GNU General Public License as published by
# * the Free Software Foundation; either version 2 of the License, or
# * (at your option) any later version.
# *
# * This program is distributed in the hope that it will be useful,
# * but WITHOUT ANY WARRANTY; without even the implied warranty of
# * GNU General Public License for more details.
# *
# * You should have received a copy of the GNU General Public License
# * along with this program; if not, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307  USA
# *
# *  All comments concerning this program package may be sent to the
# *  e-mail address ''
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# **************************************************************************
import logging
logger = logging.getLogger()

from metadataviewer.dao.model import IDAO

[docs]class StarFile(IDAO): """ Class to handle STAR or XMD files. """ def __init__(self, inputFile): self._file = self.__loadFile(inputFile) self._tableCount = {} self._tableData = {} self._labels = {} self._names = [] self._labelsTypes = {} self._aliases = {} def __loadFile(self, inputFile): try: return open(inputFile, 'r') except Exception as e: logger.error("The file could not be opened. Make sure the path is " "correct: \n %s" % e) return None
[docs] def fillTable(self, table, objectManager): """Create the table structure""" self._loadStarFileInfo(table)
[docs] def fillPage(self, page, actualColumn, orderAsc): """ Fill a page taking into account the page number and size. Variables actualColumn and orderAsc control the table order """ table = page.getTable() tableName = table.getName() if table.hasSortingChanged(): self.sort(tableName, actualColumn, orderAsc) # moving to the first row of the page pageNumber = page.getPageNumber() pageSize = page.getPageSize() firstRow = pageNumber * pageSize - pageSize endRow = pageNumber * pageSize # getting more rows logger.debug("Creating the page with rows: %d -> %d " % (firstRow, endRow)) for row in self._iterRowLines(tableName, firstRow, endRow): if row: page.addRow(row)
[docs] def getTableRowCount(self, tableName): """Get the number of rows of a given table""" return self._tableCount[tableName]
[docs] def getTableNames(self): """ Return all the names of the data_ blocks found in the file and fill all labels and data of every table name """ if not self._names: f = self._file line = f.readline() logger.debug("Reading the star file completely and filling " "the model().") while line: # While searching for a data line, we will store the offsets # for any data_ line that we find if line.startswith('data_'): tn = line.strip().replace('data_', '') self._names.append(tn) data = self._getData() self._tableCount[tn] = data[0] self._labels[tn] = ['id'] + data[1] self._labelsTypes[tn] = data[2] self._tableData[tn] = data[3] self._aliases[tn] = tn line = f.readline() return list(self._names)
[docs] def getTableAliases(self): """Get the tables aliases""" return self._aliases
def _getData(self): """ Method to get all information of the table (labels, data,...)""" self._findLabelLine() data = [] line, labels = self._getLabels() count = 0 f = self._file firstRow = line.split() labelsTypes = [int] for i in range(len(firstRow)): labelsTypes.append(_guessType(firstRow[i])) while line and not line.startswith('\n'): line = str(count+1) + ' ' + line data.append(line.split()) count += 1 line = f.readline().strip() return count, labels, labelsTypes, data def _getLabels(self): """Get the table labels""" logger.debug("Getting the table labels...") line = self._line labels = [] while line.startswith('\n'): line = self._file.readline() while line.startswith('_'): parts = line.split() labels.append(parts[0][1:]) line = self._file.readline() while line.startswith('\n'): line = self._file.readline() return line, labels def _loadStarFileInfo(self, table): """Create the table structure""" logger.debug("Creating the table columns...") colNames = self._labels[table.getName()] values = self._tableData[table.getName()][0] table.createColumns(colNames, values) table.setAlias(table.getName()) def _findLabelLine(self): """Find the first labels line in the star file""" line = '' foundLoop = False rawLine = self._file.readline() while rawLine: if rawLine.startswith('_'): line = rawLine break elif rawLine.startswith('loop_'): foundLoop = True rawLine = self._file.readline() self._line = line.strip() self._foundLoop = foundLoop def _iterRowLines(self, tableName, firstRow, endRow): """Iter over the table in a range of rows """ if self._tableCount[tableName] == 1: yield 1, self._tableData[tableName][0] return if firstRow + endRow > self._tableCount[tableName]: endRow = self._tableCount[tableName] for i in range(firstRow, endRow): values = self._tableData[tableName][i] yield int(values[0]), values
[docs] def close(self): if getattr(self, '_file', None): self._file.close() self._file = None
[docs] @classmethod def getCompatibleFileTypes(cls): """Return a list of compatible extension of files""" logger.debug("Selected StarFile DAO") return ['star', 'xmd']
[docs] def sort(self, tableName, column, sortAsc=True): """ Sort the table in place using the provided column. :param column is a number, it is the index of one column. """ _columType = self._labelsTypes[tableName][column] orderList = sorted(self._tableData[tableName], key=lambda x: _columType(x[column]), reverse=not sortAsc) self._tableData[tableName] = orderList
[docs] def getSelectedRangeRowsIds(self, tableName, startRow, numberOfRows, column, reverse=True): """Return a range of rows starting at 'startRow' an amount of 'numberOfRows' """ logger.debug("Reading the table %s and selected a range of rows %d - %d" % (tableName, startRow+1, numberOfRows + 1)) col = 0 for i in range(len(self._labels[tableName])): if self._labels[tableName][i] == 'id': col = i break table = self._tableData[tableName] rowsIds = [int(table[row][col]) for row in range(startRow-1, startRow+numberOfRows)] return rowsIds
[docs] def getTableWithAdditionalInfo(self): """Return a tuple with the table that need to show additional info and the column that we need to show""" return None
# -----------------------------------Utils methods ----------------------- def _guessType(strValue): try: int(strValue) return int except ValueError: try: float(strValue) return float except ValueError: return str