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# below makes the pixmap half transparent |
# painter = QtGui.QPainter(pixmap) |
# painter.setCompositionMode(painter.CompositionMode_DestinationIn) |
# painter.fillRect(pixmap.rect(), QtGui.QColor(0, 0, 0, 127)) |
# painter.end() |
drag.setPixmap(pixmap) |
drag.setHotSpot(QtCore.QPoint(pixmap.width()/2, pixmap.height()/2)) |
drag.setPixmap(pixmap) |
self.dragActive.emit(True) |
result = drag.exec_(QtCore.Qt.MoveAction) |
QtGui.QApplication.restoreOverrideCursor()" |
19,"def database(self): |
"""""" |
Enters all the metadata into a database |
"""""" |
import sqlite3 |
try: |
os.remove('{}/metadatabase.sqlite'.format(self.reportpath)) |
except OSError: |
pass |
# Set the name of the database |
db = sqlite3.connect('{}/metadatabase.sqlite'.format(self.reportpath)) |
# Create a cursor to allow access to the database |
cursor = db.cursor() |
# Set up the db |
cursor.execute(''' |
CREATE TABLE IF NOT EXISTS Samples ( |
id INTEGER NOT NULL PRIMARY KEY AUTOINCREMENT UNIQUE, |
name TEXT UNIQUE |
) |
''') |
# Create a variable to store the names of the header values for each individual table |
# This will store a set of all the headers from all the strains, as there can be some variability present, as |
# not all analyses are available for all taxonomic groups |
columns = dict() |
for sample in self.metadata: |
# Create a metadata object to store the new tables |
data = MetadataObject() |
data.name = sample.name |
# Insert each strain name into the Samples table |
cursor.execute(''' |
INSERT OR IGNORE INTO Samples (name) |
VALUES ( ? ) |
''', (sample.name, )) |
# Each header in the .json file represents a major category e.g. ARMI, GeneSeekr, commands, etc. and |
# will be made into a separate table |
for header in sample.datastore.items(): |
# Allow for certain analyses, such as core genome, not being performed on all strains |
try: |
# Key and value: data description and data value e.g. targets present: 1012, etc. |
for key, value in sorted(header[1].datastore.items()): |
# Only the values consisting of dictionaries are of interest |
if type(value) == dict: |
# Clean the column names so there are no issues entering names into the database |
cleanedcolumn = self.columnclean(key) |
# Set the table name |
tablename = '{}_{}'.format(header[0].replace('.', '_'), cleanedcolumn) |
# Create the table (if it doesn't already exist) |
cursor.execute(''' |
CREATE TABLE IF NOT EXISTS {} ( |
sample_id INTEGER |
) |
'''.format(tablename)) |
# Add the attributes with the dictionaries (values) to the metadata object |
setattr(data, tablename, GenObject(value)) |
for gene, result in sorted(value.items()): |
# Add the data header to the dictionary |
try: |
columns[tablename].add(gene) |
# Initialise the dictionary the first time a table name is encountered |
except KeyError: |
columns[tablename] = set() |
columns[tablename].add(str(gene)) |
except (AttributeError, IndexError): |
pass |
self.tabledata.append(data) |
# Iterate through the dictionary containing all the data headers |
for table, setofheaders in sorted(columns.items()): |
# Each header will be used as a column in the appropriate table |
for cleanedcolumn in sorted(setofheaders): |
# Alter the table by adding each header as a column |
cursor.execute(''' |
ALTER TABLE {} |
ADD COLUMN {} TEXT |
'''.format(table, cleanedcolumn)) |
# Iterate through the samples and pull out the data for each table/column |
# for sample in self.metadata: |
for sample in self.tabledata: |
# Find the id associated with each sample in the Sample table |
cursor.execute(''' |
SELECT id from Samples WHERE name=? |
''', (sample.name,)) |
sampleid = cursor.fetchone()[0] |
# Add the sample_id to the table |
cursor.execute(''' |