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Removed directory argument from Database methods in favor of instance…
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… attribute (Issue #87)
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@hover2pi
hover2pi committed May 11, 2017
1 parent d32dffc commit 0991a57
Showing 1 changed file with 72 additions and 73 deletions.
145 changes: 72 additions & 73 deletions astrodbkit/astrodb.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@
import math
import pandas as pd
import numpy as np
import datetime
import matplotlib.pyplot as plt
import astropy.io.fits as pf
import astropy.io.ascii as ii
Expand Down Expand Up @@ -54,15 +55,15 @@ def create_database(dbpath):


class Database:
def __init__(self, dbpath, directory='tabledata'):
def __init__(self, dbpath, directory=''):
"""
Initialize the database.
Parameters
----------
dbpath: str
The path to the .db or .sql database file.
directory: str
directory: str (optional)
Folder in which individual tables are stored (Default: tabledata)
Returns
Expand All @@ -81,52 +82,55 @@ def __init__(self, dbpath, directory='tabledata'):
if dbpath.endswith('.sql'):
self.sqlpath = dbpath
self.dbpath = dbpath.replace('.sql', '.db')

# If the .db file already exists, rename it with the date
if os.path.isfile(self.dbpath):
import datetime
date = datetime.datetime.now().strftime("%Y-%m-%d_%H:%M")
print("Renaming existing file {} to {}".format(self.dbpath, self.dbpath.replace('.db', date+'.db')))
os.system("mv {} {}".format(self.dbpath, self.dbpath.replace('.db', date+'.db')))

# Make the new database from the .sql files
# First the schema...
os.system("sqlite3 {} < {}".format(self.dbpath, self.sqlpath))

# Prepare to deactivate the triggers (all, just in case)
trigger_names = os.popen(
"""echo "SELECT name FROM sqlite_master WHERE type='trigger';" | sqlite3 {}"""
.format(self.dbpath)).read().replace('\n', ' ').split()
trigger_sql = os.popen(
"""echo "SELECT sql FROM sqlite_master WHERE type='trigger';" | sqlite3 {}"""
.format(self.dbpath)).read()
if len(trigger_names) > 0:
for trigger_name in trigger_names:
os.system("""echo "DROP TRIGGER {};" | sqlite3 {}""".format(trigger_name, self.dbpath))

# Then load the table data...
print('Populating database...')
# Grabbing only tables, not tables and views
# tables = os.popen('sqlite3 {} ".tables"'.format(self.dbpath)).read().replace('\n',' ').split()
tables = os.popen("""echo "SELECT name FROM sqlite_master WHERE type='table';" | sqlite3 {}"""
.format(self.dbpath)).read().replace('\n',' ').split()
for table in tables:
print('Loading {}'.format(table))
os.system('sqlite3 {0} ".read {1}/{2}.sql"'.format(self.dbpath, directory, table))

# Reactivate the triggers
if len(trigger_sql) > 0:
for new_trigger in trigger_sql.split('END'):
if new_trigger == '\n': continue
# print(new_trigger + 'END;')
os.system("""echo "{}" | sqlite3 {}""".format(new_trigger + 'END;', self.dbpath))


elif dbpath.endswith('.db'):
self.sqlpath = dbpath.replace('.db', '.sql')
self.dbpath = dbpath
else:
self.sqlpath = dbpath + '.sql'
self.dbpath = dbpath

# Save the directory to the tabledata as an attribute
self.directory = directory or os.path.join(os.path.dirname(self.dbpath), 'tabledata')

# If the .db file already exists, copy and rename it
if os.path.isfile(self.dbpath):

date = datetime.datetime.now().strftime("%Y-%m-%d_%H-%M")
print("Renaming existing file {} to {}".format(self.dbpath, self.dbpath.replace('.db', date+'.db')))
os.system("mv {} {}".format(self.dbpath, self.dbpath.replace('.db', date+'.db')))

# Make the new database from the .sql files
# First the schema...
os.system("sqlite3 {} < {}".format(self.dbpath, self.sqlpath))

# Prepare to deactivate the triggers (all, just in case)
trigger_names = os.popen(
"""echo "SELECT name FROM sqlite_master WHERE type='trigger';" | sqlite3 {}"""
.format(self.dbpath)).read().replace('\n', ' ').split()
trigger_sql = os.popen(
"""echo "SELECT sql FROM sqlite_master WHERE type='trigger';" | sqlite3 {}"""
.format(self.dbpath)).read()
if len(trigger_names) > 0:
for trigger_name in trigger_names:
os.system("""echo "DROP TRIGGER {};" | sqlite3 {}""".format(trigger_name, self.dbpath))

# Then load the table data...
print('Populating database...')
# Grabbing only tables, not tables and views
# tables = os.popen('sqlite3 {} ".tables"'.format(self.dbpath)).read().replace('\n',' ').split()
tables = os.popen("""echo "SELECT name FROM sqlite_master WHERE type='table';" | sqlite3 {}"""
.format(self.dbpath)).read().replace('\n',' ').split()
for table in tables:
print('Loading {}'.format(table))
os.system('sqlite3 {0} ".read {1}/{2}.sql"'.format(self.dbpath, self.directory, table))

# Reactivate the triggers
if len(trigger_sql) > 0:
for new_trigger in trigger_sql.split('END'):
if new_trigger == '\n': continue
# print(new_trigger + 'END;')
os.system("""echo "{}" | sqlite3 {}""".format(new_trigger + 'END;', self.dbpath))

# Create .sql schema file if it doesn't exist
os.system('touch {}'.format(self.sqlpath.replace(' ', '\ ')))
Expand Down Expand Up @@ -202,26 +206,26 @@ def add_changelog(self, user="", mod_tables="", user_desc=""):

def add_data(self, data, table, delimiter='|', bands='', verbose=False):
"""
Adds data to the specified database table. Column names must match table fields to insert,
however order and completeness don't matter.
Adds data to the specified database table. Column names must match table fields to insert,
however order and completeness don't matter.
Parameters
----------
data: str, sequence
The path to an ascii file or a list of lists. The first row or element must
be the list of column names
table: str
The name of the table into which the data should be inserted
delimiter: str
The string to use as the delimiter when parsing the ascii file
bands: sequence
Sequence of band to look for in the data header when digesting columns of
multiple photometric measurements (e.g. ['MKO_J','MKO_H','MKO_K']) into individual
rows of data for database insertion
verbose: bool
Print diagnostic messages
Parameters
----------
data: str, sequence
The path to an ascii file or a list of lists. The first row or element must
be the list of column names
table: str
The name of the table into which the data should be inserted
delimiter: str
The string to use as the delimiter when parsing the ascii file
bands: sequence
Sequence of band to look for in the data header when digesting columns of
multiple photometric measurements (e.g. ['MKO_J','MKO_H','MKO_K']) into individual
rows of data for database insertion
verbose: bool
Print diagnostic messages
"""
"""
# Store raw entry
entry, del_records = data, []

Expand Down Expand Up @@ -515,7 +519,7 @@ def clean_up(self, table, verbose=False):
print('\nFinished clean up on {} table.'.format(table.upper()))

# @property
def close(self, silent=False, directory='tabledata'):
def close(self, silent=False):
"""
Close the database and ask to save and delete the file
Expand All @@ -526,7 +530,7 @@ def close(self, silent=False, directory='tabledata'):
"""
if not silent:
saveme = get_input("Save database contents to '{}/'? (y, [n]) \n"
"To save under a folder name, run db.save() before closing. ".format(directory))
"To save under a folder name, run db.save() before closing. ".format(self.directory))
if saveme.lower() == 'y':
self.save()

Expand Down Expand Up @@ -1467,14 +1471,9 @@ def references(self, criteria, publications='publications', column_name='publica

if fetch: return data_tables

def save(self, directory='tabledata'):
def save(self):
"""
Dump the entire contents of the database into a folder **directory** as ascii files
Parameters
==========
directory: str
Directory name to store individual table data
Dump the entire contents of the database into the tabledata director as ascii files
"""
from subprocess import call

Expand All @@ -1493,12 +1492,12 @@ def save(self, directory='tabledata'):
os.system("echo '.output {}\n.schema' | sqlite3 {}".format(self.sqlpath, self.dbpath))

# Write the table files to the tabledata directory
os.system("mkdir -p {}".format(directory))
os.system("mkdir -p {}".format(self.directory))
tables = self.query("select tbl_name from sqlite_master where type='table'")['tbl_name']
tablepaths = [self.sqlpath]
for table in tables:
print('Generating {}...'.format(table))
tablepath = '{0}/{1}.sql'.format(directory, table)
tablepath = '{0}/{1}.sql'.format(self.directory, table)
tablepaths.append(tablepath)
with open(tablepath, 'w') as f:
for line in self.conn.iterdump():
Expand All @@ -1509,7 +1508,7 @@ def save(self, directory='tabledata'):
else:
f.write(u'{}\n'.format(line))

print("Tables saved to directory {}/".format(directory))
print("Tables saved to directory {}/".format(self.directory))
print("""=======================================================================================
You can now run git to commit and push these changes, if needed.
For example, if on the master branch you can do the following:
Expand All @@ -1518,7 +1517,7 @@ def save(self, directory='tabledata'):
git push origin master
You can then issue a pull request on GitHub to have these changes reviewed and accepted
======================================================================================="""
.format(self.sqlpath, directory))
.format(self.sqlpath, self.directory))

# Collect name and commit message from the user and push to Github
# if git:
Expand Down

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