I'm using xlwt in python to create a Excel spreadsheet. You could interchange this for almost anything else that generates a file; it's what I want to do with the file that's important.
from xlwt import *
w = Workbook()
#... do something
w.save('filename.xls')
I want to I have two use cases for the file: I stream it out to the user's browser or I attach it to an email. In both cases the file only needs to exist the duration of the web request that generates it.
What I'm getting at, the reason for starting this thread is saving to a real file on the filesystem has its own hurdles (stopping overwriting, cleaning up the file once done). Is there somewhere I could "save" it where it lives only in memory and only for the duration of the request?
cStringIO
(or mmap if it should be mutable)
Generalising the answer, as you suggested: If the "anything else that generates a file" won't accept a file-like object as well as a filepath, then you can reduce the hassle by using tempfile.NamedTemporaryFile
Related
I apologize for the length of this. I am a relative Neophyte to Excel VBA and even more junior with Python. I have run into an issue with an error that occasionally occurs in python using OpenPyXl (just trying that for the first time).
Background: I have a series of python scripts (12) running and querying an API to gather data and populate 12 different, though similar, workbooks. Separately, I have a equal number of Excel instances periodically looking for that data and doing near-real-time analysis and reporting. Another python script looks for key information to be reported from the spreadsheets and will text it to me when identified. The problem seems to occur between the data gathering python scripts and a copy command in the data analysis workbooks.
The way the python data gathering scripts "talk" to the analysis workbooks is via the sheets they build in their workbooks. The existing vba in the analysis workbooks will copy the data workbooks to another directory (so that they can be opened and manipulated without impacting their use by the python scripts) and then interpret and copy the data into the Excel analysis workbook. Although I recently tested a method to read the data directly from those python-created workbooks without opening them, the vba will require some major surgery to convert to that method and is likely not going to happen soon.
TL,DR: There are data workbooks and analysis workbooks. Python builds the data workbooks and the analysis workbooks use VBA to copy the data workbooks to another directory and load specific data from the copied data workbooks. There is a one-to-one correspondence between the data and analysis workbooks.
Based on the above, I believe that the only "interference" that occurs with the data workbooks is when the macro in the analysis workbook copies the workbook. I thought this would be a relatively safe level of interference, but it apparently is not.
The copy is done in VBA with this set of commands (the actual VBA sub is about 500 lines):
fso.CopyFile strFromFilePath, strFilePath, True
where fso is set thusly:
Set fso = CreateObject("Scripting.FileSystemObject")
and the strFromFilePath and strFilePath both include a fully qualified file name (with their respective paths). This has not generated any errors on the VBA side.
The data is copied about once a minute (though it varies from 40 seconds to about 5 minutes) and seems to work fine from a VBA perspective.
What fails is the python side about 1% of the time (which is probably 12 or fewer times daily. While that seems small, the associated data capture process halts until I notice and restart it. This means anywhere from 1 to all 12 of the data capture processes will fail at some point each day.
Here is what a failure looks like:
Traceback (most recent call last):
File "<pyshell#2>", line 1, in <module>
monitor('DLD',1,13,0)
File "<string>", line 794, in monitor
File "C:\Users\abcd\AppData\Local\Programs\Python\Python39\lib\site-packages\openpyxl\workbook\workbook.py", line 407, in save
save_workbook(self, filename)
File "C:\Users\abcd\AppData\Local\Programs\Python\Python39\lib\site-packages\openpyxl\writer\excel.py", line 291, in save_workbook
archive = ZipFile(filename, 'w', ZIP_DEFLATED, allowZip64=True)
File "C:\Users\abcd\AppData\Local\Programs\Python\Python39\lib\zipfile.py", line 1239, in __init__
self.fp = io.open(file, filemode)
PermissionError: [Errno 13] Permission denied: 'DLD20210819.xlsx'
and I believe it occurs as a result of the following lines of python code (which comes after a while statement with various if conditions to populate the worksheets). The python script itself is about 200 lines long:
time.sleep(1) # no idea why wb.save sometimes fails; trying a delay
wb.save(FileName)
Notice, I left in one of the attempts to correct this. I have tried waiting as much as 3 seconds with no noticeable difference.
I admit I have no idea how to detect errors thrown by OpenPyXl and am quite unskilled at python error handling, but I had tried this code yesterday:
retries = 1
success = False
while not success and retries < 3:
try:
wb.save
success = True
except PermissionError as saveerror:
print ('>>> Save Error: ',saveerror)
wait = 3
print('=== Waiting %s secs and re-trying... ===' % wait)
#sys.stdout.flush()
time.sleep(wait)
retries += 1
My review of the output tells me that the except code never executed while testing the data capture routine over 3000 times. However, the "save" also never happened so the analysis spreadsheets did not receive any information until later when the python code saved the workbook and closed it.
I also tried adding a wb.close after setting the success variable to true, but got the same results.
I am considering either rewriting the VBA to try to grab the data directly from the unopened data workbooks without first copying them (which actually sounds more dangerous) or using an external synching tool to copy them outside of VBA (which could potentially cause exactly the same problem).
Does anyone have an idea of what may be happening and how to address it? It works nearly all the time but just fails several times a day.
Can someone help me to better understand how to trap the error thrown by OpenPyXl so that I can have it retry rather than just abending?
Any suggestions are appreciated. Thank you for reading.
Not sure if this is the best way, but the comment from simpleApp gave me an idea that I may want to use a technique I used elsewhere in the VBA. Since I am new to these tools, perhaps someone can suggest a cleaner approach, but I am going to try using a semaphore file to signal when I am copying the file to alert the python script that it should avoid saving.
In the below I am separating out the directory the prefix and the suffix. The prefix would be different for each of the 12 or more instances I am running and I have not figured out where I want to put these files nor what suffix I should use, so I made them variables.
For example, in the VBA I will have something like this to create a file saying currently available:
Dim strSemaphoreFolder As String
Dim strFilePrefix As String
Dim strFileDeletePath As String
Dim strFileInUseName As String
Dim strFileAvailableName As String
Dim strSemaphoreFileSuffix As String
Dim fso As Scripting.FileSystemObject
Dim fileTemp As TextStream
Set fso = CreateObject("Scripting.FileSystemObject")
strSemaphoreFileSuffix = ".txt"
strSemaphoreFolder = "c:\temp\monitor\"
strFilePrefix = "RJD"
strFileDeletePath = strSemaphoreFolder & strFilePrefix & "*" & strSemaphoreFileSuffix
' Clean up remnants from prior activities
If Len(Dir(strFileDeletePath)) > 0 Then
Kill strFileDeletePath
End If
' files should be gone
' Set the In-use and Available Names
strFileInUseName = strFilePrefix & "InUse" & strSemaphoreFileSuffix
strFileAvailableName = strFilePrefix & "Available" & strSemaphoreFileSuffix
' Create an available file
Set fileTemp = fso.CreateTextFile(strSemaphoreFolder & strFileAvailableName, True)
fileTemp.Close
' available file should be there
Then, when I am about to copy the file, I will briefly change the filename to indicate that the file is in use, perform the potentially problematic copy and then change it back with something like this:
' Temporarily name the semaphore file to "In Use"
Name strSemaphoreFolder & strFileAvailableName As strSemaphoreFolder & strFileInUseName
fso.CopyFile strFromFilePath, strFilePath, True
' After copying the file name it back to "Available"
Name strSemaphoreFolder & strFileInUseName As strSemaphoreFolder & strFileAvailableName
Over in the Python script, before I do the wb.save command, I will insert a check to see whether the file indicates that it is available or in use with something like this:
prefix = 'RJD'
directory = 'c:\\temp\\monitor\\'
suffix = '.txt'
filepathname = directory + prefix + 'Available' + suffix
while not (os.path.isfile(directory + prefix + 'Available' + suffix)):
time.sleep(1)
wb.save
Does this seem like it would work?
I am thinking that it should avoid the failure if I have properly identified it as an attempt to save the file in the Python script while the VBA script is telling the operating system to copy it.
Thoughts?
afterthoughts:
Using the technique I described, I probably need to create the "Available" semaphore file in the Python script and simply assume it will be there in the VBA script since the Python script is collecting the data and may be doing so before the VBA is even started.
A better alternative may be to simply check for the existence of the "In Use" file which will never be there unless the VBA wants it there, like this:
while (os.path.isfile(directory + prefix + 'InUse' + suffix)):
time.sleep(1)
wb.save
I'm attempting to read in a series of files for processing contained in a single directory using RedVox:
input_directory = "/home/ben/Documents/Data/F1D1/21" # file location
rdvx_data = DataWindow(input_dir=input_directory, apply_correction=False, debug=True) # using RedVox to read in the files
print(os.listdir(input_directory)) # verifying the files actually exist...
# returns "['file1.rdvxz', 'file2.rdvxz', file3.rdvxz', ...etc]", they exist
# write audio portion to file
rdvx_data.to_json_file(base_dir=output_rpd_directory,
file_name=output_filename)
# this never runs, because rdvx_data.stations = [] (verified through debugging)
for station in rdvx_data.stations:
# some code here
Enabling debugging through arguments as seen above does not provide an extra details. In fact, there is no error message whatsoever. It writes the JSON file and pickle to disk, but the JSON file is full of null values and the pickle object is just a shell, no contents. So the files definitely exist, os.listdir() sees them, but RedVox does not.
I assume this is some very silly error or lack of understanding on my part. Any help is greatly appreciated. I have not worked with RedVox previously, nor do I have much understanding of what these files contain other than some audio data and some other data. I've simply been tasked with opening them to work on a model to analyze the data within.
SOLVED: Not sure why the previous code doesn't work (it was handed to me), however, I worked around the DataWindow call and went straight to calling the "redvox.api900.reader" object:
from redvox.api900 import reader
dataset_dir = "/home/*****/Documents/Data/F1D1/21/"
rdvx_files = glob(dataset_dir+"*.rdvxz")
for file in rdvx_files:
wrapped_packet = reader.read_rdvxz_file(file)
From here I can view all of the sensor data within:
if wrapped_packet.has_microphone_sensor():
microphone_sensor = wrapped_packet.microphone_sensor()
print("sample_rate_hz", microphone_sensor.sample_rate_hz())
Hope this helps anyone else who's confused.
I have old code below that gzips a file and stores it as json into S3, using the IO library ( so a file does not save locally). I am having trouble converting this same approach (ie using IO library for a buffer) to create a .txt file and push into S3 and later retrieve. I know how to create txt files and push into s3 is as well, but not how to use IO in the process.
The value I would want to be stored in the text value would just be a variable with a string value of 'test'
Goal: Use IO library and save string variable as a text file into S3 and be able to pull it down again.
x = 'test'
inmemory = io.BytesIO()
with gzip.GzipFile(fileobj=inmemory, mode='wb') as fh:
with io.TextIOWrapper(fh, encoding='utf-8',errors='replace') as wrapper:
wrapper.write(json.dumps(x, ensure_ascii=False,indent=2))
inmemory.seek(0)
s3_resource.Object(s3bucket, s3path + '.json.gz').upload_fileobj(inmemory)
inmemory.close()
Also any documentation with that anyone likes with specific respect to the IO library and writing to files, because the actual documentation ( f = io.StringIO("some initial text data")
ect..https://docs.python.org/3/library/io.html ) It just did not give me enough at my current level.
Duplicate.
For sake of brevity, it turns out there's a way to override the putObject call so that it takes in a string of text instead of a file.
The original post is answered in Java, but this additional thread should be sufficient for a Python-specific answer.
In our lab we store our data in hdf5 files trough the python package h5py.
At the beginning of an experiment we create an hdf5 file and store array after array of array of data in the file (among other things). When an experiment fails or is interrupted the file is not correctly closed.
Because our experiments run from iPython the reference to the data object remains (somewhere) in memory.
Is there a way to scan for all open h5py data objects and close them?
This is how it could be done (I could not figure out how to check for closed-ness of the file without exceptions, maybe you will find):
import gc
for obj in gc.get_objects(): # Browse through ALL objects
if isinstance(obj, h5py.File): # Just HDF5 files
try:
obj.close()
except:
pass # Was already closed
Another idea:
Dpending how you use the files, what about using the context manager and the with keyword like this?
with h5py.File("some_path.h5") as f:
f["data1"] = some_data
When the program flow exits the with-block, the file is closed regardless of what happens, including exceptions etc.
pytables (which h5py uses) keeps track of all open files and provides an easy method to force-close all open hdf5 files.
import tables
tables.file._open_files.close_all()
That attribute _open_files also has helpful methods to give you information and handlers for the open files.
I've found that hFile.bool() returns True if open, and False otherwise. This might be the simplest way to check.
In other words, do this:
hFile = h5py.File(path_to_file)
if hFile.__bool__():
hFile.close()
I am trying to change the value of a keyword in the header of a FITS file.
Quite simple, this is the code:
import pyfits
hdulist = pyfits.open('test.fits') # open a FITS file
prihdr = hdulist[1].header
print prihdr['AREASCAL']
effarea = prihdr['AREASCAL']/5.
print effarea
prihdr['AREASCAL'] = effarea
print prihdr['AREASCAL']
I print the steps many times to check the values are correct. And they are.
The problem is that, when I check the FITS file afterwards, the keyword value in the header is not changed. Why does this happen?
You are opening the file in read-only mode. This won't prevent you from modifying any of the in-memory objects, but closing or flushing to the file (as suggested in other answers to this question) won't make any changes to the file. You need to open the file in update mode:
hdul = pyfits.open(filename, mode='update')
Or better yet use the with statement:
with pyfits.open(filename, mode='update') as hdul:
# Make changes to the file...
# The changes will be saved and the underlying file object closed when exiting
# the 'with' block
You need to close the file, or explicitly flush it, in order to write the changes back:
hdulist.close()
or
hdulist.flush()
Interestingly, there's a tutorial for that in the astropy tutorials github. Here is the ipython notebook viewer version of that tutorial that explains it all.
Basically, you are noticing that the python instance does not interact with disk instance. You have to save a new file or overwrite the old one explicitly.