Discussion on: Automatic Reporting in Python - Part 3: Packaging It Up

[goyder]

Howdy! Glad you've found it useful.

If you could provide a full dump of the error code, I can better take a guess at the issue.

However, looking through the code, I now realise it assumes that an outputs folder is available in the folder. You could either:

• Manually create an outputs folder (not a thorough fix)
• Modify the code to check if the target folder exists, and create it if it doesn't, before writing to it.

[Leif-Erik]

Yeah it is really useful. I am a python noob, so it was like jumping out to swim in the deep end. But I have learned a lot by just playing around with it, trying to find out what everything does. Are you planning on doing a guide on how to include images/figures in a html report?

Below is the error I get.

Success When I have the files in the same folder as the script

PS C:\Users\lpe061\Dropbox\Python\Automatic Reporting> python Autoreport.py LAS318_results.csv LAS319_results.csv LAS320_results.csv
Successfully wrote "report.html" to folder "outputs".

When the files are in the "datasets" folder

PS C:\Users\lpe061\Dropbox\Python\Automatic Reporting> python Autoreport.py LAS318_results.csv LAS319_results.csv LAS320_results.csv
Traceback (most recent call last):
File "Autoreport.py", line 239, in
main()
File "Autoreport.py", line 202, in main
SampleResults(sample_name, results_filepath))
File "Autoreport.py", line 29, in init
self.df_results = csv_to_df(filepath) # Filesystem access
File "Autoreport.py", line 167, in csv_to_df
df = pd.read_csv(filepath, index_col=0)
File "C:\Users\lpe061\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\io\parsers.py", line 678, in parser_f
return read(filepath_or_buffer, kwds)
File "C:\Users\lpe061\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\io\parsers.py", line 440, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "C:\Users\lpe061\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\io\parsers.py", line 787, in __init_
self.make_engine(self.engine)
File "C:\Users\lpe061\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\io\parsers.py", line 1014, in _make_engine
self._engine = CParserWrapper(self.f, **self.options)
File "C:\Users\lpe061\AppData\Local\Continuum\anaconda3\lib\site-packages\pandas\io\parsers.py", line 1708, in __init_
self.reader = parsers.TextReader(src, **kwds)
File "pandas_libs\parsers.pyx", line 384, in pandas._libs.parsers.TextReader.cinit_
File "pandas_libs\parsers.pyx", line 695, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: File b'LAS318_results.csv' does not exist
PS C:\Users\lpe061\Dropbox\Python\Automatic Reporting>

[goyder]

Hey Leif,

Thanks for the comparison of functional/non-functional calls - gives me a lot more context on where the issue might be.

You'll need to provide a relative path to the datasets (relative to the script) to get it to run if you have have your datasets under the folder - i.e. run python Autoreport.py datasets/LAS318_results.csv datasets/LAS319_results.csv datasets/LAS320_results.csv. In its current form, the script won't search any subfolders.

(It's curious to me that the FileNotFoundError is returning a byte string, indicated the b in front of the filepath... that makes me raise an eyebrow.)

I hadn't planned on adding any additional examples around how to publish images in the reports, but in previous projects I've added similar features. The key questions that I worked through were:

• How do I present the images in the report? Do I present them all, just provide links, or have some kind of interactive tool?
• Where do I store the images for access? Do I keep a local copy of all the images (and if so, how do I manage moving the report around)? Should I push all the images to be hosted somewhere else - or even inside the .html file somehow?

These questions are a little outside of Python and more into web dev, which I am definitely not an expert in. They're all very interesting options to explore, however.