Test report of gui.py - petermr/pygetpapers GitHub Wiki

Tester1: Radhu Ladani

OS: Windows 10

Date: 29th April 2021

Prerequisites

  • git pull the repositories: CEVOpen, dictionary, opendiagram

Open gui.pyfile (\openDiagram\physchem\python\gui.py)

  • Make changes to the gui.py file such that the HOME directs to your home directory. And in most cases, the home directory is your project directory. It should look like this:
        DICTIONARY_HOME = "/Users/DELL/dictionary"
        CEV_DICTIONARY_HOME = "/Users/DELL/CEVOpen/dictionary"
  • Save the changes in the gui.py file.

Run gui.py in my case at path C:\Users\DELL\Radhu\openDiagram\physchem\python on commandline

  • Command Line: C:\Users\DELL\openDiagram\physchem\python>python gui.py
  • After this tk window open with such options including:
    • output dir for output folder where numbers of paper will download
    • create dictboxes for query term selection such as country, ethics, invasive, plant_part, parkinsons
    • output XML, output PDF, output metadata CSV, no download, output SUPP, make sections this different checkbox provide result according user's cretareia.
    • maximum hits(-k) option provide user's to download specific number of papers

tk

Example query

  • Once you select your query it's give following auto generate query on commandline and gives following result:
args ['pygetpapers', '-q', '("Brazil" OR "India" OR "South Africa") AND ("Alliaria petiolata" OR "Lantana camara" OR "Mikania micrantha")', '-o', 'C:\\Users\\DELL\\temp', '-k', '10', '-x', '-c']       
HITS  673\r
CompletedProcess(args=['pygetpapers', '-q', '("Brazil" OR "India" OR "South Africa") AND ("Alliaria petiolata" OR "Lantana camara" OR "Mikania micrantha")', '-o', 'C:\\Users\\DELL\\temp', '-k', '10', '-x', '-c'], returncode=0, stdout=b'', stderr=b'INFO: Total Hits are 673\r
WARNING: Author list not found for paper 3\r
WARNING: Author list not found for paper 5\r
WARNING: Keywords not found for paper 8\r
WARNING: Keywords not found for paper 9\r
INFO: Saving XML files to C:\\Users\\DELL\\temp\\*\\fulltext.xml\r
INFO: */Wrote xml for PMC8042356/\r
INFO: */Wrote xml for PMC7998567/\r
INFO: */Wrote xml for PMC7455955/\r
INFO: */Wrote xml for PMC7359623/\r
INFO: */Wrote xml for PMC7554841/\r
INFO: */Wrote xml for PMC7287757/\r
INFO: */Wrote xml for PMC7760039/\r
INFO: */Wrote xml for PMC7201468/\r
INFO: */Wrote xml for PMC7748911/\r
INFO: */Wrote xml for PMC7676390/\r
')
  • Selection of checkbox into the tk window generate query: ['pygetpapers', '-q', '("Brazil" OR "India" OR "South Africa") AND ("Alliaria petiolata" OR "Lantana camara" OR "Mikania micrantha")', '-o', 'C:\\Users\\DELL\\temp', '-k', '10', '-x', '-c']
  • This query created "temp" in the current directory and in this folder .XML of 10 papers were downloaded with CSV metadata file

Tester2: Kanishka Parashar

OS: Windows 10

Date: 30April 2021

  • Git pull all repositories : CEVOpen, OpenDiagram, Dictionary by commandline commands

Open gui.py file (C:\Users\HP PC\openDiagram\physchem\python\gui.py) in VS code

  • Make changes to the gui.py files such that the HOME directs to your home directory. like-
DICTIONARY_HOME= "/Users/HP PC/dictionary"
CEV_DICTIONARY_HOME= "/Users/HP PC/CEVOpen/dictionary"
  • Save changes in the gui.py file.

Run gui.py in cmd, copy path C:\Users\HP PC\openDiagram\physchem\python and give command C:\Users\HP PC\openDiagram\physchem\python>python gui.py

  • A tk window will appear on screen
  • Screenshot (85)
  • It will include :
  • output dir for output/result where papers will be downloded
  • create dictboxes for query selection as country, ethics, invasive, plant_part, parkinsons
  • output as : XML, PDF, CSV, SUPP, make sections
  • maximum hits (-k) this for the limit or number of papers the person wants to download
  • A query box to write a query

Query Example:

  • After giving command in cmd to run gui.py a tk window will appear on the screen.
  • set the output directory in my case it is C:\Users\HP PC\temp\temp1
  • Select a query from the box, in my case invasie another box will appear on the same tk window showing list of plants, select as per your choice, set the limit (k) in my case it is set to 10
  • mark the section box as per your choice.
  • write query in the query box , essential oils in my case.
  • After this click on run pygetpapers query box
  • you will get results for end search
  • Screenshot (86)
  • Your papers will be downloaded at the given output directory
  • Screenshot (87)

Your cmd will appear like:

C:\Users\HP PC\openDiagram\physchem\python>python gui.py
ROOT .
/Users/HP PC/CEVOpen/dictionary\Invasive_species\invasive_plant.xml
entries 460
HITS  33\r
txt .!frame8.!frame
making sections ['ami', '-p', 'C:\\Users\\HP PC\\temp\\temp1', 'section']
Exception in Tkinter callback
Traceback (most recent call last):
  File "C:\Users\HP PC\AppData\Local\Programs\Python\Python39\lib\tkinter\__init__.py", line 1884, in __call__
    return self.func(*args)
  File "C:\Users\HP PC\openDiagram\physchem\python\gui.py", line 426, in create_query_and_run
    self.create_sections()
  File "C:\Users\HP PC\openDiagram\physchem\python\gui.py", line 434, in create_sections
    stdout_lines, _ = self.run_subprocess_get_lines(args)
  File "C:\Users\HP PC\openDiagram\physchem\python\gui.py", line 389, in run_subprocess_get_lines
    completed_process = subprocess.run(args, capture_output=True)
  File "C:\Users\HP PC\AppData\Local\Programs\Python\Python39\lib\subprocess.py", line 501, in run
    with Popen(*popenargs, **kwargs) as process:
  File "C:\Users\HP PC\AppData\Local\Programs\Python\Python39\lib\subprocess.py", line 947, in __init__
    self._execute_child(args, executable, preexec_fn, close_fds,
  File "C:\Users\HP PC\AppData\Local\Programs\Python\Python39\lib\subprocess.py", line 1416, in _execute_child
    hp, ht, pid, tid = _winapi.CreateProcess(executable, args,
FileNotFoundError: [WinError 2] The system cannot find the file specified