`--restart` fails - Githubissues

ShweataNHegde commented 3 years ago

Describe the bug From what I understand, --restart works just like how --updatenow works. We would have to specify the output directory (already existing Cproject) and give it --restart. But the error says that --restart flag requires an argument.

To Reproduce INPUT:

C:\Users\shweata>pygetpapers -q "invasive plant species" -o lantana_test_5 --restart -c

OUTPUT:

usage: pygetpapers [-h] [--config CONFIG] [-v] [-q QUERY] [-o OUTPUT] [--save_query] [-x] [-p] [-s] [-z] [--references REFERENCES] [-n] [--citations CITATIONS]
                   [-l LOGLEVEL] [-f LOGFILE] [-k LIMIT] [-r RESTART] [-u] [--onlyquery] [-c] [--makehtml] [--synonym] [--startdate STARTDATE] [--enddate ENDDATE]
                   [--terms TERMS] [--api API] [--filter FILTER]
pygetpapers: error: argument -r/--restart: expected one argument

petermr commented 3 years ago

I think we need to outline what we want these functions to do. And what information the CProject holds. It should maintain state as much as possible e.g.

pygetpapers -o ebola -q ebola -k 1000 -x should remember:

the query
the cursor
final state (or if interrupted, the completed downloads)

I can think of:

restart after a crash or deliberate break (this is what I assume 'restart" means). The value of this is that in a long download on a slow line you might want to break the download and pick up from where you left off
```
pygetpapers -o foo -q pandemic -k 1000 -x
<break after 300>
pygetpapers -o foo --restart
("foo/eupmc_results.json" should contain the cursor??
```
expand additional information by types, e.g. add -p to a completed xml download
```
pygetpapers -o foo -q pandemic -k 100 -x
<terminates OK>
pygetpapers -o foo --expand -p
```
(where expand is the required new command - I don't think "update" is right. And do we even need it?)
update in case the repo has more data
```
pygetpapers -o ebola -q ebola -k 1000 -x --start-date 2021-01-01
<wait a few months>
pygetpapers -o ebola --update
```
(not even sure we need update).
```
pygetpapers -o ebola
```
should be able to work out what it can do, and what it needs to do.

I think we need a Wikipage about this.

On Fri, Aug 6, 2021 at 6:01 PM ShweataNHegde @.***> wrote:

Describe the bug From what I understand, --restart works just like how --update now works. We would have to specify the output directory (already existing Cproject) and give it --restart. But the error says that --restart` flag requires an argument.

To Reproduce INPUT:

C:\Users\shweata>pygetpapers -q "invasive plant species" -o lantana_test_5 --restart -c

OUTPUT:

usage: pygetpapers [-h] [--config CONFIG] [-v] [-q QUERY] [-o OUTPUT] [--save_query] [-x] [-p] [-s] [-z] [--references REFERENCES] [-n] [--citations CITATIONS] [-l LOGLEVEL] [-f LOGFILE] [-k LIMIT] [-r RESTART] [-u] [--onlyquery] [-c] [--makehtml] [--synonym] [--startdate STARTDATE] [--enddate ENDDATE] [--terms TERMS] [--api API] [--filter FILTER] pygetpapers: error: argument -r/--restart: expected one argument

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ShweataNHegde commented 3 years ago

@ayush4921,

I'm now running on version:

 C:\Users\shweata>pygetpapers -v
INFO: You are running pygetpapers version 0.0.8.7

I tried reproducing the same query as earlier, here's the error I get:

C:\Users\shweata>pygetpapers -q "invasive plant species" -o lantana_test_5 --restart -c
Traceback (most recent call last):
  File "c:\users\shweata\appdata\local\programs\python\python38\lib\runpy.py", line 194, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "c:\users\shweata\appdata\local\programs\python\python38\lib\runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "C:\Users\shweata\AppData\Local\Programs\Python\Python38\Scripts\pygetpapers.exe\__main__.py", line 7, in <module>
  File "c:\users\shweata\appdata\local\programs\python\python38\lib\site-packages\pygetpapers\pygetpapers.py", line 604, in main
    callpygetpapers.handlecli()
  File "c:\users\shweata\appdata\local\programs\python\python38\lib\site-packages\pygetpapers\pygetpapers.py", line 568, in handlecli
    self.handle_restart(args)
  File "c:\users\shweata\appdata\local\programs\python\python38\lib\site-packages\pygetpapers\pygetpapers.py", line 235, in handle_restart
    self.europe_pmc.eupmc_restart(args, restart_file_path)
TypeError: eupmc_restart() takes 2 positional arguments but 3 were given

What am I getting wrong?

ayush4921 commented 3 years ago

This issue has been fixed

petermr / pygetpapers

`--restart` fails #27