It would be nice, but maybe impossible) if argument names are reasonably consistent between pygetpapers, docanalysis and py4ami. (This is a problem in UNIX tools where there is little consistency
-q is passed to pygetpapers with the same meaning as standalone pygetpapers.
I assumed (wrongly) that -o was the same , but it has a different role (output CSV).
Some parameters imply or depend on others:
-q implies --run_pygetpapers (could the latter be omitted)
can --run_sectioning be run independently ofpygetpapers`. Is it idempotent (i.e. if it's run a second time does it have no effect?
can --section drive --run_sectioning making the latter redundant?
can --make_ami_dict have repeated arguments (dictiomaries)?`
docanalysis
[...]
optional arguments:
-h, --help show this help message and exit
--run_pygetpapers queries EuropePMC via pygetpapers
--run_sectioning make sections
-q QUERY, --query QUERY
query to pygetpapers
--project_name PROJECT_NAME
name of CProject folder
-d DICTIONARY, --dictionary DICTIONARY
Ami Dictionary to tag sentences and support supervised entity extraction
-o OUTPUT, --output OUTPUT
Output CSV file [default=entities.csv]
--make_ami_dict MAKE_AMI_DICT
if provided will make ami dict with given title
-l LOGLEVEL, --loglevel LOGLEVEL
[All] Provide logging level. Example --log warning
<<info,warning,debug,error,critical>>, default='info'
-f LOGFILE, --logfile LOGFILE
[All] save log to specified file in output directory as well as printing to
terminal
--section [SECTION [SECTION ...]]
Which section to get
--entities [ENTITIES [ENTITIES ...]]
Which entities to get. Default(ALL)
--spacy_model SPACY_MODEL
Optional. (spacy, scispacy). Default(spacy)
--html HTML Saves output in html format to given path
It would be nice, but maybe impossible) if argument names are reasonably consistent between
pygetpapers
,docanalysis
andpy4ami
. (This is a problem in UNIX tools where there is little consistency-q
is passed topygetpapers
with the same meaning as standalonepygetpapers
. I assumed (wrongly) that-o
was the same , but it has a different role (output CSV).Some parameters imply or depend on others:
-q
implies--run_pygetpapers
(could the latter be omitted)--run_sectioning be run independently of
pygetpapers`. Is it idempotent (i.e. if it's run a second time does it have no effect?--section
drive--run_sectioning
making the latter redundant?--make_ami_dict
have repeated arguments (dictiomaries)?`