Reworked interface

[nevrome]

Here's a suggestion for a better interface in accordance to #4.

./sidora.R -h
usage: sidora.cli [--] [--help] [--as_tsv] [--entity_type ENTITY_TYPE]
       [--entity_id ENTITY_ID] [--credentials CREDENTIALS] [--cache_dir
       CACHE_DIR] module

MPI-SHH Pandora DB command line interface test

positional arguments:
  module             One of: summary, list, view, projects, tags

flags:
  -h, --help         show this help message and exit
  -a, --as_tsv       For module: list - Return the list as
                     tab-separated data

optional arguments:
  -t, --entity_type  For module: summary, list, view - One of: project,
                     tag, site, individual
  -i, --entity_id    For module: summary, list, view - Identifier of
                     one or multiple: projects, tags, sites,
                     individuals
  -c, --credentials  path to the credentials file [default:
                     .credentials]
  -d, --cache_dir    path to table cache directory [default:
                     /tmp/sidora.cli_table_cache]

./sidora.R summary -t site -i "..."


|Site_Id |Name          |Country            |Tags                         |Projects    |
|:-------|:-------------|:------------------|:----------------------------|:-----------|
|...|...|...|...|...|
      +--------+---------+----------+---------+----------+----------+---------++
      |                                                                        |
      |                                                                        |
      |                                                                        |
   50 +                                                                        +
L     |                                   +                                    |
a     |                                                                        |
t     |                                                                        |
i     |                                                                        |
t   0 +                                                                        +
u     |                                                                        |
d     |                                                                        |
e     |                                                                        |
  -50 +                                                                        +
      |                                                                        |
      |                                                                        |
      |                                                                        |
      +--------+---------+----------+---------+----------+----------+---------++
              30        35         40        45         50         55        60
                                      Longitude

./sidora.R list -t site -i "...","..."


|Site_Id |Name           |Country            |Tags                         |Projects    |
|:-------|:--------------|:------------------|:----------------------------|:-----------|
|...|...|...|...|...|
|...|...|...|...|...|

./sidora.R view -t site -i "..."


|Site_Id |Name |Country |Tags |Projects |
|:-------|:----|:-------|:----|:--------|
There is no entity with that entity_id. Did you mean one of the following entities?
- ... 
- ...
- ... 
- ... 
- ... 

I think it's neat. Fight me! 😄

[nevrome]

But of course: Everything at an early prototyping stage.

[nevrome]

./sidora.R summary -t site -i "..."


|Site_Id |Name           |Country |Tags          |Projects    |
|:-------|:--------------|:-------|:-------------|:-----------|
|...|...|...|...|...|

             . .   ...  ...........                   .       ...
.  ................. .  ..  .....          ......  ..... .......................
     .   ..........    ...               ... ..........................    .
            .............  .            ..X............................
            ............              ..   .. ..... .................
               .......                ..... ..  ...................
                ..   .              ............ ....  ..........
                    .               .............        .    ..   .
                       .....             ..........          ..  .
                      ..........           ......              .      ..
                       ........            ......                    . .
                        .......            .....  .              ........
                        .....               ...                   ........
                        ..
                       ..                              .

                                                   ..     ..............
       .................          ..........................................
................................................................................

I love it.

[stschiff]

Amazing. Love it!!! Just a question about --as_tsv: Shouldn't that be a sub-option for the "list" subcommand (or module?) Or are you currently not working with subcommand-specific options? Perhaps that's making things too complicated, but it would be somewhat more logical to have command-specific options, in my view. Just thinking loud.

[stschiff]

I'm not following every bit here. I'd like to review more carefully the command line option interface at some point, but I don't see myself doing that anytime soon, so I suggest we move on and I check it out, or discuss with you, at some later timepoints.

[nevrome]

argparser does not support real subcommands. I did not use r-argparse, because it has some extra Python dependencies. So sub-options are not a thing here. I think that's not really a problem: Unused options are just ignored with the current setup.

I think I will merge this now and I have two additional things on my mind:

1. I'm still not sure if this should just be an R package. All the view_, list_ and summary_* modules should probably be functions of a package. A package that is not supposed to be used in R, but only with a command line script that we could put into the inst directory.
2. I suggest we use the next hackhour session to fill some of these modules with life. This is a task that can easily be split up and in an hour we can already have a very satisfying cli tool with some minimal views for all sorts of Pandora entities. I think Thiseas already started to work on the summary_sites thing last friday.

[TCLamnidis]

Out of curiosity, how does the map react if you place a point in an area that does not get drawn by default (e.g. New Zealand)? Is that point added, or do you currently simply replace . with X?

[nevrome]

Ah - a classic. I'm confident from the implementation that all and every sample point will be plotted no matter if it is on land or not. The code just splits the word into a grid and checks if there is a (or multiple) sample in a particular cell. If so, then we get an X.