[hail] teach tables how to HTML #5666
Conversation
hail/build.gradle
Outdated
| @@ -279,7 +279,7 @@ task testPython(type: Exec, dependsOn: shadowJar) { | |||
| '--color=no', | |||
| '-r a', | |||
| '--html=build/reports/pytest.html', | |||
| '--self-contained-html', | |||
| '--self-contained-html', '-vv', '--maxfail=1', | |||
hail/python/hail/table.py
Outdated
| t = t.flatten() | ||
| fields = list(t.row) | ||
|
|
||
| formatted_t = t.select(**{k: hl_format(v) for (k, v) in t.row.items()}) |
There was a problem hiding this comment.
This won't work - it'll try to call hl_format on expressions. hl_format needs to be called on strings after the take localizes them to python
There was a problem hiding this comment.
This isn't hl.format, its hl_format, which is defined above to escape after calling Table._hl_repr. This is basically the same code as what show previously did except I removed truncation and added cgi.escape.
There was a problem hiding this comment.
wait, but isn't this calling cgi.escape inside of a TableMapRows (select) above? How does that work?
There was a problem hiding this comment.
lmao nice: https://github.com/python/cpython/blob/3.5/Lib/html/__init__.py#L12
replace just works.
There was a problem hiding this comment.
import html
print(html.escape(hl.str("tlocus<GRCh37>"))._ir)(Apply replace (Apply replace (Apply replace (Apply replace (Apply replace (Str "tlocus<GRCh37>") (Str "&") (Str "&")) (Str "<") (Str "<")) (Str ">") (Str ">")) (Str "\"") (Str """)) (Str "'") (Str "'"))
There was a problem hiding this comment.
I don't really like this -- I think there's nothing that prevents the cgi or html implementation from changing and breaking this, and Hail string manipulation is also extremely slow right now.
Can we just call hl_format on each string coming out in line 1367?
hail/python/hail/table.py
Outdated
|
|
||
| if has_more: | ||
| n_rows = len(rows) | ||
| s += f"<p>showing top { n_rows } { 'row' if n_rows == 1 else 'rows' }</p>\n" |
There was a problem hiding this comment.
we have a plural utility function in hail.utils.misc
| handler(self._show(n, width, truncate, types)) | ||
| if n is None or width is None: | ||
| import shutil | ||
| (columns, lines) = shutil.get_terminal_size((80, 10)) |
|
e.g. Jupyter. Looks like Jupyter also supports terminal size, and it chooses 40 in this case, which means Jupyter told us 50 lines, which seems a bit much. In reality you can fit about 35 HTML table lines in that browser window including the Jupiter header (which eats about 5 lines).
|
|
IPython |
|
doctest failure from show() changing the width, it seems |
hail/python/hail/table.py
Outdated
| s = "{" + hl.delimit(hl.map(lambda x: Table._hl_repr(x[0]) + ":" + Table._hl_repr(x[1]), hl.array(v)), ",") + "}" | ||
| elif v.dtype == hl.tstr: | ||
| s = hl.str('"') + hl.expr.functions._escape_string(v) + '"' | ||
| elif isinstance(v.dtype, (hl.tstruct, hl.tarray)): |
There was a problem hiding this comment.
you didn't change this code, but this should be ttuple not tarray
hail/python/hail/table.py
Outdated
| elif v.dtype == hl.tstr: | ||
| s = hl.str('"') + hl.expr.functions._escape_string(v) + '"' | ||
| elif isinstance(v.dtype, (hl.tstruct, hl.ttuple)): | ||
| s = "(" + hl.delimit([Table._hl_repr(v[i]) for i in range(len(v))], ",") + ")" |
There was a problem hiding this comment.
needs to check for empty array - that can't be type-imputed
There was a problem hiding this comment.
(this is your test failure)
Take a look at the docs for
IPython.display.display.I preserve the user's ability to specify a custom handler. The handler is no longer given a string but an object that has a sensible
__str__and__repr__. Moreover, this object has a_repr_html_which Jupyter uses to display an HTML table. Detecting what frontend is being run is done byIPython.display.display.I use the
_Showshim class to avoid having tables themselves print as HTML.I also check for terminal size and use that to pick
nandwidth.Should
_hl_reprlive here?Resolves #5663, #2847