Commit 566a87d0 authored by Matthias Bernt's avatar Matthias Bernt
Browse files

fix type annotations for assertions 

the functions always get a str (from the xml attributes)
parent a15fd1fc

lib/galaxy/tool_util/verify/asserts/_util.py

+29 −4
Original line number Diff line number Diff line 
from math import inf

from typing import (

    Any,

    Callable,

    Optional

)



from galaxy.util import asbool

from galaxy.util.bytesize import parse_bytesize





def _assert_number(count, n, delta, min, max, negate, n_text, min_max_text):

def _assert_number(

    count,

    n: Optional[str],

    delta: str,

    min: Optional[str],

    max: Optional[str],

    negate: str,

    n_text,

    min_max_text

):

    """

    helper function for assering that count is in

    - [n-delta:n+delta]
@@ -26,12 +40,12 @@ def _assert_number(count, n, delta, min, max, negate, n_text, min_max_text): 
        )

    if min is not None or max is not None:

        if min is None:

            min = -inf  # also replacing min/max for output

            min = "-inf"  # also replacing min/max for output

            min_bytes = -inf

        else:

            min_bytes = parse_bytesize(min)

        if max is None:

            max = inf

            max = "inf"

            max_bytes = inf

        else:

            max_bytes = parse_bytesize(max)
@@ -42,7 +56,18 @@ def _assert_number(count, n, delta, min, max, negate, n_text, min_max_text): 




def _assert_presence_number(

    output, text, n, delta, min, max, negate, check_presence_foo, count_foo, presence_text, n_text, min_max_text

    output,

    text,

    n: Optional[str],

    delta: str,

    min: Optional[str],

    max: Optional[str],

    negate: str,

    check_presence_foo: Callable[[Any, Any], bool],

    count_foo: Callable[[Any, Any], int],

    presence_text: str,

    n_text: str,

    min_max_text: str

):

    """

    helper function to assert that

lib/galaxy/tool_util/verify/asserts/archive.py

+6 −6
Original line number Diff line number Diff line
@@ -55,12 +55,12 @@ def assert_has_archive_member( 
    path,

    verify_assertions_function,

    children,

    all="false",

    n: Optional[int] = None,

    delta: int = 0,

    min: Optional[int] = None,

    max: Optional[int] = None,

    negate: bool = False,

    all="False",

    n: Optional[str] = None,

    delta: str = "0",

    min: Optional[str] = None,

    max: Optional[str] = None,

    negate: str = "False",

):

    """Recursively checks the specified children assertions against the text of

    the first element matching the specified path found within the archive.

lib/galaxy/tool_util/verify/asserts/size.py

+5 −5
Original line number Diff line number Diff line
@@ -5,11 +5,11 @@ from ._util import _assert_number 


def assert_has_size(

    output_bytes,

    value: Optional[int] = None,

    delta: int = 0,

    min: Optional[int] = None,

    max: Optional[int] = None,

    negate: bool = False,

    value: Optional[str] = None,

    delta: str = "0",

    min: Optional[str] = None,

    max: Optional[str] = None,

    negate: str = "False",

):

    """

    Asserts the specified output has a size of the specified value,

lib/galaxy/tool_util/verify/asserts/tabular.py

+5 −5
Original line number Diff line number Diff line
@@ -20,13 +20,13 @@ def get_first_line(output, comment): 


def assert_has_n_columns(

    output,

    n: Optional[int] = None,

    delta: int = 0,

    min: Optional[int] = None,

    max: Optional[int] = None,

    n: Optional[str] = None,

    delta: str = "0",

    min: Optional[str] = None,

    max: Optional[str] = None,

    sep="\t",

    comment="",

    negate: bool = False,

    negate: str = "False",

):

    """Asserts the tabular output contains n columns. The optional

    sep argument specifies the column seperator used to determine the

lib/galaxy/tool_util/verify/asserts/text.py

+25 −25
Original line number Diff line number Diff line
@@ -10,11 +10,11 @@ from ._util import ( 
def assert_has_text(

    output,

    text,

    n: Optional[int] = None,

    delta: int = 0,

    min: Optional[int] = None,

    max: Optional[int] = None,

    negate: bool = False,

    n: Optional[str] = None,

    delta: str = "0",

    min: Optional[str] = None,

    max: Optional[str] = None,

    negate: str = "False",

):

    """Asserts specified output contains the substring specified by

    the argument text. The exact number of occurrences can be
@@ -46,11 +46,11 @@ def assert_not_has_text(output, text): 
def assert_has_line(

    output,

    line,

    n: Optional[int] = None,

    delta: int = 0,

    min: Optional[int] = None,

    max: Optional[int] = None,

    negate: bool = False,

    n: Optional[str] = None,

    delta: str = "0",

    min: Optional[str] = None,

    max: Optional[str] = None,

    negate: str = "False",

):

    """Asserts the specified output contains the line specified by the

    argument line. The exact number of occurrences can be optionally
@@ -74,11 +74,11 @@ def assert_has_line( 


def assert_has_n_lines(

    output,

    n: Optional[int] = None,

    delta: int = 0,

    min: Optional[int] = None,

    max: Optional[int] = None,

    negate: bool = False,

    n: Optional[str] = None,

    delta: str = "0",

    min: Optional[str] = None,

    max: Optional[str] = None,

    negate: str = "False",

):

    """Asserts the specified output contains ``n`` lines allowing

    for a difference in the number of lines (delta)
@@ -100,11 +100,11 @@ def assert_has_n_lines( 
def assert_has_text_matching(

    output,

    expression,

    n: Optional[int] = None,

    delta: int = 0,

    min: Optional[int] = None,

    max: Optional[int] = None,

    negate: bool = False,

    n: Optional[str] = None,

    delta: str = "0",

    min: Optional[str] = None,

    max: Optional[str] = None,

    negate: str = "False",

):

    """Asserts the specified output contains text matching the

    regular expression specified by the argument expression.
@@ -130,11 +130,11 @@ def assert_has_text_matching( 
def assert_has_line_matching(

    output,

    expression,

    n: Optional[int] = None,

    delta: int = 0,

    min: Optional[int] = None,

    max: Optional[int] = None,

    negate: bool = False,

    n: Optional[str] = None,

    delta: str = "0",

    min: Optional[str] = None,

    max: Optional[str] = None,

    negate: str = "False",

):

    """Asserts the specified output contains a line matching the

    regular expression specified by the argument expression. If n is given