Commit 738b477a authored by Sveinung Gundersen's avatar Sveinung Gundersen Committed by Cage, Gregory
Browse files

Merge 'Fixed linting, import sorting and unrelated mypy error (due to... 

Merge 'Fixed linting, import sorting and unrelated mypy error (due to deprecated method)' into branch
parent 5a71488b

lib/galaxy/model/__init__.py

+1 −0
Original line number Diff line number Diff line
@@ -146,6 +146,7 @@ from galaxy.security.validate_user_input import validate_password_str 
from galaxy.util import (

    directory_hash_id,

    enum_values,

    hex_to_lowercase_alphanum,

    listify,

    ready_name_for_url,

    unicodify,

lib/galaxy/model/migrations/alembic/versions_gxy/8a19186a6ee7_add_columns_to_interactivetool_entry_point.py

0 → 100644
+41 −0
Original line number Diff line number Diff line 
"""add label, requires_path_in_url and requires_path_in_header_named columns to interactivetool_entry_point



Revision ID: 8a19186a6ee7

Revises: ddbdbc40bdc1

Create Date: 2023-11-15 12:53:32.888292



"""

from sqlalchemy import (

    Boolean,

    Column,

    Text,

)



from galaxy.model.migrations.util import (

    add_column,

    drop_column,

)



# revision identifiers, used by Alembic.

revision = "8a19186a6ee7"

down_revision = "ddbdbc40bdc1"

branch_labels = None

depends_on = None



# database object names used in this revision

table_name = "interactivetool_entry_point"

label_column_name = "label"

requires_path_in_url_colname = "requires_path_in_url"

requires_path_in_header_named_colname = "requires_path_in_header_named"





def upgrade():

    add_column(table_name, Column(label_column_name, Text()))

    add_column(table_name, Column(requires_path_in_url_colname, Boolean(), default=False))

    add_column(table_name, Column(requires_path_in_header_named_colname, Text()))





def downgrade():

    drop_column(table_name, requires_path_in_header_named_colname)

    drop_column(table_name, requires_path_in_url_colname)

    drop_column(table_name, label_column_name)

lib/galaxy/security/idencoding.py

+17 −0
Original line number Diff line number Diff line
@@ -11,6 +11,8 @@ from Crypto.Random import get_random_bytes 


import galaxy.exceptions

from galaxy.util import (

    hex_to_lowercase_alphanum,

    lowercase_alphanum_to_hex,

    smart_str,

    unicodify,

)
@@ -146,3 +148,18 @@ def _last_bits(secret): 
    if len(last_bits) > MAXIMUM_ID_SECRET_LENGTH:

        last_bits = last_bits[-MAXIMUM_ID_SECRET_LENGTH:]

    return last_bits





class IdAsLowercaseAlphanumEncodingHelper:

    """

    Helper class to encode IDs as lowercase alphanumeric strings, and vice versa

    """



    def __init__(self, security: IdEncodingHelper):

        self.security = security



    def encode_id(self, id: int) -> str:

        return hex_to_lowercase_alphanum(self.security.encode_id(id))



    def decode_id(self, id: str) -> int:

        return self.security.decode_id(lowercase_alphanum_to_hex(id).rjust(16, "0"))

lib/galaxy/util/__init__.py

+22 −2
Original line number Diff line number Diff line
@@ -538,7 +538,7 @@ def pretty_print_time_interval(time=False, precise=False, utc=False): 
        now = datetime.utcnow()

    else:

        now = datetime.now()

    if type(time) is int:

    if isinstance(time, (int, float)):

        diff = now - datetime.fromtimestamp(time)

    elif isinstance(time, datetime):

        diff = now - time
@@ -979,7 +979,7 @@ def parse_resource_parameters(resource_param_file): 
        resource_definitions_root = resource_definitions.getroot()

        for parameter_elem in resource_definitions_root.findall("param"):

            name = parameter_elem.get("name")

            resource_parameters[name] = parameter_elem

            resource_parameters[name] = etree.tostring(parameter_elem)



    return resource_parameters
@@ -1882,3 +1882,23 @@ def enum_values(enum_class): 
    Values are in member definition order.

    """

    return [value.value for value in enum_class.__members__.values()]





def hex_to_lowercase_alphanum(hex_string: str) -> str:

    """

    Convert a hexadecimal string encoding into a lowercase 36-base alphanumeric string using the

    characters a-z and 0-9

    """

    import numpy as np



    return np.base_repr(int(hex_string, 16), 36).lower()





def lowercase_alphanum_to_hex(lowercase_alphanum: str) -> str:

    """

    Convert a lowercase 36-base alphanumeric string encoding using the characters a-z and 0-9 to a

    hexadecimal string

    """

    import numpy as np



    return np.base_repr(int(lowercase_alphanum, 36), 16).lower()