Commit 3167b913 authored by John Davis's avatar John Davis
Browse files

Handle missing import

parent a6f3d74f

lib/galaxy/datatypes/isa.py

+20 −7
Original line number Diff line number Diff line
@@ -17,12 +17,22 @@ from typing import ( 
    TYPE_CHECKING,

)



logger = logging.getLogger(__name__)



ISA_MISSING_MODULE_MESSAGE = "Please install the missing isatools dependency from `isa-rwval @ git+https://github.com/nsoranzo/isa-rwval.git@master`"



try:

    # Imports isatab after turning off warnings inside logger settings to avoid pandas warning making uploads fail.

    logging.getLogger("isatools.isatab").setLevel(logging.ERROR)

    from isatools import (

        isajson,

        isatab_meta,

    )

except ImportError:

    isajson = None

    isatab_meta = None

    logger.exception(ISA_MISSING_MODULE_MESSAGE)



from markupsafe import escape



from galaxy import util
@@ -55,7 +65,6 @@ _MAX_LINES_HISTORY_PEEK = 11 
# Configure logger {{{1

################################################################



logger = logging.getLogger(__name__)



# Function for opening correctly a CSV file for csv.reader() for both Python 2 and 3 {{{1

################################################################
@@ -346,6 +355,8 @@ class IsaTab(_Isa): 
    ################################################################



    def _make_investigation_instance(self, filename: str) -> "Investigation":

        if not isatab_meta:

            return

        # Parse ISA-Tab investigation file

        parser = isatab_meta.InvestigationParser()

        isa_dir = os.path.dirname(filename)
@@ -379,6 +390,8 @@ class IsaJson(_Isa): 
    ################################################################



    def _make_investigation_instance(self, filename: str) -> "Investigation":

        if not isajson:

            return

        # Parse JSON file

        with open(filename, newline="", encoding="utf8") as fp:

            isa = isajson.load(fp)