Unverified Commit 7fc1ba06 authored by mvdbeek's avatar mvdbeek
Browse files

Fix conditional dependency path resolution 

The path resolution logic was not correct. A relative path within
galaxy.yml is relative to the config directory. To fix this we now rely
on GalaxyAppConfiguration which does all of the path resolution exactly
as Galaxy would.

I noticed this when I added a file source and the conditional depdency
logic would not attempt to install the correctly defined conditional
dependency. I did have `file_sources_config_file` set in my galaxy
config. This would have only worked if I left that setting undefined and
we correctly joined the path with the config dir or if I had set an
absolute path.
parent 79681d8f

lib/galaxy/dependencies/__init__.py

+10 −13
Original line number Diff line number Diff line
@@ -13,6 +13,7 @@ from os.path import ( 
import yaml

from dparse import parse



from galaxy.config import GalaxyAppConfiguration

from galaxy.util import (

    asbool,

    etree,
@@ -41,6 +42,7 @@ class ConditionalDependencies: 
            self.config = load_app_properties(config_file=self.config_file)

        else:

            self.config = config

        self.config_object = GalaxyAppConfiguration(**self.config)

        self.parse_configs()

        self.get_conditional_requirements()
@@ -58,7 +60,7 @@ class ConditionalDependencies: 
        if "job_config" in self.config:

            load_job_config_dict(self.config.get("job_config"))

        else:

            job_conf_path = self.config.get("job_config_file")

            job_conf_path = self.config_object.job_config_file

            if not job_conf_path:

                job_conf_path = join(dirname(self.config_file), "job_conf.yml")

                if not exists(job_conf_path):
@@ -85,9 +87,7 @@ class ConditionalDependencies: 
                except OSError:

                    pass



        object_store_conf_path = self.config.get(

            "object_store_config_file", join(dirname(self.config_file), "object_store_conf.xml")

        )

        object_store_conf_path = self.config_object.object_store_config_file

        try:

            if ".xml" in object_store_conf_path:

                for store in parse_xml(object_store_conf_path).iter("object_store"):
@@ -117,7 +117,7 @@ class ConditionalDependencies: 
            pass



        # Parse auth conf

        auth_conf_xml = self.config.get("auth_config_file", join(dirname(self.config_file), "auth_conf.xml"))

        auth_conf_xml = self.config_object.auth_config_file

        try:

            for auth in parse_xml(auth_conf_xml).findall("authenticator"):

                auth_type = auth.find("type")
@@ -128,9 +128,7 @@ class ConditionalDependencies: 


        # Parse oidc_backends_config_file specifically for PKCE support.

        self.pkce_support = False

        oidc_backend_conf_xml = self.config.get(

            "oidc_backends_config_file", join(dirname(self.config_file), "oidc_backends_config.xml")

        )

        oidc_backend_conf_xml = self.config_object.oidc_backends_config_file

        try:

            for pkce_support_element in parse_xml(oidc_backend_conf_xml).iterfind("./provider/pkce_support"):

                if pkce_support_element.text == "true":
@@ -140,7 +138,7 @@ class ConditionalDependencies: 
            pass



        # Parse error report config

        error_report_yml = self.config.get("error_report_file", join(dirname(self.config_file), "error_report.yml"))

        error_report_yml = self.config_object.error_report_file

        try:

            with open(error_report_yml) as f:

                error_reporters = yaml.safe_load(f)
@@ -149,9 +147,8 @@ class ConditionalDependencies: 
            pass



        # Parse file sources config

        file_sources_conf_yml = self.config.get(

            "file_sources_config_file", join(dirname(self.config_file), "file_sources_conf.yml")

        )

        file_sources_conf_yml = self.config_object.file_sources_config_file



        if exists(file_sources_conf_yml):

            with open(file_sources_conf_yml) as f:

                file_sources_conf = yaml.safe_load(f)
@@ -160,7 +157,7 @@ class ConditionalDependencies: 
        self.file_sources = [c.get("type", None) for c in file_sources_conf]



        # Parse vault config

        vault_conf_yml = self.config.get("vault_config_file", join(dirname(self.config_file), "vault_conf.yml"))

        vault_conf_yml = self.config_object.vault_config_file

        if exists(vault_conf_yml):

            with open(vault_conf_yml) as f:

                vault_conf = yaml.safe_load(f)