Mercurial > repos > yating-l > jbrowsearchivecreator
changeset 30:2191bd0798a9 draft
planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty
| author | yating-l |
|---|---|
| date | Fri, 13 Oct 2017 16:19:03 -0400 |
| parents | f5fbe894af85 |
| children | 127037c49bc8 |
| files | apollo/ApolloInstance.py jbrowseArchiveCreator.xml tool_dependencies.xml |
| diffstat | 3 files changed, 8 insertions(+), 4 deletions(-) [+] |
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--- a/apollo/ApolloInstance.py Fri Oct 13 16:00:38 2017 -0400 +++ b/apollo/ApolloInstance.py Fri Oct 13 16:19:03 2017 -0400 @@ -13,9 +13,11 @@ def createApolloUser(self, apollo_user, admin=None): p = subtools.arrow_create_user(apollo_user.user_email, apollo_user.firstname, apollo_user.lastname, apollo_user.password, admin) - user_info = json.loads(p) - user_id = user_info.get('userId') - if not user_id: + print p + if p: + user_info = json.loads(p) + user_id = user_info.get('userId') + if not p or not user_id: self.logger.debug("Cannot create new user: %s; The user may already exist", apollo_user.user_email) user_id = subtools.arrow_get_users(apollo_user.user_email) self.logger.debug("Got user_id for new or existing user: user_id = %s", str(user_id))
--- a/jbrowseArchiveCreator.xml Fri Oct 13 16:00:38 2017 -0400 +++ b/jbrowseArchiveCreator.xml Fri Oct 13 16:19:03 2017 -0400 @@ -34,9 +34,10 @@ ## Ask the user to enter the genome name #silent $data_parameter_dict.update({"genome_name": str($genome_name)}) #silent $data_parameter_dict.update({"apollo_host": str($apollo_host)}) -if $apollo_users_settings.apollo_users_selector == "yes": +#if $apollo_users_settings.apollo_users_selector == "yes": #set apollo_user = {"firstname": str($apollo_users_settings.firstname), "lastname": str($apollo_users_settings.lastname), "password": str($apollo_users_settings.password), "user_email": str($apollo_users_settings.user_email)} $data_parameter_dict.update({"apollo_user": $apollo_user}) +#end if ## Function to retrieve the data of the inputs #def prepare_json($datatype, $input_to_prepare, $order_index, $extra_data_dict={})
--- a/tool_dependencies.xml Fri Oct 13 16:00:38 2017 -0400 +++ b/tool_dependencies.xml Fri Oct 13 16:19:03 2017 -0400 @@ -91,6 +91,7 @@ </action> <action type="set_environment"> <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/apollo</environment_variable> + <environment_variable action="append_to" name="PATH">$INSTALL_DIR/apollo</environment_variable> </action> </actions> </install>