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Merge pull request #7018 from qiagu/join1

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Add datatype sniff button to edit dataset attributes page
This commit is contained in:
Martin Cech
2018-11-30 16:55:52 -05:00
committed by GitHub
parent 8c8fc364e1 4ff3c95e38
commit 030cf02fc8
2 changed files with 28 additions and 0 deletions
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client/galaxy/scripts/mvc/dataset/dataset-edit-attributes.js
+8
View File
@@ -179,6 +179,14 @@ var View = Backbone.View.extend({
onclick: function() {
self._submit("datatype", form);
}
}),
submit_datatype_detect: new Ui.Button({
tooltip: _l("Detect the datatype and change it."),
title: _l("Detect datatype"),
icon: "fa-undo",
onclick: function() {
self._submit("datatype_detect", form);
}
})
}
});
lib/galaxy/webapps/galaxy/controllers/dataset.py
+20
View File
@@ -17,6 +17,7 @@ from galaxy import (
util,
web
)
from galaxy.datatypes import sniff
from galaxy.datatypes.display_applications.util import decode_dataset_user, encode_dataset_user
from galaxy.exceptions import RequestParameterInvalidException
from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings
@@ -25,6 +26,7 @@ from galaxy.util import (
sanitize_text,
smart_str
)
from galaxy.util.checkers import check_binary
from galaxy.util.sanitize_html import sanitize_html
from galaxy.web import form_builder
from galaxy.web.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesExtendedMetadataMixin
@@ -459,6 +461,24 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE
message = 'Changed the type to %s.' % datatype
else:
return self.message_exception(trans, 'You are unable to change datatypes in this manner. Changing %s to %s is not allowed.' % (data.extension, datatype))
elif operation == 'datatype_detect':
# The user clicked the 'Detect datatype' button on the 'Change data type' form
if data.datatype.allow_datatype_change:
# prevent modifying datatype when dataset is queued or running as input/output
if not __ok_to_edit_metadata(data.id):
return self.message_exception(trans, 'This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them.')
else:
path = data.dataset.file_name
is_binary = check_binary(path)
datatype = sniff.guess_ext(path, trans.app.datatypes_registry.sniff_order, is_binary=is_binary)
trans.app.datatypes_registry.change_datatype(data, datatype)
trans.sa_session.flush()
trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute(
trans.app.datatypes_registry.set_external_metadata_tool, trans, incoming={'input1': data},
overwrite=False) # overwrite is False as per existing behavior
message = 'Detection was finished and changed the datatype to %s.' % datatype
else:
return self.message_exception(trans, 'Changing datatype "%s" is not allowed.' % (data.extension))
elif operation == 'autodetect':
# The user clicked the Auto-detect button on the 'Edit Attributes' form
# prevent modifying metadata when dataset is queued or running as input/output