Infrastructure for writing to pluggable Galaxy file sources.

client/src/components/FilesDialog/FilesDialog.vue

@@ -60,6 +60,10 @@ export default {
             default: "file",
             validator: (prop) => ["file", "directory"].includes(prop),
         },
+        requireWritable: {
+            type: Boolean,
+            default: false,
+        },
     },
     data() {
         return {
@@ -129,16 +133,19 @@ export default {
                 this.services
                     .getFileSources()
                     .then((items) => {
-                        this.items = items.map((item) => {
-                            return {
-                                id: item.id,
-                                label: item.label,
-                                details: item.doc,
-                                isLeaf: false,
-                                url: item.uri_root,
-                                labelTitle: item.uri_root,
-                            };
-                        });
+                        items = items
+                            .filter((item) => !this.requireWritable || item.writable)
+                            .map((item) => {
+                                return {
+                                    id: item.id,
+                                    label: item.label,
+                                    details: item.doc,
+                                    isLeaf: false,
+                                    url: item.uri_root,
+                                    labelTitle: item.uri_root,
+                                };
+                            });
+                        this.items = items;
                         this.formatRows();
                         this.optionsShow = true;
                         this.showTime = false;

client/src/mvc/form/form-parameters.js

@@ -10,6 +10,7 @@ import SelectContent from "mvc/ui/ui-select-content";
 import SelectLibrary from "mvc/ui/ui-select-library";
 import SelectFtp from "mvc/ui/ui-select-ftp";
 import RulesEdit from "mvc/ui/ui-rules-edit";
+import FileSource from "mvc/ui/ui-file-source";
 import ColorPicker from "mvc/ui/ui-color-picker";
 import DataPicker from "mvc/ui/ui-data-picker";
 
@@ -37,6 +38,7 @@ export default Backbone.Model.extend({
         ftpfile: "_fieldFtp",
         upload: "_fieldUpload",
         rules: "_fieldRulesEdit",
+        directory_uri: "_fieldDirectoryUri",
         data_dialog: "_fieldDialog",
     },
 
@@ -238,6 +240,14 @@ export default Backbone.Model.extend({
         });
     },
 
+    _fieldDirectoryUri: function (input_def) {
+        return new FileSource.View({
+            id: `field-${input_def.id}`,
+            onchange: input_def.onchange,
+            target: input_def.target,
+        });
+    },
+
     _fieldRulesEdit: function (input_def) {
         return new RulesEdit.View({
             id: `field-${input_def.id}`,

client/src/mvc/ui/ui-file-source.js

@@ -0,0 +1,100 @@
+import Backbone from "backbone";
+import { filesDialog } from "utils/data";
+import _l from "utils/localization";
+import Ui from "mvc/ui/ui-misc";
+
+var View = Backbone.View.extend({
+    initialize: function (options) {
+        this.model = new Backbone.Model();
+        this.target = options.target;
+        const props = {
+            mode: "directory",
+            requireWritable: true,
+        };
+        // create insert edit button
+        this.browse_button = new Ui.Button({
+            title: _l("Select"),
+            icon: "fa fa-edit",
+            tooltip: _l("Select URI"),
+            onclick: () => {
+                filesDialog((uri) => {
+                    this._handleRemoteFilesUri(uri);
+                }, props);
+            },
+        });
+
+        // add change event. fires on trigger
+        this.on("change", () => {
+            if (options.onchange) {
+                options.onchange(this.value());
+            }
+        });
+
+        // create elements
+        this.setElement(this._template(options));
+        this.$text = this.$(".ui-uri-preview");
+        this.$(".ui-file-select-button").append(this.browse_button.$el);
+        this.listenTo(this.model, "change", this.render, this);
+        this.render();
+    },
+
+    _handleRemoteFilesUri: function (uri) {
+        this._setValue(uri);
+    },
+
+    render: function () {
+        const value = this._value;
+        if (value) {
+            if (value.url !== this.$text.text()) {
+                this.$text.text(value.url);
+            }
+        } else {
+            this.$text.text("select...");
+        }
+    },
+
+    /** Main Template */
+    _template: function (options) {
+        return `
+            <div class="ui-rules-edit clearfix">
+                <span class="ui-uri-preview" />
+                <span class="ui-file-select-button float-left" />
+            </div>
+        `;
+    },
+
+    /** Return/Set current value */
+    value: function (new_value) {
+        if (new_value !== undefined) {
+            this._setValue(new_value);
+        } else {
+            return this._getValue();
+        }
+    },
+
+    /** Update input element options */
+    update: function (input_def) {
+        this.target = input_def.target;
+    },
+
+    /** Returns current value */
+    _getValue: function () {
+        return this._value.url;
+    },
+
+    /** Sets current value */
+    _setValue: function (new_value) {
+        if (new_value) {
+            if (typeof new_value == "string") {
+                new_value = JSON.parse(new_value);
+            }
+            this._value = new_value;
+            this.model.trigger("error", null);
+            this.model.trigger("change");
+        }
+    },
+});
+
+export default {
+    View: View,
+};

client/src/mvc/ui/ui-rules-edit.js

@@ -23,7 +23,7 @@ var View = Backbone.View.extend({
             tooltip: _l("Edit Rules"),
             onclick: () => {
                 if (view.target) {
-                    view._fetcCollectionAndEdit();
+                    view._fetchCollectionAndEdit();
                 } else {
                     view._showRuleEditor(null);
                 }
@@ -55,7 +55,7 @@ var View = Backbone.View.extend({
         this.collapsible_disabled = true;
     },
 
-    _fetcCollectionAndEdit: function () {
+    _fetchCollectionAndEdit: function () {
         const view = this;
         const url = `${getAppRoot()}api/dataset_collections/${view.target.id}?instance_type=history`;
         axios

lib/galaxy/files/__init__.py

@@ -68,7 +68,7 @@ def get_file_source_path(self, uri):
         if "://" not in uri:
             raise exceptions.RequestParameterInvalidException("Invalid uri [%s]" % uri)
         scheme, rest = uri.split("://", 1)
-        if scheme not in self.get_schemas():
+        if scheme not in self.get_schemes():
             raise exceptions.RequestParameterInvalidException("Unsupported URI scheme [%s]" % scheme)
 
         if scheme != "gxfiles":
@@ -107,30 +107,30 @@ def validate_uri_root(self, uri, user_context):
             if not user_ftp_dir or not os.path.exists(user_ftp_dir):
                 raise exceptions.ObjectNotFound('Your FTP directory does not exist, attempting to upload files to it may cause it to be created.')
 
-    def get_file_source(self, id_prefix, schema):
+    def get_file_source(self, id_prefix, scheme):
         for file_source in self._file_sources:
-            # gxfiles uses prefix to find plugin, other schema are assumed to have
+            # gxfiles uses prefix to find plugin, other scheme are assumed to have
             # at most one file_source.
-            if schema != file_source.get_schema():
+            if scheme != file_source.get_scheme():
                 continue
-            prefix_match = schema != "gxfiles" or file_source.get_prefix() == id_prefix
+            prefix_match = scheme != "gxfiles" or file_source.get_prefix() == id_prefix
             if prefix_match:
                 return file_source
 
     def looks_like_uri(self, path_or_uri):
         # is this string a URI this object understands how to realize
         if path_or_uri.startswith("gx") and "://" in path_or_uri:
-            for scheme in self.get_schemas():
+            for scheme in self.get_schemes():
                 if path_or_uri.startswith("%s://" % scheme):
                     return True
 
         return False
 
-    def get_schemas(self):
-        schemas = set()
+    def get_schemes(self):
+        schemes = set()
         for file_source in self._file_sources:
-            schemas.add(file_source.get_schema())
-        return schemas
+            schemes.add(file_source.get_scheme())
+        return schemes
 
     def plugins_to_dict(self, for_serialization=False, user_context=None):
         rval = []

lib/galaxy/files/sources/__init__.py

@@ -6,20 +6,27 @@
 
 from galaxy.util.template import fill_template
 
+DEFAULT_SCHEME = "gxfiles"
+DEFAULT_WRITABLE = False
+
 
 @six.add_metaclass(abc.ABCMeta)
 class FilesSource(object):
     """
     """
 
-    @abc.abstractproperty
+    @abc.abstractmethod
     def get_uri_root(self):
         """Return a prefix for the root (e.g. gxfiles://prefix/)."""
 
-    @abc.abstractproperty
-    def get_schema(self):
+    @abc.abstractmethod
+    def get_scheme(self):
         """Return a prefix for the root (e.g. the gxfiles in gxfiles://prefix/path)."""
 
+    @abc.abstractmethod
+    def get_writable(self):
+        """Return a boolean indicating if this target is writable."""
+
     # TODO: off-by-default
     @abc.abstractmethod
     def list(self, source_path="/", recursive=False, user_context=None):
@@ -29,6 +36,10 @@ def list(self, source_path="/", recursive=False, user_context=None):
     def realize_to(self, source_path, native_path, user_context=None):
         """Realize source path (relative to uri root) to local file system path."""
 
+    def write_from(self, target_path, native_path, user_context=None):
+        """Write file at native path to target_path (relative to uri root).
+        """
+
     @abc.abstractmethod
     def to_dict(self, for_serialization=False, user_context=None):
         """Return a dictified representation of this FileSource instance.
@@ -43,13 +54,16 @@ class BaseFilesSource(FilesSource):
     def get_prefix(self):
         return self.id
 
-    def get_schema(self):
+    def get_scheme(self):
         return "gxfiles"
 
+    def get_writable(self):
+        return self.writable
+
     def get_uri_root(self):
         prefix = self.get_prefix()
-        schema = self.get_schema()
-        root = "%s://" % schema
+        scheme = self.get_scheme()
+        root = "%s://" % scheme
         if prefix:
             root = uri_join(root, prefix)
         return root
@@ -63,7 +77,8 @@ def _parse_common_config_opts(self, kwd):
         self.id = kwd.pop("id")
         self.label = kwd.pop("label", None) or self.id
         self.doc = kwd.pop("doc", None)
-        self.schema = kwd.pop("schema", "gxfiles")
+        self.scheme = kwd.pop("scheme", DEFAULT_SCHEME)
+        self.writable = kwd.pop("writable", DEFAULT_WRITABLE)
         # If coming from to_dict, strip API helper values
         kwd.pop("uri_root", None)
         kwd.pop("type", None)
@@ -76,6 +91,7 @@ def to_dict(self, for_serialization=False, user_context=None):
             "uri_root": self.get_uri_root(),
             "label": self.label,
             "doc": self.doc,
+            "writable": self.writable,
         }
         if for_serialization:
             rval.update(self._serialization_props(user_context=user_context))
@@ -96,6 +112,15 @@ def _serialization_props(self):
         Used in to_dict method if for_serialization is True.
         """
 
+    def write_from(self, target_path, native_path, user_context=None):
+        if not self.get_writable():
+            raise Exception("Cannot write to a non-writable file source.")
+        self._write_from(target_path, native_path, user_context=user_context)
+
+    @abc.abstractmethod
+    def _write_from(self, target_path, native_path, user_context=None):
+        pass
+
     def _evaluate_prop(self, prop_val, user_context):
         rval = prop_val
         if isinstance(prop_val, str) and "$" in prop_val:

lib/galaxy/files/sources/_pyfilesystem2.py

@@ -42,6 +42,10 @@ def realize_to(self, source_path, native_path, user_context=None):
         with open(native_path, 'wb') as write_file:
             self._open_fs(user_context=user_context).download(source_path, write_file)
 
+    def _write_from(self, target_path, native_path, user_context=None):
+        with open(native_path, 'rb') as read_file:
+            self._open_fs(user_context=user_context).upload(target_path, read_file)
+
     def _resource_info_to_dict(self, dir_path, resource_info):
         name = resource_info.name
         path = os.path.join(dir_path, name)

lib/galaxy/files/sources/galaxy.py

@@ -12,6 +12,7 @@ def __init__(self, label="FTP Directory", doc="Galaxy User's FTP Directory", roo
             root=root,
             label=label,
             doc=doc,
+            writable=True,
         )
         posix_kwds.update(kwd)
         if "delete_on_realize" not in posix_kwds:
@@ -22,7 +23,7 @@ def __init__(self, label="FTP Directory", doc="Galaxy User's FTP Directory", roo
     def get_prefix(self):
         return None
 
-    def get_schema(self):
+    def get_scheme(self):
         return "gxftp"
 
 
@@ -42,7 +43,7 @@ def __init__(self, label="Library Import Directory", doc="Galaxy's library impor
     def get_prefix(self):
         return None
 
-    def get_schema(self):
+    def get_scheme(self):
         return "gximport"
 
 
@@ -62,7 +63,7 @@ def __init__(self, label="Library User Import Directory", doc="Galaxy's user lib
     def get_prefix(self):
         return None
 
-    def get_schema(self):
+    def get_scheme(self):
         return "gxuserimport"