Tmp extra

.gitignore

@@ -188,3 +188,8 @@ involucro
 .DS_Store
 *.rej
 *~
+
+# Syncthing
+.stignore
+.stfolder
+.stversions

client/src/components/Tool/ToolInteractiveClient.vue

@@ -14,6 +14,9 @@
             @onSetError="onSetError"
             @updatePreferredObjectStoreId="onUpdatePreferredObjectStoreId">
             <template v-slot:extra-tool-options-items>
+                <b-dropdown-item @click="openClientTool">
+                    <FontAwesomeIcon icon="fa-table-list" /><span v-localize>Open Client tool form</span>
+                </b-dropdown-item>
                 <b-dropdown-item :disabled="!serviceToolExists" @click="openServiceTool">
                     <FontAwesomeIcon icon="fa-wrench" /><span v-localize>Open Service tool</span>
                 </b-dropdown-item>
@@ -428,6 +431,10 @@ export default {
             }
             return iframeSrc;
         },
+        openClientTool() {
+            // const { data } = await axios.post(this.serviceToolEntryPointTarget, this.clientToolParams);
+            this.$router.push(`/root?tool_id=${this.toolConfig.id}&tool_version=${this.toolConfig.version}`);
+        },
         openServiceTool() {
             this.$router.push(`/root?tool_id=${this.serviceToolId}&tool_version=${this.serviceToolVersion}`);
         },

lib/galaxy/managers/interactivetool.py

@@ -163,7 +163,10 @@ def create_entry_points(self, job, tool, entry_points=None, flush=True):
                 tool_port=entry["port"],
                 entry_url=entry["url"],
                 name=entry["name"],
+                label=entry["label"],
                 requires_domain=entry["requires_domain"],
+                requires_path_in_url=entry["requires_path_in_url"],
+                requires_path_in_header_named=entry["requires_path_in_header_named"],
                 short_token=self.app.config.interactivetools_shorten_url,
             )
             self.sa_session.add(ep)

lib/galaxy/model/__init__.py

@@ -2663,17 +2663,21 @@ class InteractiveToolEntryPoint(Base, Dictifiable, RepresentById):
     protocol = Column(TEXT)
     entry_url = Column(TEXT)
     requires_domain = Column(Boolean, default=True)
+    requires_path_in_url = Column(Boolean, default=False)
+    requires_path_in_header_named = Column(TEXT)
     info = Column(MutableJSONType, nullable=True)
     configured = Column(Boolean, default=False)
     deleted = Column(Boolean, default=False)
     created_time = Column(DateTime, default=now)
     modified_time = Column(DateTime, default=now, onupdate=now)
+    label = Column(TEXT)
     job = relationship("Job", back_populates="interactivetool_entry_points", uselist=False)
 
     dict_collection_visible_keys = [
         "id",
         "job_id",
         "name",
+        "label",
         "active",
         "created_time",
         "modified_time",
@@ -2683,15 +2687,25 @@ class InteractiveToolEntryPoint(Base, Dictifiable, RepresentById):
         "id",
         "job_id",
         "name",
+        "label",
         "active",
         "created_time",
         "modified_time",
         "output_datasets_ids",
     ]
 
-    def __init__(self, requires_domain=True, configured=False, deleted=False, short_token=False, **kwd):
+    def __init__(
+        self,
+        requires_domain=True,
+        requires_path_in_url=False,
+        configured=False,
+        deleted=False,
+        short_token=False,
+        **kwd,
+    ):
         super().__init__(**kwd)
         self.requires_domain = requires_domain
+        self.requires_path_in_url = requires_path_in_url
         self.configured = configured
         self.deleted = deleted
         if short_token:

lib/galaxy/model/migrations/alembic/versions_gxy/8a19186a6ee7_add_columns_to_interactivetool_entry_point.py

@@ -0,0 +1,37 @@
+"""add label, requires_path_in_url and requires_path_in_header_named columns to interactivetool_entry_point
+
+Revision ID: 8a19186a6ee7
+Revises: 92fb564c7095
+Create Date: 2023-10-15 22:09:32.888292
+
+"""
+from sqlalchemy import Column, Text, Boolean
+
+from galaxy.model.migrations.util import (
+    add_column,
+    drop_column,
+)
+
+# revision identifiers, used by Alembic.
+revision = "8a19186a6ee7"
+down_revision = "92fb564c7095"
+branch_labels = None
+depends_on = None
+
+# database object names used in this revision
+table_name = "interactivetool_entry_point"
+label_column_name = "label"
+requires_path_in_url_colname = "requires_path_in_url"
+requires_path_in_header_named_colname = "requires_path_in_header_named"
+
+
+def upgrade():
+    add_column(table_name, Column(label_column_name, Text()))
+    add_column(table_name, Column(requires_path_in_url_colname, Boolean(), default=False))
+    add_column(table_name, Column(requires_path_in_header_named_colname, Text()))
+
+
+def downgrade():
+    drop_column(table_name, requires_path_in_header_named_colname)
+    drop_column(table_name, requires_path_in_url_colname)
+    drop_column(table_name, label_column_name)

lib/galaxy/tool_util/parser/xml.py

@@ -303,8 +303,25 @@ def parse_interactivetool(self):
             name = ep_el.get("name", None)
             if name:
                 name = name.strip()
+            label = ep_el.get("label", None)
+            if label:
+                label = label.strip()
             requires_domain = string_as_bool(ep_el.attrib.get("requires_domain", False))
-            rtt.append(dict(port=port, url=url, name=name, requires_domain=requires_domain))
+            requires_path_in_url = string_as_bool(ep_el.attrib.get("requires_path_in_url", False))
+            requires_path_in_header_named = ep_el.get("requires_path_in_header_named", None)
+            if requires_path_in_header_named:
+                requires_path_in_header_named = requires_path_in_header_named.strip()
+            rtt.append(
+                dict(
+                    port=port,
+                    url=url,
+                    name=name,
+                    label=label,
+                    requires_domain=requires_domain,
+                    requires_path_in_url=requires_path_in_url,
+                    requires_path_in_header_named=requires_path_in_header_named,
+                )
+            )
         return rtt
 
     def parse_hidden(self):

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -370,7 +370,7 @@ to provide access to graphical tools in real-time.
 
 ```xml
 <entry_points>
-  <entry_point name="Example name">
+  <entry_point name="Example name" label="example">
     <port>80</port>
     <url>landing/${template_enabled}/index.html</url>
   </entry_point>
@@ -385,12 +385,43 @@ to provide access to graphical tools in real-time.
     </xs:sequence>
         <xs:attribute name="name" type="xs:string" use="required">
           <xs:annotation>
-            <xs:documentation xml:lang="en">This value defines the name of the entry point.</xs:documentation>
+            <xs:documentation xml:lang="en">The name of the entry point.</xs:documentation>
           </xs:annotation>
         </xs:attribute>
-        <xs:attribute name="requires_domain" type="PermissiveBoolean" default="false">
+        <xs:attribute name="label" type="xs:string" use="optional">
           <xs:annotation>
-            <xs:documentation xml:lang="en">This value declares if domain-based proxying is required. Default is False. Currently only works when True.</xs:documentation>
+            <xs:documentation xml:lang="en">A unique label to identify the entry point. Used by interactive client tools to connect.</xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
+        <xs:attribute name="requires_domain" type="PermissiveBoolean" default="true">
+          <xs:annotation>
+            <xs:documentation xml:lang="en">Whether domain-based proxying is required for the entry point. Default is True.</xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
+        <xs:attribute name="requires_path_in_url" type="PermissiveBoolean" default="false">
+          <xs:annotation>
+            <xs:documentation xml:lang="en"><![CDATA[
+Whether the InteractiveTool proxy will add the entry point path to the URL provided to the interactive tool. Only
+relevant when path-based proxying is configured (``requires_domain=False``). A value of False implies that the web service
+for the interactive tool fully operates with relative links. A value of True implies that the unique entry point path,
+which is autogenerated each run, must be somehow provided to the web service. This can be done by injecting the path
+into an environment variable by setting the attribute ``inject="entry_point_path"`` in the tool XML.
+Alternatively, the attribute ``requires_path_in_header_named`` can be set to provide the path in the specified HTTP header.
+The entry point path should in any case be used to configure the web service in the interactive tool to serve the content
+from the provided URL path. Default value of ``requires_path_in_url`` is False.
+]]>
+            </xs:documentation>
+          </xs:annotation>
+        </xs:attribute>
+        <xs:attribute name="requires_path_in_header_named" type="xs:string" default="">
+          <xs:annotation>
+            <xs:documentation xml:lang="en"><![CDATA[
+Whether the InteractiveTool proxy will add the entry point path to an HTTP header. An empty string as value (default) means
+that the path will not be provided in an HTTP header. Any other string value will define the name of the HTTP header
+where the path will be injected by the proxy. See the documentation of ``requires_path_in_url`` for more information.
+Default value of ``requires_path_in_header_named`` is False.
+]]>
+            </xs:documentation>
           </xs:annotation>
         </xs:attribute>
   </xs:complexType>

lib/galaxy/tools/evaluation.py

@@ -522,7 +522,15 @@ def populate_interactivetools(self):
         it = []
         for ep in getattr(self.tool, "ports", []):
             ep_dict = {}
-            for key in "port", "name", "url", "requires_domain":
+            for key in (
+                "port",
+                "name",
+                "label",
+                "url",
+                "requires_domain",
+                "requires_path_in_url",
+                "requires_path_in_header_named",
+            ):
                 val = ep.get(key, None)
                 if val is not None and not isinstance(val, bool):
                     val = fill_template(

lib/tool_shed/test/test_data/repos/emboss_5_0470/0/emboss_format_corrector.py

@@ -1,53 +1,55 @@
-#EMBOSS format corrector
+# EMBOSS format corrector
 
 import operator
-#from galaxy import datatypes
 
-#Properly set file formats after job run
-def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr):
-#Properly set file formats before job run
-#def exec_before_job(trans, inp_data, out_data, param_dict,tool):
-    #why isn't items an ordered list?
+# from galaxy import datatypes
+
+
+# Properly set file formats after job run
+def exec_after_process(app, inp_data, out_data, param_dict, tool, stdout, stderr):
+    # Properly set file formats before job run
+    # def exec_before_job(trans, inp_data, out_data, param_dict,tool):
+    # why isn't items an ordered list?
     items = out_data.items()
-    #lets sort it ourselves....
+    # lets sort it ourselves....
     items = sorted(items, key=operator.itemgetter(0))
-    #items is now sorted...
-    
-    #normal filetype correction
-    data_count=1
+    # items is now sorted...
+
+    # normal filetype correction
+    data_count = 1
     for name, data in items:
-        outputType = param_dict.get( 'out_format'+str(data_count), None )
-        #print "data_count",data_count, "name", name, "outputType", outputType
-        if outputType !=None:
-            if outputType == 'ncbi':
+        outputType = param_dict.get("out_format" + str(data_count), None)
+        # print "data_count",data_count, "name", name, "outputType", outputType
+        if outputType != None:
+            if outputType == "ncbi":
                 outputType = "fasta"
-            elif outputType == 'excel':
+            elif outputType == "excel":
                 outputType = "tabular"
-            elif outputType == 'text':
+            elif outputType == "text":
                 outputType = "txt"
             data = app.datatypes_registry.change_datatype(data, outputType)
-            app.model.context.add( data )
+            app.model.context.add(data)
             app.model.context.flush()
-        data_count+=1
-    
-    #html filetype correction
-    data_count=1
+        data_count += 1
+
+    # html filetype correction
+    data_count = 1
     for name, data in items:
-        wants_plot = param_dict.get( 'html_out'+str(data_count), None )
+        wants_plot = param_dict.get("html_out" + str(data_count), None)
         ext = "html"
         if wants_plot == "yes":
             data = app.datatypes_registry.change_datatype(data, ext)
-            app.model.context.add( data )
+            app.model.context.add(data)
             app.model.context.flush()
-        data_count+=1
-    
-    #png file correction
-    data_count=1
+        data_count += 1
+
+    # png file correction
+    data_count = 1
     for name, data in items:
-        wants_plot = param_dict.get( 'plot'+str(data_count), None )
+        wants_plot = param_dict.get("plot" + str(data_count), None)
         ext = "png"
         if wants_plot == "yes":
             data = app.datatypes_registry.change_datatype(data, ext)
-            app.model.context.add( data )
+            app.model.context.add(data)
             app.model.context.flush()
-        data_count+=1
+        data_count += 1