Merge branch 'release_24.1' into dev

client/src/api/schema/schema.ts

@@ -9212,6 +9212,11 @@ export interface components {
              * @description TODO
              */
             api_type?: "file" | null;
+            /**
+             * Copied From History Dataset Association Id
+             * @description ID of HDA this HDA was copied from.
+             */
+            copied_from_history_dataset_association_id?: string | null;
             /** Copied From Ldda Id */
             copied_from_ldda_id?: string | null;
             /**
@@ -9457,6 +9462,11 @@ export interface components {
              * @enum {string}
              */
             api_type: "file";
+            /**
+             * Copied From History Dataset Association Id
+             * @description ID of HDA this HDA was copied from.
+             */
+            copied_from_history_dataset_association_id?: string | null;
             /** Copied From Ldda Id */
             copied_from_ldda_id?: string | null;
             /**

client/src/components/Login/RegisterForm.vue

@@ -79,7 +79,7 @@ async function submit() {
             Toast.info(response.data.message);
         }
 
-        window.location.href = props.redirect || withPrefix("/");
+        window.location.href = props.redirect ? withPrefix(props.redirect) : withPrefix("/");
     } catch (error: any) {
         disableCreate.value = false;
         messageText.value = errorMessageAsString(error, "Registration failed for an unknown reason.");

client/src/components/User/ExternalIdentities/ExternalLogin.vue

@@ -254,6 +254,12 @@ function getIdpPreference() {
                             <img :src="iDPInfo['icon']" height="45" :alt="idp" />
                         </BButton>
                     </span>
+                    <span v-else-if="iDPInfo['custom_button_text']">
+                        <BButton class="d-block mt-3" @click="submitOIDCLogin(idp)">
+                            <i :class="oIDCIdps[idp]" />
+                            Sign in with {{ iDPInfo["custom_button_text"] }}
+                        </BButton>
+                    </span>
                     <span v-else>
                         <BButton class="d-block mt-3" @click="submitOIDCLogin(idp)">
                             <i :class="oIDCIdps[idp]" />

lib/galaxy/authnz/managers.py

@@ -96,6 +96,9 @@ def _parse_oidc_config(self, config_file):
     def _get_idp_icon(self, idp):
         return self.oidc_backends_config[idp].get("icon") or DEFAULT_OIDC_IDP_ICONS.get(idp)
 
+    def _get_idp_button_text(self, idp):
+        return self.oidc_backends_config[idp].get("custom_button_text")
+
     def _parse_oidc_backends_config(self, config_file):
         self.oidc_backends_config = {}
         self.oidc_backends_implementation = {}
@@ -122,7 +125,10 @@ def _parse_oidc_backends_config(self, config_file):
                 if idp in BACKENDS_NAME:
                     self.oidc_backends_config[idp] = self._parse_idp_config(child)
                     self.oidc_backends_implementation[idp] = "psa"
-                    self.app.config.oidc[idp] = {"icon": self._get_idp_icon(idp)}
+                    self.app.config.oidc[idp] = {
+                        "icon": self._get_idp_icon(idp),
+                        "custom_button_text": self._get_idp_button_text(idp),
+                    }
                 elif idp in KEYCLOAK_BACKENDS:
                     self.oidc_backends_config[idp] = self._parse_custos_config(child)
                     self.oidc_backends_implementation[idp] = "custos"
@@ -159,6 +165,10 @@ def _parse_idp_config(self, config_xml):
             rtv["extra_scopes"] = listify(config_xml.find("extra_scopes").text)
         if config_xml.find("tenant_id") is not None:
             rtv["tenant_id"] = config_xml.find("tenant_id").text
+        if config_xml.find("oidc_endpoint") is not None:
+            rtv["oidc_endpoint"] = config_xml.find("oidc_endpoint").text
+        if config_xml.find("custom_button_text") is not None:
+            rtv["custom_button_text"] = config_xml.find("custom_button_text").text
         if config_xml.find("pkce_support") is not None:
             rtv["pkce_support"] = asbool(config_xml.find("pkce_support").text)
         if config_xml.find("accepted_audiences") is not None:

lib/galaxy/authnz/psa_authnz.py

@@ -45,6 +45,7 @@
     "okta": "social_core.backends.okta_openidconnect.OktaOpenIdConnect",
     "azure": "social_core.backends.azuread_tenant.AzureADV2TenantOAuth2",
     "egi_checkin": "social_core.backends.egi_checkin.EGICheckinOpenIdConnect",
+    "oidc": "social_core.backends.open_id_connect.OpenIdConnectAuth",
 }
 
 BACKENDS_NAME = {
@@ -54,6 +55,7 @@
     "okta": "okta-openidconnect",
     "azure": "azuread-v2-tenant-oauth2",
     "egi_checkin": "egi-checkin",
+    "oidc": "oidc",
 }
 
 AUTH_PIPELINE = (
@@ -133,6 +135,7 @@ def _setup_idp(self, oidc_backend_config):
         self.config["KEY"] = oidc_backend_config.get("client_id")
         self.config["SECRET"] = oidc_backend_config.get("client_secret")
         self.config["TENANT_ID"] = oidc_backend_config.get("tenant_id")
+        self.config["OIDC_ENDPOINT"] = oidc_backend_config.get("oidc_endpoint")
         self.config["redirect_uri"] = oidc_backend_config.get("redirect_uri")
         self.config["EXTRA_SCOPES"] = oidc_backend_config.get("extra_scopes")
         if oidc_backend_config.get("prompt") is not None:

lib/galaxy/authnz/xsd/oidc_backends_config.xsd

@@ -121,6 +121,20 @@
                                     </xs:documentation>
                                 </xs:annotation>
                             </xs:element>
+                            <xs:element name="oidc_endpoint" minOccurs="0" type="xs:anyURI">
+                                <xs:annotation>
+                                    <xs:documentation>
+                                        OIDC endpoint for the IdP
+                                    </xs:documentation>
+                                </xs:annotation>
+                            </xs:element>
+                            <xs:element name="custom_button_text" minOccurs="0" type="xs:string">
+                                <xs:annotation>
+                                    <xs:documentation>
+                                        Can be used to set a custom text value for the "Sign in with " button for your chosen IdP.
+                                    </xs:documentation>
+                                </xs:annotation>
+                            </xs:element>
                             <xs:element name="pkce_support" minOccurs="0" type="xs:boolean">
                                 <xs:annotation>
                                     <xs:documentation>

lib/galaxy/config/sample/oidc_backends_config.xml.sample

@@ -201,6 +201,26 @@ Please mind `http` and `https`.
         <tenant_id> ... </tenant_id>
     </provider>
 
+    <provider name="oidc">
+        <!-- This example section uses the generic OIDC backend from python-social-auth. This should work with any provider that
+        supports the OIDC standard.
+        -->
+        <client_id> ... </client_id>
+        <client_secret> ... </client_secret>
+        <redirect_uri>http://localhost:8080/authnz/oidc/callback</redirect_uri>
+        <oidc_endpoint> ... </oidc_endpoint>
+        <!-- enter the url of a OIDC endpoint that supports autoconfiguration here. Enter the URL minus the ".well-known/openid-configuration" part.
+        For example: If the complete url pointing to your endpoint's autoconfig file is "https:example.com/my-realm/.well-known/openid-configuration",
+        then simply enter "https://example.com/my-realm".
+         -->
+         <custom_button_text> ... </custom_button_text>
+         <!-- This is an optional field where you can provide a custom text for the sign in button on the Galaxy front page
+          that you can click to authenticate with your IdP. If you don't provide a custom button text, the sign in button
+          will just read the default value of your IdP name. For example: "Sign in with oidc" or "Sign in with Azure".
+          However, if for example you enter the value "your university account" here, the button will display "Sign in with your university account".
+         -->
+    </provider>
+
     <!-- Documentation: https://docs.egi.eu/providers/check-in/sp -->
     <provider name="egi_checkin">
 	<!-- Client id and secret can be obtained by registering your client at EGI Check-in

lib/galaxy/managers/datasets.py

@@ -632,7 +632,7 @@ def add_serializers(self):
             "file_size": lambda item, key, **context: self.serializers["size"](item, key, **context),
             "nice_size": lambda item, key, **context: item.get_size(nice_size=True, calculate_size=False),
             # common to lddas and hdas - from mapping.py
-            "copied_from_history_dataset_association_id": self.serialize_id,
+            "copied_from_history_dataset_association_id": lambda item, key, **context: item.id,
             "copied_from_library_dataset_dataset_association_id": self.serialize_id,
             "info": lambda item, key, **context: item.info.strip() if isinstance(item.info, str) else item.info,
             "blurb": lambda item, key, **context: item.blurb,

lib/galaxy/model/__init__.py

@@ -5277,6 +5277,7 @@ def copy_from(self, other_hda, new_dataset=None, include_tags=True, include_meta
         if include_tags and self.history:
             self.copy_tags_from(self.user, other_hda)
         self.dataset = new_dataset or other_hda.dataset
+        self.copied_from_history_dataset_association_id = other_hda.id
         if old_dataset:
             old_dataset.full_delete()
 
@@ -8223,6 +8224,7 @@ def copy_to(self, copied_step, step_mapping, user=None):
             if stored_subworkflow and stored_subworkflow.user == user:
                 # This should be fine and reduces the number of stored subworkflows
                 copied_step.subworkflow = subworkflow
+                copied_subworkflow = subworkflow
             else:
                 # Can this even happen, building a workflow with a subworkflow you don't own ?
                 copied_subworkflow = subworkflow.copy()
@@ -8231,8 +8233,8 @@ def copy_to(self, copied_step, step_mapping, user=None):
                 )
                 copied_subworkflow.stored_workflow = stored_workflow
                 copied_step.subworkflow = copied_subworkflow
-                for subworkflow_step, copied_subworkflow_step in zip(subworkflow.steps, copied_subworkflow.steps):
-                    subworkflow_step_mapping[subworkflow_step.id] = copied_subworkflow_step
+            for subworkflow_step, copied_subworkflow_step in zip(subworkflow.steps, copied_subworkflow.steps):
+                subworkflow_step_mapping[subworkflow_step.id] = copied_subworkflow_step
 
         for old_conn, new_conn in zip(self.input_connections, copied_step.input_connections):
             new_conn.input_step_input = copied_step.get_or_add_input(old_conn.input_name)

lib/galaxy/schema/schema.py

@@ -912,6 +912,9 @@ class HDADetailed(HDASummary, WithModelClass):
             description="The list of sources associated with this dataset.",
         ),
     ]
+    copied_from_history_dataset_association_id: Annotated[
+        Optional[EncodedDatabaseIdField], Field(None, description="ID of HDA this HDA was copied from.")
+    ]
 
 
 class HDAExtended(HDADetailed):

lib/galaxy/tools/__init__.py

@@ -2999,7 +2999,9 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
                 # if change_datatype PJA is associated with expression tool output the new output already has
                 # the desired datatype, so we use it. If the extension is "data" there's no change_dataset PJA and
                 # we want to use the existing extension.
-                new_ext = output.extension if output.extension != "data" else copy_object.extension
+                new_ext = (
+                    output.extension if output.extension not in ("data", "expression.json") else copy_object.extension
+                )
                 require_metadata_regeneration = copy_object.extension != new_ext
                 output.copy_from(copy_object, include_metadata=not require_metadata_regeneration)
                 output.extension = new_ext
@@ -3014,8 +3016,12 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job=None, **kw
                     else:
                         # TODO: move exec_after_process into metadata script so this doesn't run on the headnode ?
                         output.init_meta()
-                        output.set_meta()
-                        output.set_metadata_success_state()
+                        try:
+                            output.set_meta()
+                            output.set_metadata_success_state()
+                        except Exception:
+                            output.state = model.HistoryDatasetAssociation.states.FAILED_METADATA
+                            log.exception("Exception occured while setting metdata")
 
     def parse_environment_variables(self, tool_source):
         """Setup environment variable for inputs file."""

lib/galaxy/util/__init__.py

@@ -30,8 +30,7 @@
     timezone,
 )
 from decimal import Decimal
-from email.mime.multipart import MIMEMultipart
-from email.mime.text import MIMEText
+from email.message import EmailMessage
 from hashlib import md5
 from os.path import relpath
 from pathlib import Path
@@ -1634,10 +1633,8 @@ def send_mail(frm, to, subject, body, config, html=None, reply_to=None):
         return
 
     to = listify(to)
-    if html:
-        msg = MIMEMultipart("alternative")
-    else:
-        msg = MIMEText(body, "plain", "utf-8")
+    msg = EmailMessage()
+    msg.set_content(body)
 
     msg["To"] = ", ".join(to)
     msg["From"] = frm
@@ -1652,45 +1649,40 @@ def send_mail(frm, to, subject, body, config, html=None, reply_to=None):
         return
 
     if html:
-        mp_text = MIMEText(body, "plain", "utf-8")
-        mp_html = MIMEText(html, "html", "utf-8")
-        msg.attach(mp_text)
-        msg.attach(mp_html)
+        msg.add_alternative(html, subtype="html")
 
     smtp_ssl = asbool(getattr(config, "smtp_ssl", False))
     if smtp_ssl:
         s = smtplib.SMTP_SSL(config.smtp_server)
     else:
         s = smtplib.SMTP(config.smtp_server)
-    if not smtp_ssl:
-        try:
-            s.starttls()
-            log.debug("Initiated SSL/TLS connection to SMTP server: %s", config.smtp_server)
-        except RuntimeError as e:
-            log.warning("SSL/TLS support is not available to your Python interpreter: %s", unicodify(e))
-        except smtplib.SMTPHeloError as e:
-            log.error("The server didn't reply properly to the HELO greeting: %s", unicodify(e))
-            s.close()
-            raise
-        except smtplib.SMTPException as e:
-            log.warning("The server does not support the STARTTLS extension: %s", unicodify(e))
-    if config.smtp_username and config.smtp_password:
-        try:
-            s.login(config.smtp_username, config.smtp_password)
-        except smtplib.SMTPHeloError as e:
-            log.error("The server didn't reply properly to the HELO greeting: %s", unicodify(e))
-            s.close()
-            raise
-        except smtplib.SMTPAuthenticationError as e:
-            log.error("The server didn't accept the username/password combination: %s", unicodify(e))
-            s.close()
-            raise
-        except smtplib.SMTPException as e:
-            log.error("No suitable authentication method was found: %s", unicodify(e))
-            s.close()
-            raise
-    s.sendmail(frm, to, msg.as_string())
-    s.quit()
+    try:
+        if not smtp_ssl:
+            try:
+                s.starttls()
+                log.debug("Initiated SSL/TLS connection to SMTP server: %s", config.smtp_server)
+            except RuntimeError as e:
+                log.warning("SSL/TLS support is not available to your Python interpreter: %s", e)
+            except smtplib.SMTPHeloError as e:
+                log.error("The server didn't reply properly to the HELO greeting: %s", e)
+                raise
+            except smtplib.SMTPException as e:
+                log.warning("The server does not support the STARTTLS extension: %s", e)
+        if config.smtp_username and config.smtp_password:
+            try:
+                s.login(config.smtp_username, config.smtp_password)
+            except smtplib.SMTPHeloError as e:
+                log.error("The server didn't reply properly to the HELO greeting: %s", e)
+                raise
+            except smtplib.SMTPAuthenticationError as e:
+                log.error("The server didn't accept the username/password combination: %s", e)
+                raise
+            except smtplib.SMTPException as e:
+                log.error("No suitable authentication method was found: %s", e)
+                raise
+        s.send_message(msg)
+    finally:
+        s.quit()
 
 
 def force_symlink(source, link_name):

lib/galaxy/webapps/galaxy/services/datasets.py

@@ -403,7 +403,11 @@ def show(
             # Default: return dataset as dict.
             if hda_ldda == DatasetSourceType.hda:
                 return self.hda_serializer.serialize_to_view(
-                    dataset, view=serialization_params.view or "detailed", user=trans.user, trans=trans
+                    dataset,
+                    view=serialization_params.view or "detailed",
+                    keys=serialization_params.keys,
+                    user=trans.user,
+                    trans=trans,
                 )
             else:
                 dataset_dict = dataset.to_dict()

lib/galaxy_test/api/test_workflows.py

@@ -887,6 +887,43 @@ def test_update_name(self):
         workflow_dict = self.workflow_populator.download_workflow(workflow_id)
         assert workflow_dict["license"] == "AAL"
 
+    def test_update_name_for_workflow_with_subworkflows(self):
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+label: old name
+inputs:
+  dataset: data
+steps:
+  subworkflow:
+    in:
+      dataset: dataset
+    outputs:
+      output:
+        outputSource: cat1/out_file1
+    run:
+      class: GalaxyWorkflow
+      inputs:
+        dataset:
+          type: data
+      steps:
+        cat1:
+          tool_id: cat1
+          in:
+            input1: dataset
+  cat1:
+    tool_id: cat1
+    in:
+      input1: subworkflow/output
+"""
+        )
+        self.workflow_populator.download_workflow(workflow_id)
+        new_name = "my cool new name"
+        data = {"name": new_name}
+        self._update_workflow(workflow_id, data).raise_for_status()
+        post_update_workflow = self.workflow_populator.download_workflow(workflow_id)
+        assert post_update_workflow["name"] == new_name
+
     def test_update_name_empty(self):
         # Update doesn't allow empty names.
 

lib/galaxy_test/base/populators.py

@@ -1009,14 +1009,17 @@ def get_history_dataset_source_transform_actions(self, history_id: str, **kwd) -
         assert isinstance(transform, list)
         return {t["action"] for t in transform}
 
-    def get_history_dataset_details(self, history_id: str, **kwds) -> Dict[str, Any]:
+    def get_history_dataset_details(self, history_id: str, keys: Optional[str] = None, **kwds) -> Dict[str, Any]:
         dataset_id = self.__history_content_id(history_id, **kwds)
-        details_response = self.get_history_dataset_details_raw(history_id, dataset_id)
+        details_response = self.get_history_dataset_details_raw(history_id, dataset_id, keys=keys)
         details_response.raise_for_status()
         return details_response.json()
 
-    def get_history_dataset_details_raw(self, history_id: str, dataset_id: str) -> Response:
-        details_response = self._get_contents_request(history_id, f"/datasets/{dataset_id}")
+    def get_history_dataset_details_raw(self, history_id: str, dataset_id: str, keys: Optional[str] = None) -> Response:
+        data = None
+        if keys:
+            data = {"keys": keys}
+        details_response = self._get_contents_request(history_id, f"/datasets/{dataset_id}", data=data)
         return details_response
 
     def get_history_dataset_extra_files(self, history_id: str, **kwds) -> list: