From c933732b1d7323706d841c923fc87cdc824194a6 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 4 May 2022 11:32:09 -0400
Subject: [PATCH 1/6] Fix stray non-breaking typo in workflows.py.

---
 lib/galaxy/webapps/galaxy/services/workflows.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/lib/galaxy/webapps/galaxy/services/workflows.py b/lib/galaxy/webapps/galaxy/services/workflows.py
index 4f056978b83..c8c754d2f67 100644
--- a/lib/galaxy/webapps/galaxy/services/workflows.py
+++ b/lib/galaxy/webapps/galaxy/services/workflows.py
@@ -115,7 +115,6 @@ class WorkflowsService(ServiceBase):
             parsed_search = parse_filters_structured(search_query, INDEX_SEARCH_FILTERS)
 
             def tag_filter(term_text: str, quoted: bool):
-                term_text = term.text
                 if ":" in term_text:
                     key, value = term_text.rsplit(":", 1)
                     if not quoted:

From d2e555d0a73b66d0d0fa0781c161dbd4db9afb61 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Fri, 29 Apr 2022 12:00:52 -0400
Subject: [PATCH 2/6] Docs for workflow index filter tags.

---
 lib/galaxy/webapps/galaxy/api/__init__.py  | 57 ++++++++++++++++++++++
 lib/galaxy/webapps/galaxy/api/workflows.py | 29 +++++++++--
 2 files changed, 81 insertions(+), 5 deletions(-)

diff --git a/lib/galaxy/webapps/galaxy/api/__init__.py b/lib/galaxy/webapps/galaxy/api/__init__.py
index 33d136bb7c9..9bcd7894e92 100644
--- a/lib/galaxy/webapps/galaxy/api/__init__.py
+++ b/lib/galaxy/webapps/galaxy/api/__init__.py
@@ -3,10 +3,12 @@ This module *does not* contain API routes. It exclusively contains dependencies
 """
 import inspect
 from enum import Enum
+from string import Template
 from typing import (
     Any,
     AsyncGenerator,
     cast,
+    NamedTuple,
     Optional,
     Tuple,
     Type,
@@ -410,3 +412,58 @@ async def try_get_request_body_as_json(request: Request) -> Optional[Any]:
         body = await request.json()
         return body
     return None
+
+
+search_description_template = Template(
+    """A mix of free text and GitHub-style tags used to filter the index operation.
+
+## Query Structure
+
+GitHub-style filter tags (not be confused with Galaxy tags) are tags of the form
+`<tag_name>:<text_no_spaces>` or `<tag_name>:'<text with potential spaces>'`. The tag name
+*generally* (but not exclusively) corresponds to the name of an attribute on the model
+being indexed (i.e. a column in the database).
+
+If the tag is quoted, the attribute will be filtered exactly. If the tag is unquoted,
+generally a partial match will be used to filter the query (i.e. in terms of the implementation
+this means the database operation `ILIKE` will typically be used).
+
+Once the tagged filters are extracted from the search query, the remaing text is just
+used to search various documented attributes of the object.
+
+## GitHub-style Tags Available
+
+${tags}
+
+## Free Text
+
+Free text search terms will be searched against the following attributes of the
+${model_name}s: ${freetext}.
+
+"""
+)
+
+
+class IndexQueryTag(NamedTuple):
+    tag: str
+    description: str
+    alias: Optional[str] = None
+
+    def as_markdown(self):
+        desc = self.description
+        alias = self.alias
+        if alias:
+            desc += f" (The tag `{alias}` can be used a short hand alias for this tag to filter on this attribute.)"
+        return f"`{self.tag}`\n: {desc}"
+
+
+def search_query_param(model_name: str, tags: list, free_text_fields: list) -> Optional[str]:
+    tags_markdown_str = "\n\n".join([t.as_markdown() for t in tags])
+    description = search_description_template.safe_substitute(
+        model_name=model_name, tags=tags_markdown_str, freetext=", ".join([f"`{t}`" for t in free_text_fields])
+    )
+    return Query(
+        default=None,
+        title="Search query.",
+        description=description,
+    )
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index e45e838710a..df23c878b2c 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -85,7 +85,9 @@ from . import (
     BaseGalaxyAPIController,
     depends,
     DependsOnTrans,
+    IndexQueryTag,
     Router,
+    search_query_param,
 )
 
 log = logging.getLogger(__name__)
@@ -1442,10 +1444,27 @@ OffsetQueryParam: Optional[int] = Query(
     title="Number of workflows to skip in sorted query (to enable pagination).",
 )
 
-SearchQueryParam: Optional[str] = Query(
-    default=None,
-    title="Search query.",
-    description="Free text used to filter the query. Filters on a name and tags, Github-style tags can be used to be more specific. Free-text search is case-insensitive.",
+query_tags = [
+    IndexQueryTag("name", "The stored workflow's name.", "n"),
+    IndexQueryTag(
+        "tag",
+        "The workflow's tag, if the tag contains a colon an approach will be made to match the key and value of the tag separately.",
+        "t",
+    ),
+    IndexQueryTag(
+        "is:published",
+        "Include only published workflows in the final result. Be sure the the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.",
+    ),
+    IndexQueryTag(
+        "is:share_with_me",
+        "Include only workflows shared with the requesting user.  Be sure the the query parameter `show_shared` is set to `true` if to include shared workflows.",
+    ),
+]
+
+SearchQueryParam: Optional[str] = search_query_param(
+    model_name="Stored Workflow",
+    tags=query_tags,
+    free_text_fields=["name", "tag"],
 )
 
 SkipStepCountsQueryParam: bool = Query(
@@ -1480,7 +1499,7 @@ class FastAPIWorkflows:
         search: Optional[str] = SearchQueryParam,
         skip_step_counts: bool = SkipStepCountsQueryParam,
     ) -> List[Dict[str, Any]]:
-        """Return the sharing status of the item."""
+        """Lists stored workflows viewable by the user."""
         payload = WorkflowIndexPayload(
             show_published=show_published,
             show_hidden=show_hidden,

From caa5c56a0a9eabdaaf357f1a86fae84d8a8d6962 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 May 2022 19:46:23 -0400
Subject: [PATCH 3/6] Allow filtering workflows on sharing tags.

Implement is:published and is:shared_with_me in the query 'search' parameter.
---
 .../src/components/Workflow/WorkflowList.vue  | 23 ++++++++++++----
 .../src/components/Workflow/Workflows.test.js | 26 +++++++++++++++++++
 .../webapps/galaxy/services/workflows.py      |  9 +++++++
 lib/galaxy_test/api/test_workflows.py         | 18 +++++++++++++
 4 files changed, 71 insertions(+), 5 deletions(-)

diff --git a/client/src/components/Workflow/WorkflowList.vue b/client/src/components/Workflow/WorkflowList.vue
index 63d0803d263..a52c960bfd0 100644
--- a/client/src/components/Workflow/WorkflowList.vue
+++ b/client/src/components/Workflow/WorkflowList.vue
@@ -62,8 +62,18 @@
                     <Tags :index="row.index" :tags="row.item.tags" @input="onTags" @tag-click="onTagClick" />
                 </template>
                 <template v-slot:cell(published)="row">
-                    <font-awesome-icon v-if="row.item.published" v-b-tooltip.hover title="Published" icon="globe" />
-                    <font-awesome-icon v-if="row.item.shared" v-b-tooltip.hover title="Shared" icon="share-alt" />
+                    <font-awesome-icon
+                        v-if="row.item.published"
+                        v-b-tooltip.hover
+                        title="Published"
+                        icon="globe"
+                        @click="appendFilter('is:published')" />
+                    <font-awesome-icon
+                        v-if="row.item.shared"
+                        v-b-tooltip.hover
+                        title="Shared"
+                        icon="share-alt"
+                        @click="appendFilter('is:shared_with_me')" />
                 </template>
                 <template v-slot:cell(show_in_tool_panel)="row">
                     <b-link @click="bookmarkWorkflow(row.item, false)" v-if="row.item.show_in_tool_panel">
@@ -246,11 +256,14 @@ export default {
         },
         onTagClick: function (tag) {
             const tagFilter = `tag:'${tag.text}'`;
+            this.appendFilter(tagFilter);
+        },
+        appendFilter(text) {
             const initialFilter = this.filter;
             if (initialFilter.length === 0) {
-                this.filter = tagFilter;
-            } else if (initialFilter.indexOf(tagFilter) < 0) {
-                this.filter = `${tagFilter} ${initialFilter}`;
+                this.filter = text;
+            } else if (initialFilter.indexOf(text) < 0) {
+                this.filter = `${text} ${initialFilter}`;
             }
         },
         onAdd: function (workflow) {
diff --git a/client/src/components/Workflow/Workflows.test.js b/client/src/components/Workflow/Workflows.test.js
index d9a5f8bf845..691ecbcaf1a 100644
--- a/client/src/components/Workflow/Workflows.test.js
+++ b/client/src/components/Workflow/Workflows.test.js
@@ -124,5 +124,31 @@ describe("WorkflowList.vue", () => {
             flushPromises();
             expect(wrapper.vm.filter).toBe("tag:'tagmoo'");
         });
+
+        it("update filter when published icon is clicked", async () => {
+            axiosMock
+                .onGet("/api/workflows", {
+                    params: { limit: 50, offset: 0, skip_step_counts: true, search: "is:published" },
+                })
+                .reply(200, mockWorkflowsData, { total_matches: "1" });
+            const rows = wrapper.findAll("tbody > tr").wrappers;
+            const row = rows[0];
+            row.find(".fa-globe").trigger("click");
+            flushPromises();
+            expect(wrapper.vm.filter).toBe("is:published");
+        });
+
+        it("update filter when shared with me icon is clicked", async () => {
+            axiosMock
+                .onGet("/api/workflows", {
+                    params: { limit: 50, offset: 0, skip_step_counts: true, search: "is:shared_with_me" },
+                })
+                .reply(200, mockWorkflowsData, { total_matches: "1" });
+            const rows = wrapper.findAll("tbody > tr").wrappers;
+            const row = rows[0];
+            row.find(".fa-share-alt").trigger("click");
+            flushPromises();
+            expect(wrapper.vm.filter).toBe("is:shared_with_me");
+        });
     });
 });
diff --git a/lib/galaxy/webapps/galaxy/services/workflows.py b/lib/galaxy/webapps/galaxy/services/workflows.py
index c8c754d2f67..d77d5d5ebec 100644
--- a/lib/galaxy/webapps/galaxy/services/workflows.py
+++ b/lib/galaxy/webapps/galaxy/services/workflows.py
@@ -45,6 +45,7 @@ INDEX_SEARCH_FILTERS = {
     "tag": "tag",
     "n": "name",
     "t": "tag",
+    "is": "is",
 }
 
 
@@ -148,6 +149,14 @@ class WorkflowsService(ServiceBase):
                         query = query.filter(tag_filter(term.text, term.quoted))
                     elif key == "name":
                         query = query.filter(name_filter(q, term.quoted))
+                    elif key == "is":
+                        if q == "published":
+                            query = query.filter(model.StoredWorkflow.published == true())
+                        elif q == "shared_with_me":
+                            if not show_shared:
+                                message = "Can only use tag is:shared_with_me if show_shared parameter also true."
+                                raise exceptions.RequestParameterInvalidException(message)
+                            query = query.filter(model.StoredWorkflowUserShareAssociation.user == user)
                 elif isinstance(term, RawTextTerm):
                     query = query.filter(
                         or_(
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index b85cfb57b7d..fbcb2e5a76f 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -538,6 +538,24 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         assert workflow_id in self.workflow_populator.index_ids(show_published=True)
         assert workflow_id not in self.workflow_populator.index_ids(show_published=False)
 
+    def test_index_search_is_tags(self):
+        my_workflow_id_1 = self.workflow_populator.simple_workflow("sitags_m_1")
+        my_email = self.dataset_populator.user_email()
+        with self._different_user():
+            their_workflow_id_1 = self.workflow_populator.simple_workflow("sitags_shwm_1")
+            self.workflow_populator.share_with_user(their_workflow_id_1, my_email)
+            published_workflow_id_1 = self.workflow_populator.simple_workflow("sitags_p_1", publish=True)
+
+        index_ids = self.workflow_populator.index_ids(search="is:published", show_published=True)
+        assert published_workflow_id_1 in index_ids
+        assert their_workflow_id_1 not in index_ids
+        assert my_workflow_id_1 not in index_ids
+
+        index_ids = self.workflow_populator.index_ids(search="is:shared_with_me")
+        assert published_workflow_id_1 not in index_ids
+        assert their_workflow_id_1 in index_ids
+        assert my_workflow_id_1 not in index_ids
+
     def test_index_parameter_invalid_combinations(self):
         # these can all be called by themselves and return 200...
         response = self._get("workflows?show_hidden=true")

From 836ae624957646a0e85feb961e2400eb5e60c703 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Mon, 2 May 2022 18:49:03 -0400
Subject: [PATCH 4/6] Move workflows index query operations into the manager
 layer.

---
 lib/galaxy/managers/workflows.py              | 145 +++++++++++++++++-
 lib/galaxy/schema/schema.py                   |   3 +-
 lib/galaxy/webapps/galaxy/api/workflows.py    |   6 +-
 .../webapps/galaxy/services/workflows.py      | 145 +-----------------
 4 files changed, 154 insertions(+), 145 deletions(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 6b324df9c31..cc9b4f6d139 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -9,6 +9,7 @@ from typing import (
     Dict,
     List,
     Optional,
+    Tuple,
 )
 
 from gxformat2 import (
@@ -18,9 +19,16 @@ from gxformat2 import (
     python_to_workflow,
 )
 from pydantic import BaseModel
-from sqlalchemy import and_
+from sqlalchemy import (
+    and_,
+    desc,
+    false,
+    or_,
+    true,
+)
 from sqlalchemy.orm import (
     joinedload,
+    Query,
     subqueryload,
 )
 
@@ -31,7 +39,9 @@ from galaxy import (
 )
 from galaxy.job_execution.actions.post import ActionBox
 from galaxy.managers import sharable
+from galaxy.managers.context import ProvidesUserContext
 from galaxy.model.item_attrs import UsesAnnotations
+from galaxy.schema.schema import WorkflowIndexQueryPayload
 from galaxy.structured_app import MinimalManagerApp
 from galaxy.tools.parameters import (
     params_to_incoming,
@@ -48,6 +58,11 @@ from galaxy.util.json import (
     safe_loads,
 )
 from galaxy.util.sanitize_html import sanitize_html
+from galaxy.util.search import (
+    FilteredTerm,
+    parse_filters_structured,
+    RawTextTerm,
+)
 from galaxy.web import url_for
 from galaxy.workflow.modules import (
     is_tool_module_type,
@@ -69,6 +84,15 @@ from .executables import artifact_class
 log = logging.getLogger(__name__)
 
 
+INDEX_SEARCH_FILTERS = {
+    "name": "name",
+    "tag": "tag",
+    "n": "name",
+    "t": "tag",
+    "is": "is",
+}
+
+
 class WorkflowsManager(sharable.SharableModelManager):
     """Handle CRUD type operations related to workflows. More interesting
     stuff regarding workflow execution, step sorting, etc... can be found in
@@ -83,6 +107,121 @@ class WorkflowsManager(sharable.SharableModelManager):
         super().__init__(app)
         self.app = app
 
+    def index_query(
+        self, trans: ProvidesUserContext, payload: WorkflowIndexQueryPayload, include_total_count: bool = False
+    ) -> Tuple[Query, Optional[int]]:
+        show_published = payload.show_published
+        show_hidden = payload.show_hidden
+        show_deleted = payload.show_deleted
+        show_shared = payload.show_shared
+
+        if show_shared is None:
+            show_shared = not show_hidden and not show_deleted
+
+        if show_shared and show_deleted:
+            message = "show_shared and show_deleted cannot both be specified as true"
+            raise exceptions.RequestParameterInvalidException(message)
+        if show_shared and show_hidden:
+            message = "show_shared and show_hidden cannot both be specified as true"
+            raise exceptions.RequestParameterInvalidException(message)
+
+        filters = [
+            model.StoredWorkflow.user == trans.user,
+        ]
+        user = trans.user
+        if user and show_shared:
+            filters.append(model.StoredWorkflowUserShareAssociation.user == user)
+
+        if show_published or user is None and show_published is None:
+            filters.append((model.StoredWorkflow.published == true()))
+
+        query = trans.sa_session.query(model.StoredWorkflow)
+        if show_shared:
+            query = query.outerjoin(model.StoredWorkflow.users_shared_with)
+        query = query.outerjoin(model.StoredWorkflow.tags)
+
+        latest_workflow_load = joinedload("latest_workflow")
+        if not payload.skip_step_counts:
+            latest_workflow_load = latest_workflow_load.undefer("step_count")
+        latest_workflow_load = latest_workflow_load.lazyload("steps")
+
+        query = query.options(joinedload(model.StoredWorkflow.annotations))
+        query = query.options(latest_workflow_load)
+        query = query.filter(or_(*filters))
+        query = query.filter(model.StoredWorkflow.table.c.hidden == (true() if show_hidden else false()))
+        query = query.filter(model.StoredWorkflow.table.c.deleted == (true() if show_deleted else false()))
+        if payload.search:
+            search_query = payload.search
+            parsed_search = parse_filters_structured(search_query, INDEX_SEARCH_FILTERS)
+
+            def tag_filter(term_text: str, quoted: bool):
+                if ":" in term_text:
+                    key, value = term_text.rsplit(":", 1)
+                    if not quoted:
+                        return and_(
+                            model.StoredWorkflowTagAssociation.user_tname.ilike(key),
+                            model.StoredWorkflowTagAssociation.user_value.ilike(f"%{value}%"),
+                        )
+                    else:
+                        return and_(
+                            model.StoredWorkflowTagAssociation.user_tname == key,
+                            model.StoredWorkflowTagAssociation.user_value == value,
+                        )
+                else:
+                    if not quoted:
+                        return model.StoredWorkflowTagAssociation.user_tname.ilike(f"%{term_text}%")
+                    else:
+                        return model.StoredWorkflowTagAssociation.user_tname == term_text
+
+            def name_filter(text, quoted):
+                if not quoted:
+                    filter = model.StoredWorkflow.name.ilike(f"%{text}%")
+                else:
+                    filter = model.StoredWorkflow.name == text
+                return filter
+
+            for term in parsed_search.terms:
+                if isinstance(term, FilteredTerm):
+                    key = term.filter
+                    q = term.text
+                    if key == "tag":
+                        query = query.filter(tag_filter(term.text, term.quoted))
+                    elif key == "name":
+                        query = query.filter(name_filter(q, term.quoted))
+                    elif key == "is":
+                        if q == "published":
+                            query = query.filter(model.StoredWorkflow.published == true())
+                        elif q == "shared_with_me":
+                            if not show_shared:
+                                message = "Can only use tag is:shared_with_me if show_shared parameter also true."
+                                raise exceptions.RequestParameterInvalidException(message)
+                            query = query.filter(model.StoredWorkflowUserShareAssociation.user == user)
+                elif isinstance(term, RawTextTerm):
+                    query = query.filter(
+                        or_(
+                            name_filter(term.text, False),
+                            tag_filter(term.text, False),
+                        )
+                    )
+        if include_total_count:
+            total_matches = query.count()
+        else:
+            total_matches = None
+        if payload.sort_by is None:
+            if user:
+                query = query.order_by(desc(model.StoredWorkflow.user == user))
+            query = query.order_by(desc(model.StoredWorkflow.table.c.update_time))
+        else:
+            sort_column = getattr(model.StoredWorkflow, payload.sort_by)
+            if payload.sort_desc:
+                sort_column = sort_column.desc()
+            query = query.order_by(sort_column)
+        if payload.limit is not None:
+            query = query.limit(payload.limit)
+        if payload.offset is not None:
+            query = query.offset(payload.offset)
+        return query, total_matches
+
     def get_stored_workflow(self, trans, workflow_id, by_stored_id=True):
         """Use a supplied ID (UUID or encoded stored workflow ID) to find
         a workflow.
@@ -286,7 +425,7 @@ class WorkflowsManager(sharable.SharableModelManager):
 
     def build_invocations_query(
         self,
-        trans,
+        trans: ProvidesUserContext,
         stored_workflow_id=None,
         history_id=None,
         job_id=None,
@@ -296,7 +435,7 @@ class WorkflowsManager(sharable.SharableModelManager):
         offset=None,
         sort_by=None,
         sort_desc=None,
-    ):
+    ) -> Tuple[Query, int]:
         """Get invocations owned by the current user."""
         sa_session = trans.sa_session
         invocations_query = sa_session.query(model.WorkflowInvocation)
diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
index fd77a1316af..e82d6629e2d 100644
--- a/lib/galaxy/schema/schema.py
+++ b/lib/galaxy/schema/schema.py
@@ -1048,12 +1048,11 @@ class WorkflowSortByEnum(str, Enum):
     none = None
 
 
-class WorkflowIndexPayload(Model):
+class WorkflowIndexQueryPayload(Model):
     show_deleted: bool = False
     show_hidden: bool = False
     show_published: Optional[bool] = None
     show_shared: Optional[bool] = None
-    missing_tools: bool = False
     sort_by: Optional[WorkflowSortByEnum] = Field(title="Sort By", description="Sort workflows by this attribute")
     sort_desc: Optional[bool] = Field(
         title="Sort descending", description="Explicitly sort by descending if sort_by is specified."
diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
index df23c878b2c..97da931c766 100644
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -48,7 +48,6 @@ from galaxy.schema.schema import (
     ShareWithPayload,
     ShareWithStatus,
     SharingStatus,
-    WorkflowIndexPayload,
     WorkflowSortByEnum,
 )
 from galaxy.structured_app import StructuredApp
@@ -76,7 +75,10 @@ from galaxy.webapps.galaxy.services.invocations import (
     InvocationSerializationParams,
     InvocationsService,
 )
-from galaxy.webapps.galaxy.services.workflows import WorkflowsService
+from galaxy.webapps.galaxy.services.workflows import (
+    WorkflowIndexPayload,
+    WorkflowsService,
+)
 from galaxy.workflow.extract import extract_workflow
 from galaxy.workflow.modules import module_factory
 from galaxy.workflow.run import queue_invoke
diff --git a/lib/galaxy/webapps/galaxy/services/workflows.py b/lib/galaxy/webapps/galaxy/services/workflows.py
index d77d5d5ebec..52cf83c8145 100644
--- a/lib/galaxy/webapps/galaxy/services/workflows.py
+++ b/lib/galaxy/webapps/galaxy/services/workflows.py
@@ -7,46 +7,23 @@ from typing import (
     Tuple,
 )
 
-from sqlalchemy import (
-    and_,
-    desc,
-    false,
-    or_,
-    true,
-)
-from sqlalchemy.orm import joinedload
-
-from galaxy import (
-    exceptions,
-    model,
-    web,
-)
+from galaxy import web
 from galaxy.managers.context import ProvidesUserContext
 from galaxy.managers.workflows import (
     WorkflowContentsManager,
     WorkflowSerializer,
     WorkflowsManager,
 )
-from galaxy.schema.schema import WorkflowIndexPayload
+from galaxy.schema.schema import WorkflowIndexQueryPayload
 from galaxy.tool_shed.tool_shed_registry import Registry
-from galaxy.util.search import (
-    FilteredTerm,
-    parse_filters_structured,
-    RawTextTerm,
-)
 from galaxy.webapps.galaxy.services.base import ServiceBase
 from galaxy.webapps.galaxy.services.sharable import ShareableService
 
 log = logging.getLogger(__name__)
 
 
-INDEX_SEARCH_FILTERS = {
-    "name": "name",
-    "tag": "tag",
-    "n": "name",
-    "t": "tag",
-    "is": "is",
-}
+class WorkflowIndexPayload(WorkflowIndexQueryPayload):
+    missing_tools: bool = False
 
 
 class WorkflowsService(ServiceBase):
@@ -69,118 +46,10 @@ class WorkflowsService(ServiceBase):
         payload: WorkflowIndexPayload,
         include_total_count: bool = False,
     ) -> Tuple[List[Dict[str, Any]], Optional[int]]:
-        show_published = payload.show_published
-        show_hidden = payload.show_hidden
-        show_deleted = payload.show_deleted
-        missing_tools = payload.missing_tools
-        show_shared = payload.show_shared
-
-        if show_shared is None:
-            show_shared = not show_hidden and not show_deleted
-
-        if show_shared and show_deleted:
-            message = "show_shared and show_deleted cannot both be specified as true"
-            raise exceptions.RequestParameterInvalidException(message)
-        if show_shared and show_hidden:
-            message = "show_shared and show_hidden cannot both be specified as true"
-            raise exceptions.RequestParameterInvalidException(message)
-
-        rval = []
-        filters = [
-            model.StoredWorkflow.user == trans.user,
-        ]
         user = trans.user
-        if user and show_shared:
-            filters.append(model.StoredWorkflowUserShareAssociation.user == user)
-
-        if show_published or user is None and show_published is None:
-            filters.append((model.StoredWorkflow.published == true()))
-
-        query = trans.sa_session.query(model.StoredWorkflow)
-        if show_shared:
-            query = query.outerjoin(model.StoredWorkflow.users_shared_with)
-        query = query.outerjoin(model.StoredWorkflow.tags)
-
-        latest_workflow_load = joinedload("latest_workflow")
-        if not payload.skip_step_counts:
-            latest_workflow_load = latest_workflow_load.undefer("step_count")
-        latest_workflow_load = latest_workflow_load.lazyload("steps")
-
-        query = query.options(joinedload(model.StoredWorkflow.annotations))
-        query = query.options(latest_workflow_load)
-        query = query.filter(or_(*filters))
-        query = query.filter(model.StoredWorkflow.table.c.hidden == (true() if show_hidden else false()))
-        query = query.filter(model.StoredWorkflow.table.c.deleted == (true() if show_deleted else false()))
-        if payload.search:
-            search_query = payload.search
-            parsed_search = parse_filters_structured(search_query, INDEX_SEARCH_FILTERS)
-
-            def tag_filter(term_text: str, quoted: bool):
-                if ":" in term_text:
-                    key, value = term_text.rsplit(":", 1)
-                    if not quoted:
-                        return and_(
-                            model.StoredWorkflowTagAssociation.user_tname.ilike(key),
-                            model.StoredWorkflowTagAssociation.user_value.ilike(f"%{value}%"),
-                        )
-                    else:
-                        return and_(
-                            model.StoredWorkflowTagAssociation.user_tname == key,
-                            model.StoredWorkflowTagAssociation.user_value == value,
-                        )
-                else:
-                    if not quoted:
-                        return model.StoredWorkflowTagAssociation.user_tname.ilike(f"%{term_text}%")
-                    else:
-                        return model.StoredWorkflowTagAssociation.user_tname == term_text
-
-            def name_filter(text, quoted):
-                if not quoted:
-                    filter = model.StoredWorkflow.name.ilike(f"%{text}%")
-                else:
-                    filter = model.StoredWorkflow.name == text
-                return filter
-
-            for term in parsed_search.terms:
-                if isinstance(term, FilteredTerm):
-                    key = term.filter
-                    q = term.text
-                    if key == "tag":
-                        query = query.filter(tag_filter(term.text, term.quoted))
-                    elif key == "name":
-                        query = query.filter(name_filter(q, term.quoted))
-                    elif key == "is":
-                        if q == "published":
-                            query = query.filter(model.StoredWorkflow.published == true())
-                        elif q == "shared_with_me":
-                            if not show_shared:
-                                message = "Can only use tag is:shared_with_me if show_shared parameter also true."
-                                raise exceptions.RequestParameterInvalidException(message)
-                            query = query.filter(model.StoredWorkflowUserShareAssociation.user == user)
-                elif isinstance(term, RawTextTerm):
-                    query = query.filter(
-                        or_(
-                            name_filter(term.text, False),
-                            tag_filter(term.text, False),
-                        )
-                    )
-        if include_total_count:
-            total_matches = query.count()
-        else:
-            total_matches = None
-        if payload.sort_by is None:
-            if user:
-                query = query.order_by(desc(model.StoredWorkflow.user == user))
-            query = query.order_by(desc(model.StoredWorkflow.table.c.update_time))
-        else:
-            sort_column = getattr(model.StoredWorkflow, payload.sort_by)
-            if payload.sort_desc:
-                sort_column = sort_column.desc()
-            query = query.order_by(sort_column)
-        if payload.limit is not None:
-            query = query.limit(payload.limit)
-        if payload.offset is not None:
-            query = query.offset(payload.offset)
+        missing_tools = payload.missing_tools
+        query, total_matches = self._workflows_manager.index_query(trans, payload, include_total_count)
+        rval = []
         for wf in query.all():
             item = wf.to_dict(value_mapper={"id": trans.security.encode_id})
             encoded_id = trans.security.encode_id(wf.id)

From d2601426a42a37b1d9e87095990bf6e3ef1fbcf7 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 4 May 2022 11:21:11 -0400
Subject: [PATCH 5/6] index_filter_util to re-use filters from workflows in
 other index models.

---
 lib/galaxy/managers/workflows.py      | 46 +++++++++--------------
 lib/galaxy/model/index_filter_util.py | 53 +++++++++++++++++++++++++++
 2 files changed, 70 insertions(+), 29 deletions(-)
 create mode 100644 lib/galaxy/model/index_filter_util.py

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index cc9b4f6d139..96fcd06e33e 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -40,6 +40,11 @@ from galaxy import (
 from galaxy.job_execution.actions.post import ActionBox
 from galaxy.managers import sharable
 from galaxy.managers.context import ProvidesUserContext
+from galaxy.model.index_filter_util import (
+    raw_text_column_filter,
+    tag_filter,
+    text_column_filter,
+)
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.schema.schema import WorkflowIndexQueryPayload
 from galaxy.structured_app import MinimalManagerApp
@@ -154,40 +159,20 @@ class WorkflowsManager(sharable.SharableModelManager):
             search_query = payload.search
             parsed_search = parse_filters_structured(search_query, INDEX_SEARCH_FILTERS)
 
-            def tag_filter(term_text: str, quoted: bool):
-                if ":" in term_text:
-                    key, value = term_text.rsplit(":", 1)
-                    if not quoted:
-                        return and_(
-                            model.StoredWorkflowTagAssociation.user_tname.ilike(key),
-                            model.StoredWorkflowTagAssociation.user_value.ilike(f"%{value}%"),
-                        )
-                    else:
-                        return and_(
-                            model.StoredWorkflowTagAssociation.user_tname == key,
-                            model.StoredWorkflowTagAssociation.user_value == value,
-                        )
-                else:
-                    if not quoted:
-                        return model.StoredWorkflowTagAssociation.user_tname.ilike(f"%{term_text}%")
-                    else:
-                        return model.StoredWorkflowTagAssociation.user_tname == term_text
+            def w_tag_filter(term_text: str, quoted: bool):
+                return tag_filter(model.StoredWorkflowTagAssociation, term_text, quoted)
 
-            def name_filter(text, quoted):
-                if not quoted:
-                    filter = model.StoredWorkflow.name.ilike(f"%{text}%")
-                else:
-                    filter = model.StoredWorkflow.name == text
-                return filter
+            def name_filter(term):
+                return text_column_filter(model.StoredWorkflow.name, term)
 
             for term in parsed_search.terms:
                 if isinstance(term, FilteredTerm):
                     key = term.filter
                     q = term.text
                     if key == "tag":
-                        query = query.filter(tag_filter(term.text, term.quoted))
+                        query = query.filter(w_tag_filter(term.text, term.quoted))
                     elif key == "name":
-                        query = query.filter(name_filter(q, term.quoted))
+                        query = query.filter(name_filter(term))
                     elif key == "is":
                         if q == "published":
                             query = query.filter(model.StoredWorkflow.published == true())
@@ -198,9 +183,12 @@ class WorkflowsManager(sharable.SharableModelManager):
                             query = query.filter(model.StoredWorkflowUserShareAssociation.user == user)
                 elif isinstance(term, RawTextTerm):
                     query = query.filter(
-                        or_(
-                            name_filter(term.text, False),
-                            tag_filter(term.text, False),
+                        raw_text_column_filter(
+                            [
+                                model.StoredWorkflow.name,
+                                w_tag_filter(term.text, False),
+                            ],
+                            term,
                         )
                     )
         if include_total_count:
diff --git a/lib/galaxy/model/index_filter_util.py b/lib/galaxy/model/index_filter_util.py
new file mode 100644
index 00000000000..d148c996500
--- /dev/null
+++ b/lib/galaxy/model/index_filter_util.py
@@ -0,0 +1,53 @@
+"""Utility functions used to adapt galaxy.util.search to Galaxy model index queries."""
+from typing import (
+    List,
+    Union,
+)
+
+from sqlalchemy import (
+    and_,
+    or_,
+)
+from sqlalchemy.orm import InstrumentedAttribute
+from sqlalchemy.sql.expression import BinaryExpression
+
+from galaxy.util.search import (
+    FilteredTerm,
+    RawTextTerm,
+)
+
+
+def text_column_filter(column, term: FilteredTerm):
+    if term.quoted:
+        filter = column == term.text
+    else:
+        filter = column.ilike(f"%{term.text}%")
+    return filter
+
+
+RawTextSearchableT = Union[BinaryExpression, InstrumentedAttribute]
+
+
+def raw_text_column_filter(columns: List[RawTextSearchableT], term: RawTextTerm):
+    like_text = f"%{term.text}%"
+    return or_(*[c.ilike(like_text) if isinstance(c, InstrumentedAttribute) else c for c in columns])
+
+
+def tag_filter(assocation_model_class, term_text, quoted: bool = False):
+    if ":" in term_text:
+        key, value = term_text.rsplit(":", 1)
+        if not quoted:
+            return and_(
+                assocation_model_class.user_tname.ilike(key),
+                assocation_model_class.user_value.ilike(f"%{value}%"),
+            )
+        else:
+            return and_(
+                assocation_model_class.user_tname == key,
+                assocation_model_class.user_value == value,
+            )
+    else:
+        if not quoted:
+            return assocation_model_class.user_tname.ilike(f"%{term_text}%")
+        else:
+            return assocation_model_class.user_tname == term_text

From d2feecd4430561abe5d22830afaece73c19a7a0f Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Tue, 3 May 2022 14:48:47 -0400
Subject: [PATCH 6/6] Bugfix - allow filtering on multiple workflow tags at
 once.

---
 lib/galaxy/managers/workflows.py      | 12 +++++++---
 lib/galaxy_test/api/test_workflows.py | 33 +++++++++++++++++++++++++++
 2 files changed, 42 insertions(+), 3 deletions(-)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
index 96fcd06e33e..33a1b5a5676 100644
--- a/lib/galaxy/managers/workflows.py
+++ b/lib/galaxy/managers/workflows.py
@@ -27,6 +27,7 @@ from sqlalchemy import (
     true,
 )
 from sqlalchemy.orm import (
+    aliased,
     joinedload,
     Query,
     subqueryload,
@@ -160,7 +161,10 @@ class WorkflowsManager(sharable.SharableModelManager):
             parsed_search = parse_filters_structured(search_query, INDEX_SEARCH_FILTERS)
 
             def w_tag_filter(term_text: str, quoted: bool):
-                return tag_filter(model.StoredWorkflowTagAssociation, term_text, quoted)
+                nonlocal query
+                alias = aliased(model.StoredWorkflowTagAssociation)
+                query = query.outerjoin(model.StoredWorkflow.tags.of_type(alias))
+                return tag_filter(alias, term_text, quoted)
 
             def name_filter(term):
                 return text_column_filter(model.StoredWorkflow.name, term)
@@ -170,7 +174,8 @@ class WorkflowsManager(sharable.SharableModelManager):
                     key = term.filter
                     q = term.text
                     if key == "tag":
-                        query = query.filter(w_tag_filter(term.text, term.quoted))
+                        tf = w_tag_filter(term.text, term.quoted)
+                        query = query.filter(tf)
                     elif key == "name":
                         query = query.filter(name_filter(term))
                     elif key == "is":
@@ -182,11 +187,12 @@ class WorkflowsManager(sharable.SharableModelManager):
                                 raise exceptions.RequestParameterInvalidException(message)
                             query = query.filter(model.StoredWorkflowUserShareAssociation.user == user)
                 elif isinstance(term, RawTextTerm):
+                    tf = w_tag_filter(term.text, False)
                     query = query.filter(
                         raw_text_column_filter(
                             [
                                 model.StoredWorkflow.name,
-                                w_tag_filter(term.text, False),
+                                tf,
                             ],
                             term,
                         )
diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
index fbcb2e5a76f..935719c08d4 100644
--- a/lib/galaxy_test/api/test_workflows.py
+++ b/lib/galaxy_test/api/test_workflows.py
@@ -493,6 +493,39 @@ class WorkflowsApiTestCase(BaseWorkflowsApiTestCase, ChangeDatatypeTestCase):
         index_ids = self.workflow_populator.index_ids(search="tag:moocowatag")
         assert workflow_id_1 in index_ids
 
+    def test_index_search_tags_multiple(self):
+        name1 = self.dataset_populator.get_random_name()
+        name2 = self.dataset_populator.get_random_name()
+        name3 = self.dataset_populator.get_random_name()
+        workflow_id_1 = self.workflow_populator.simple_workflow(name1)
+        workflow_id_2 = self.workflow_populator.simple_workflow(name2)
+        workflow_id_3 = self.workflow_populator.simple_workflow(name3)
+        self.workflow_populator.set_tags(workflow_id_1, ["multipletagfilter1", "multipletagfilter2", "decoy1"])
+        self.workflow_populator.set_tags(workflow_id_2, ["multipletagfilter1", "decoy2"])
+        self.workflow_populator.set_tags(workflow_id_3, ["multipletagfilter2", "decoy3"])
+
+        for search in ["multipletagfilter1", "tag:ipletagfilter1", "tag:'multipletagfilter1'"]:
+            index_ids = self.workflow_populator.index_ids(search=search)
+            assert workflow_id_1 in index_ids
+            assert workflow_id_2 in index_ids
+            assert workflow_id_3 not in index_ids
+
+        for search in ["multipletagfilter2", "tag:ipletagfilter2", "tag:'multipletagfilter2'"]:
+            index_ids = self.workflow_populator.index_ids(search=search)
+            assert workflow_id_1 in index_ids
+            assert workflow_id_2 not in index_ids
+            assert workflow_id_3 in index_ids
+
+        for search in [
+            "multipletagfilter2 multipletagfilter1",
+            "tag:filter2 tag:tagfilter1",
+            "tag:'multipletagfilter2' tag:'multipletagfilter1'",
+        ]:
+            index_ids = self.workflow_populator.index_ids(search=search)
+            assert workflow_id_1 in index_ids
+            assert workflow_id_2 not in index_ids
+            assert workflow_id_3 not in index_ids
+
     def test_search_casing(self):
         name1, name2 = (
             self.dataset_populator.get_random_name().upper(),