From 5272dfab8129bfff05d8ecee4ddfa57c5fa8672a Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 12 Jan 2024 14:00:20 -0500
Subject: [PATCH 1/7] add associations tsv download to frontend

---
 frontend/src/api/associations.ts              |  2 ++
 frontend/src/pages/node/AssociationsTable.vue | 15 ++++++++-------
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/frontend/src/api/associations.ts b/frontend/src/api/associations.ts
index dc2f814de..e6f1955f0 100644
--- a/frontend/src/api/associations.ts
+++ b/frontend/src/api/associations.ts
@@ -10,6 +10,7 @@ export const getAssociations = async (
   limit = 10,
   search?: string,
   sort: Sort = null,
+  download?: "tsv" | "json",
 ) => {
   /** make query params */
   const params = {
@@ -19,6 +20,7 @@ export const getAssociations = async (
     sort: sort
       ? `${sort.key} ${sort.direction === "up" ? "asc" : "desc"}`
       : null,
+    ...(download && { format: download }),
   };
 
   /** make query */
diff --git a/frontend/src/pages/node/AssociationsTable.vue b/frontend/src/pages/node/AssociationsTable.vue
index bc5df3448..2eb08339f 100644
--- a/frontend/src/pages/node/AssociationsTable.vue
+++ b/frontend/src/pages/node/AssociationsTable.vue
@@ -108,7 +108,6 @@ import type { Cols, Sort } from "@/components/AppTable.vue";
 import { snackbar } from "@/components/TheSnackbar.vue";
 import { getBreadcrumbs } from "@/pages/node/AssociationsSummary.vue";
 import { useQuery } from "@/util/composables";
-import { downloadJson } from "@/util/download";
 
 type Props = {
   /** current node */
@@ -276,8 +275,8 @@ const {
 
 /** download table data */
 async function download() {
-  /** max rows to try to query */
-  const max = 100;
+  /** max supported rows to query */
+  const max = 500;
   const total = associations.value.total;
 
   /** warn user */
@@ -285,17 +284,19 @@ async function download() {
     `Downloading data for ${total > max ? "first " : ""}${Math.min(
       total,
       max,
-    )} table entries.` + (total >= 100 ? " This may take a minute." : ""),
+    )} table rows. This may take a minute.`,
   );
 
-  /** attempt to request all rows */
-  const response = await getAssociations(
+  /** download as many rows as possible */
+  await getAssociations(
     props.node.id,
     props.category.id,
     0,
     max,
+    search.value,
+    sort.value,
+    "tsv",
   );
-  downloadJson(response, "associations");
 }
 
 /** get associations when category or table state changes */

From 950c3acfcd7057921cf56a5cc163b41128d987a6 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 12 Jan 2024 14:04:35 -0500
Subject: [PATCH 2/7] add download flag

---
 frontend/src/api/associations.ts            | 2 +-
 frontend/src/pages/node/SectionOverview.vue | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/frontend/src/api/associations.ts b/frontend/src/api/associations.ts
index e6f1955f0..4d60fbf52 100644
--- a/frontend/src/api/associations.ts
+++ b/frontend/src/api/associations.ts
@@ -20,7 +20,7 @@ export const getAssociations = async (
     sort: sort
       ? `${sort.key} ${sort.direction === "up" ? "asc" : "desc"}`
       : null,
-    ...(download && { format: download }),
+    ...(download && { download: true, format: download }),
   };
 
   /** make query */
diff --git a/frontend/src/pages/node/SectionOverview.vue b/frontend/src/pages/node/SectionOverview.vue
index c89b3f942..75096575a 100644
--- a/frontend/src/pages/node/SectionOverview.vue
+++ b/frontend/src/pages/node/SectionOverview.vue
@@ -144,7 +144,6 @@
 </template>
 
 <script setup lang="ts">
-import type { info } from "console";
 import { computed } from "vue";
 import { omit } from "lodash";
 import type { Node } from "@/api/model";

From 295227e1ecbb1a78fad2ee713a216f1b931f8011 Mon Sep 17 00:00:00 2001
From: glass-ships <glass.ships@outlook.com>
Date: Fri, 12 Jan 2024 15:25:28 -0700
Subject: [PATCH 3/7] add download flag for assoc table

---
 backend/src/monarch_py/api/entity.py | 21 ++++++++++++++++++++-
 frontend/src/api/associations.ts     |  1 -
 2 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/backend/src/monarch_py/api/entity.py b/backend/src/monarch_py/api/entity.py
index 500f56897..353fd119b 100644
--- a/backend/src/monarch_py/api/entity.py
+++ b/backend/src/monarch_py/api/entity.py
@@ -1,13 +1,15 @@
+from io import StringIO
 from typing import List, Union
 
 from fastapi import APIRouter, Depends, HTTPException, Path, Query
+from fastapi.responses import StreamingResponse
 
 from monarch_py.api.additional_models import PaginationParams
 from monarch_py.api.config import solr
 from monarch_py.api.additional_models import OutputFormat
 from monarch_py.datamodels.model import AssociationTableResults, Node
 from monarch_py.datamodels.category_enums import AssociationCategory
-from monarch_py.utils.format_utils import to_tsv
+from monarch_py.utils.format_utils import to_json, to_tsv
 
 router = APIRouter(tags=["entity"], responses={404: {"description": "Not Found"}})
 
@@ -69,6 +71,11 @@ def _association_table(
         title="Output format for the response",
         examples=["json", "tsv"],
     ),
+    download=Query(
+        default=False,
+        title="Download the results as a file",
+        examples=[True, False],
+    ),
 ) -> Union[AssociationTableResults, str]:
     """
     Retrieves association table data for a given entity and association type
@@ -85,6 +92,18 @@ def _association_table(
     response = solr().get_association_table(
         entity=id, category=category.value, q=query, sort=sort, offset=pagination.offset, limit=pagination.limit
     )
+    if download:
+        string_response = (
+            to_tsv(response, print_output=False)
+            if format == OutputFormat.tsv
+            else to_json(response, print_output=False)
+        )
+        stream = StringIO(string_response)
+        response = StreamingResponse(
+            stream, media_type="text/csv" if format == OutputFormat.tsv else "application/json"
+        )
+        response.headers["Content-Disposition"] = f"attachment; filename=assoc-table-{id}.{format.value}"
+        return response
     if format == OutputFormat.json:
         return response
     elif format == OutputFormat.tsv:
diff --git a/frontend/src/api/associations.ts b/frontend/src/api/associations.ts
index 4d60fbf52..60809f702 100644
--- a/frontend/src/api/associations.ts
+++ b/frontend/src/api/associations.ts
@@ -26,7 +26,6 @@ export const getAssociations = async (
   /** make query */
   const url = `${apiUrl}/entity/${nodeId}/${associationCategory}`;
   const response = await request<AssociationTableResults>(url, params);
-
   return response;
 };
 

From 3a31896244bb0c33b1007e1d4ee7936654192cdf Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 12 Jan 2024 18:19:50 -0500
Subject: [PATCH 4/7] fix download

---
 frontend/src/api/associations.ts              | 31 +++++++++++++++++--
 frontend/src/api/index.ts                     |  6 +++-
 frontend/src/pages/node/AssociationsTable.vue | 23 +++++++-------
 3 files changed, 45 insertions(+), 15 deletions(-)

diff --git a/frontend/src/api/associations.ts b/frontend/src/api/associations.ts
index 4d60fbf52..7c8a4d6c6 100644
--- a/frontend/src/api/associations.ts
+++ b/frontend/src/api/associations.ts
@@ -10,7 +10,6 @@ export const getAssociations = async (
   limit = 10,
   search?: string,
   sort: Sort = null,
-  download?: "tsv" | "json",
 ) => {
   /** make query params */
   const params = {
@@ -20,7 +19,6 @@ export const getAssociations = async (
     sort: sort
       ? `${sort.key} ${sort.direction === "up" ? "asc" : "desc"}`
       : null,
-    ...(download && { download: true, format: download }),
   };
 
   /** make query */
@@ -30,8 +28,37 @@ export const getAssociations = async (
   return response;
 };
 
+/** max rows supported in single download */
+export const maxDownload = 500;
+
+/** get associations between a node and a category */
+export const downloadAssociations = async (
+  nodeId = "",
+  associationCategory = "",
+  search?: string,
+  sort: Sort = null,
+) => {
+  /** make query params */
+  const params = {
+    limit: maxDownload,
+    query: search || "",
+    sort: sort
+      ? `${sort.key} ${sort.direction === "up" ? "asc" : "desc"}`
+      : null,
+    download: true,
+    format: "tsv",
+  };
+
+  /** make query */
+  const url = `${apiUrl}/entity/${nodeId}/${associationCategory}`;
+  await request(url, params, {}, "text", true);
+};
+
 /** get top few associations */
 export const getTopAssociations = async (
   nodeId = "",
   associationCategory = "",
 ) => await getAssociations(nodeId, associationCategory, 0, 5);
+
+/** maximum associations downloadable at once */
+export const downloadLimit = 500;
diff --git a/frontend/src/api/index.ts b/frontend/src/api/index.ts
index 1824fd95d..b774fac87 100644
--- a/frontend/src/api/index.ts
+++ b/frontend/src/api/index.ts
@@ -72,10 +72,12 @@ export const request = async <Response>(
    * { id: [1,2,3] } -> ?id=1&id=2&id=3
    */
   params: Params = {},
-  /** fetch options */
+  /** fetch/request options */
   options: RequestInit = {},
   /** parse response mode */
   parse: "text" | "json" = "json",
+  /** whether open request url in new tab */
+  newTab = false,
 ): Promise<Response> => {
   /** get string of url parameters/options */
   const paramsObject = new URLSearchParams();
@@ -96,6 +98,8 @@ export const request = async <Response>(
   const paramsString = "?" + paramsObject.toString();
   const url = path + paramsString;
 
+  if (newTab) window.open(url);
+
   /** make request object */
   const request = new Request(url, options);
 
diff --git a/frontend/src/pages/node/AssociationsTable.vue b/frontend/src/pages/node/AssociationsTable.vue
index 2eb08339f..2845d06d3 100644
--- a/frontend/src/pages/node/AssociationsTable.vue
+++ b/frontend/src/pages/node/AssociationsTable.vue
@@ -93,7 +93,11 @@
 
 <script setup lang="ts">
 import { computed, onMounted, ref, watch } from "vue";
-import { getAssociations } from "@/api/associations";
+import {
+  downloadAssociations,
+  getAssociations,
+  maxDownload,
+} from "@/api/associations";
 import { getCategoryLabel } from "@/api/categories";
 import {
   AssociationDirectionEnum,
@@ -275,27 +279,22 @@ const {
 
 /** download table data */
 async function download() {
-  /** max supported rows to query */
-  const max = 500;
-  const total = associations.value.total;
-
   /** warn user */
   snackbar(
-    `Downloading data for ${total > max ? "first " : ""}${Math.min(
-      total,
-      max,
+    `Downloading data for ${
+      associations.value.total > maxDownload ? "first " : ""
+    }${Math.min(
+      associations.value.total,
+      maxDownload,
     )} table rows. This may take a minute.`,
   );
 
   /** download as many rows as possible */
-  await getAssociations(
+  await downloadAssociations(
     props.node.id,
     props.category.id,
-    0,
-    max,
     search.value,
     sort.value,
-    "tsv",
   );
 }
 

From f2ab3449a688533588db8357afe10ee110afb589 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 12 Jan 2024 18:22:00 -0500
Subject: [PATCH 5/7] remove space

---
 frontend/src/api/associations.ts | 1 -
 1 file changed, 1 deletion(-)

diff --git a/frontend/src/api/associations.ts b/frontend/src/api/associations.ts
index 7c8a4d6c6..1d2e7d4d7 100644
--- a/frontend/src/api/associations.ts
+++ b/frontend/src/api/associations.ts
@@ -24,7 +24,6 @@ export const getAssociations = async (
   /** make query */
   const url = `${apiUrl}/entity/${nodeId}/${associationCategory}`;
   const response = await request<AssociationTableResults>(url, params);
-
   return response;
 };
 

From 0055f9c13d90d4e3e6b6cd7a4ece48e2dbd64876 Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 12 Jan 2024 18:22:09 -0500
Subject: [PATCH 6/7] readd space

---
 frontend/src/api/associations.ts | 1 +
 1 file changed, 1 insertion(+)

diff --git a/frontend/src/api/associations.ts b/frontend/src/api/associations.ts
index 1d2e7d4d7..619ca5800 100644
--- a/frontend/src/api/associations.ts
+++ b/frontend/src/api/associations.ts
@@ -24,6 +24,7 @@ export const getAssociations = async (
   /** make query */
   const url = `${apiUrl}/entity/${nodeId}/${associationCategory}`;
   const response = await request<AssociationTableResults>(url, params);
+  
   return response;
 };
 

From 8aa2932d1f6d9f8cf57ce7818e61b8cfcdc7deed Mon Sep 17 00:00:00 2001
From: Vincent Rubinetti <vince.rubinetti@gmail.com>
Date: Fri, 12 Jan 2024 18:24:27 -0500
Subject: [PATCH 7/7] fix lint

---
 frontend/src/api/associations.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/frontend/src/api/associations.ts b/frontend/src/api/associations.ts
index 619ca5800..7c8a4d6c6 100644
--- a/frontend/src/api/associations.ts
+++ b/frontend/src/api/associations.ts
@@ -24,7 +24,7 @@ export const getAssociations = async (
   /** make query */
   const url = `${apiUrl}/entity/${nodeId}/${associationCategory}`;
   const response = await request<AssociationTableResults>(url, params);
-  
+
   return response;
 };