From 364574730a36928f3d11033d30424c15f98c4cec Mon Sep 17 00:00:00 2001
From: Christopher Morrison <chris.morrison@alleninstitute.org>
Date: Wed, 20 Nov 2024 14:51:12 -0800
Subject: [PATCH] Download and use new manifest.

---
 ...ng_Aging_Mouse_10x_snRNASeq_tutorial.ipynb | 51 ++++++++++++++-----
 ...e_clustering_analysis_and_annotation.ipynb | 48 +++++++++++++----
 2 files changed, 76 insertions(+), 23 deletions(-)

diff --git a/notebooks/Zeng_Aging_Mouse_10x_snRNASeq_tutorial.ipynb b/notebooks/Zeng_Aging_Mouse_10x_snRNASeq_tutorial.ipynb
index ff3fe989..d9d8964a 100644
--- a/notebooks/Zeng_Aging_Mouse_10x_snRNASeq_tutorial.ipynb
+++ b/notebooks/Zeng_Aging_Mouse_10x_snRNASeq_tutorial.ipynb
@@ -42,14 +42,6 @@
    "execution_count": 2,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/allen/aibs/informatics/chris.morrison/miniconda/envs/abc_atlas_access/lib/python3.11/site-packages/abc_atlas_access/abc_atlas_cache/cloud_cache.py:470: MissingLocalManifestWarning: This cache directory appears to contain data files, but it has no record of what those files are. Unless running as a LocalCache, files will be re-downloaded.\n",
-      "  warnings.warn(msg, MissingLocalManifestWarning)\n"
-     ]
-    },
     {
      "data": {
       "text/plain": [
@@ -62,9 +54,8 @@
     }
    ],
    "source": [
-    "# download_base = Path('../../data/abc_atlas')\n",
-    "download_base = Path('/allen/programs/celltypes/workgroups/rnaseqanalysis/lydian/ABC_handoff')\n",
-    "abc_cache = AbcProjectCache.from_local_cache(download_base)\n",
+    "download_base = Path('../../data/abc_atlas')\n",
+    "abc_cache = AbcProjectCache.from_cache_dir(download_base)\n",
     "\n",
     "abc_cache.current_manifest"
    ]
@@ -428,6 +419,13 @@
    "execution_count": 4,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "gene.csv: 100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 2.30M/2.30M [00:00<00:00, 4.56MMB/s]"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -435,6 +433,13 @@
       "Number of genes =  32285\n"
      ]
     },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
@@ -551,7 +556,15 @@
    "cell_type": "code",
    "execution_count": 5,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "example_genes_all_cells_expression.csv: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 77.0M/77.0M [00:03<00:00, 22.0MMB/s]\n"
+     ]
+    }
+   ],
    "source": [
     "gene_names = ['Slc17a7', 'Slc17a6', 'Slc17a8', 'Slc32a1', 'Slc6a5', 'Slc6a3', 'Slc6a4', 'Tac2']\n",
     "example_genes = abc_cache.get_metadata_dataframe(\n",
@@ -1048,6 +1061,13 @@
    "execution_count": 14,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "aging_degenes.csv: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.13M/1.13M [00:00<00:00, 6.69MMB/s]\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
@@ -1212,6 +1232,13 @@
    "execution_count": 15,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "cluster_mapping_pivot.csv: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 118k/118k [00:00<00:00, 854kMB/s]\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
diff --git a/notebooks/Zeng_Aging_Mouse_clustering_analysis_and_annotation.ipynb b/notebooks/Zeng_Aging_Mouse_clustering_analysis_and_annotation.ipynb
index 162405b6..882cad05 100644
--- a/notebooks/Zeng_Aging_Mouse_clustering_analysis_and_annotation.ipynb
+++ b/notebooks/Zeng_Aging_Mouse_clustering_analysis_and_annotation.ipynb
@@ -44,14 +44,6 @@
    "execution_count": 2,
    "metadata": {},
    "outputs": [
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "/allen/aibs/informatics/chris.morrison/miniconda/envs/abc_atlas_access/lib/python3.11/site-packages/abc_atlas_access/abc_atlas_cache/cloud_cache.py:470: MissingLocalManifestWarning: This cache directory appears to contain data files, but it has no record of what those files are. Unless running as a LocalCache, files will be re-downloaded.\n",
-      "  warnings.warn(msg, MissingLocalManifestWarning)\n"
-     ]
-    },
     {
      "data": {
       "text/plain": [
@@ -64,9 +56,8 @@
     }
    ],
    "source": [
-    "# download_base = Path('../../data/abc_atlas')\n",
-    "download_base = Path('/allen/programs/celltypes/workgroups/rnaseqanalysis/lydian/ABC_handoff')\n",
-    "abc_cache = AbcProjectCache.from_local_cache(download_base)\n",
+    "download_base = Path('../../data/abc_atlas')\n",
+    "abc_cache = AbcProjectCache.from_cache_dir(download_base)\n",
     "\n",
     "abc_cache.current_manifest"
    ]
@@ -144,6 +135,13 @@
    "execution_count": 5,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "cell_metadata.csv: 100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 423M/423M [00:18<00:00, 22.3MMB/s]\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
@@ -518,6 +516,13 @@
    "execution_count": 8,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "cell_annotation_colors.csv: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 76.1M/76.1M [00:03<00:00, 22.0MMB/s]\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
@@ -1132,6 +1137,13 @@
    "execution_count": 15,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "cluster.csv: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 174k/174k [00:00<00:00, 1.17MMB/s]\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
@@ -1835,6 +1847,13 @@
    "execution_count": 21,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "cell_cluster_mapping_annotations.csv: 100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 173M/173M [00:07<00:00, 22.7MMB/s]\n"
+     ]
+    },
     {
      "data": {
       "text/html": [
@@ -2195,6 +2214,13 @@
    "execution_count": 27,
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "cluster_mapping.csv: 100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 405k/405k [00:00<00:00, 2.79MMB/s]\n"
+     ]
+    },
     {
      "data": {
       "text/html": [