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Update files.ipynb with clean execution outputs
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‎examples/files.ipynb‎

Lines changed: 110 additions & 31 deletions
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@@ -23,7 +23,14 @@
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{
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"cell_type": "code",
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"execution_count": 1,
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"metadata": {},
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:48.226452Z",
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"iopub.status.busy": "2026-04-02T11:23:48.226125Z",
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"iopub.status.idle": "2026-04-02T11:23:58.272174Z",
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"shell.execute_reply": "2026-04-02T11:23:58.270996Z"
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}
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},
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"outputs": [
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{
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"name": "stderr",
@@ -38,7 +45,13 @@
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"output_type": "stream",
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"text": [
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"Authentication successful.\n",
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"DatabaseAccessor initialized. Connections will be created on first access.\n",
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"DatabaseAccessor initialized. Connections will be created on first access.\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"TMS credentials ready: frontera, stampede3, ls6\n"
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]
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}
@@ -61,7 +74,14 @@
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{
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"cell_type": "code",
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"execution_count": 2,
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"metadata": {},
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:58.277168Z",
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"iopub.status.busy": "2026-04-02T11:23:58.276640Z",
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"iopub.status.idle": "2026-04-02T11:23:58.281010Z",
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"shell.execute_reply": "2026-04-02T11:23:58.280430Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
@@ -81,7 +101,14 @@
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{
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"cell_type": "code",
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"execution_count": 3,
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"metadata": {},
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:58.283209Z",
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"iopub.status.busy": "2026-04-02T11:23:58.283045Z",
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"iopub.status.idle": "2026-04-02T11:23:58.285824Z",
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"shell.execute_reply": "2026-04-02T11:23:58.285459Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
@@ -101,7 +128,14 @@
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{
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"cell_type": "code",
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"execution_count": 4,
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"metadata": {},
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:58.287671Z",
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"iopub.status.busy": "2026-04-02T11:23:58.287484Z",
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"iopub.status.idle": "2026-04-02T11:23:58.289812Z",
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"shell.execute_reply": "2026-04-02T11:23:58.289503Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
@@ -121,7 +155,14 @@
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{
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"cell_type": "code",
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"execution_count": 5,
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"metadata": {},
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:58.291487Z",
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"iopub.status.busy": "2026-04-02T11:23:58.291345Z",
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"iopub.status.idle": "2026-04-02T11:23:58.293263Z",
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"shell.execute_reply": "2026-04-02T11:23:58.292965Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
@@ -141,7 +182,14 @@
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{
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"cell_type": "code",
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"execution_count": 6,
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"metadata": {},
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:58.294816Z",
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"iopub.status.busy": "2026-04-02T11:23:58.294673Z",
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"iopub.status.idle": "2026-04-02T11:23:58.574276Z",
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"shell.execute_reply": "2026-04-02T11:23:58.573185Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
@@ -168,34 +216,38 @@
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{
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"cell_type": "code",
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"execution_count": 7,
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"metadata": {},
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:58.577503Z",
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"iopub.status.busy": "2026-04-02T11:23:58.577281Z",
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"iopub.status.idle": "2026-04-02T11:23:58.992222Z",
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"shell.execute_reply": "2026-04-02T11:23:58.991054Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Translated '/CommunityData/' to 'tapis://designsafe.storage.community/'\n",
178-
"Listing files in system 'designsafe.storage.community' at path ''...\n"
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"Listing files in system 'designsafe.storage.community' at path '/'...\n"
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]
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},
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{
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"ename": "FileOperationError",
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"evalue": "Tapis file listing failed for 'tapis://designsafe.storage.community/': message: path is a required argument and cannot be None.",
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"output_type": "error",
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"traceback": [
186-
"\u001b[31m---------------------------------------------------------------------------\u001b[39m",
187-
"\u001b[31mInvalidInputError\u001b[39m Traceback (most recent call last)",
188-
"\u001b[36mFile \u001b[39m\u001b[32m~/dev/DesignSafe/Dapi-Tapis/dapi/dapi/files.py:548\u001b[39m, in \u001b[36mlist_files\u001b[39m\u001b[34m(t, remote_uri, limit, offset)\u001b[39m\n\u001b[32m 547\u001b[39m encoded_path = _safe_quote(path)\n\u001b[32m--> \u001b[39m\u001b[32m548\u001b[39m results = \u001b[43mt\u001b[49m\u001b[43m.\u001b[49m\u001b[43mfiles\u001b[49m\u001b[43m.\u001b[49m\u001b[43mlistFiles\u001b[49m\u001b[43m(\u001b[49m\n\u001b[32m 549\u001b[39m \u001b[43m \u001b[49m\u001b[43msystemId\u001b[49m\u001b[43m=\u001b[49m\u001b[43msystem_id\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mpath\u001b[49m\u001b[43m=\u001b[49m\u001b[43mencoded_path\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mlimit\u001b[49m\u001b[43m=\u001b[49m\u001b[43mlimit\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43moffset\u001b[49m\u001b[43m=\u001b[49m\u001b[43moffset\u001b[49m\n\u001b[32m 550\u001b[39m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 551\u001b[39m \u001b[38;5;28mprint\u001b[39m(\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[33mFound \u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mlen\u001b[39m(results)\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m items.\u001b[39m\u001b[33m\"\u001b[39m)\n",
189-
"\u001b[36mFile \u001b[39m\u001b[32m~/dev/DesignSafe/Dapi-Tapis/dapi/.venv/lib/python3.13/site-packages/tapipy/util.py:152\u001b[39m, in \u001b[36mretriable.<locals>.wrapper\u001b[39m\u001b[34m(self, _config, *args, **kwargs)\u001b[39m\n\u001b[32m 150\u001b[39m \u001b[38;5;28;01mcontinue\u001b[39;00m\n\u001b[32m--> \u001b[39m\u001b[32m152\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m exception\n\u001b[32m 154\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m exception\n",
190-
"\u001b[36mFile \u001b[39m\u001b[32m~/dev/DesignSafe/Dapi-Tapis/dapi/.venv/lib/python3.13/site-packages/tapipy/util.py:138\u001b[39m, in \u001b[36mretriable.<locals>.wrapper\u001b[39m\u001b[34m(self, _config, *args, **kwargs)\u001b[39m\n\u001b[32m 137\u001b[39m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[32m--> \u001b[39m\u001b[32m138\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mop__call__\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 139\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n",
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"\u001b[36mFile \u001b[39m\u001b[32m~/dev/DesignSafe/Dapi-Tapis/dapi/.venv/lib/python3.13/site-packages/tapipy/tapis.py:1024\u001b[39m, in \u001b[36mOperation.__call__\u001b[39m\u001b[34m(self, **kwargs)\u001b[39m\n\u001b[32m 1023\u001b[39m \u001b[38;5;28;01mif\u001b[39;00m param.get(\u001b[33m\"\u001b[39m\u001b[33mrequired\u001b[39m\u001b[33m\"\u001b[39m) \u001b[38;5;129;01mand\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m p_val:\n\u001b[32m-> \u001b[39m\u001b[32m1024\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m errors.InvalidInputError(msg=\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mparam[\u001b[33m'\u001b[39m\u001b[33mname\u001b[39m\u001b[33m'\u001b[39m]\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m is a required argument and cannot be None.\u001b[39m\u001b[33m\"\u001b[39m)\n\u001b[32m 1025\u001b[39m \u001b[38;5;66;03m# replace the parameter in the path template with the parameter value\u001b[39;00m\n",
192-
"\u001b[31mInvalidInputError\u001b[39m: message: path is a required argument and cannot be None.",
193-
"\nThe above exception was the direct cause of the following exception:\n",
194-
"\u001b[31mFileOperationError\u001b[39m Traceback (most recent call last)",
195-
"\u001b[36mCell\u001b[39m\u001b[36m \u001b[39m\u001b[32mIn[7]\u001b[39m\u001b[32m, line 3\u001b[39m\n\u001b[32m 1\u001b[39m \u001b[38;5;66;03m# List files in CommunityData\u001b[39;00m\n\u001b[32m 2\u001b[39m uri = ds.files.to_uri(\u001b[33m\"\u001b[39m\u001b[33m/CommunityData/\u001b[39m\u001b[33m\"\u001b[39m)\n\u001b[32m----> \u001b[39m\u001b[32m3\u001b[39m files = \u001b[43mds\u001b[49m\u001b[43m.\u001b[49m\u001b[43mfiles\u001b[49m\u001b[43m.\u001b[49m\u001b[43mlist\u001b[49m\u001b[43m(\u001b[49m\u001b[43muri\u001b[49m\u001b[43m)\u001b[49m\n\u001b[32m 4\u001b[39m \u001b[38;5;28;01mfor\u001b[39;00m f \u001b[38;5;129;01min\u001b[39;00m files[:\u001b[32m10\u001b[39m]:\n\u001b[32m 5\u001b[39m \u001b[38;5;28mprint\u001b[39m(\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mf.name\u001b[38;5;132;01m:\u001b[39;00m\u001b[33m50s\u001b[39m\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m \u001b[39m\u001b[38;5;132;01m{\u001b[39;00mf.type\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m\"\u001b[39m)\n",
196-
"\u001b[36mFile \u001b[39m\u001b[32m~/dev/DesignSafe/Dapi-Tapis/dapi/dapi/client.py:250\u001b[39m, in \u001b[36mFileMethods.list\u001b[39m\u001b[34m(self, *args, **kwargs)\u001b[39m\n\u001b[32m 235\u001b[39m \u001b[38;5;28;01mdef\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34mlist\u001b[39m(\u001b[38;5;28mself\u001b[39m, *args, **kwargs) -> List[Tapis]:\n\u001b[32m 236\u001b[39m \u001b[38;5;250m \u001b[39m\u001b[33;03m\"\"\"List files and directories in a Tapis storage system path.\u001b[39;00m\n\u001b[32m 237\u001b[39m \n\u001b[32m 238\u001b[39m \u001b[33;03m This is a convenience wrapper around files_module.list_files().\u001b[39;00m\n\u001b[32m (...)\u001b[39m\u001b[32m 248\u001b[39m \u001b[33;03m FileOperationError: If the listing operation fails.\u001b[39;00m\n\u001b[32m 249\u001b[39m \u001b[33;03m \"\"\"\u001b[39;00m\n\u001b[32m--> \u001b[39m\u001b[32m250\u001b[39m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[43mfiles_module\u001b[49m\u001b[43m.\u001b[49m\u001b[43mlist_files\u001b[49m\u001b[43m(\u001b[49m\u001b[38;5;28;43mself\u001b[39;49m\u001b[43m.\u001b[49m\u001b[43m_tapis\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43margs\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m*\u001b[49m\u001b[43m*\u001b[49m\u001b[43mkwargs\u001b[49m\u001b[43m)\u001b[49m\n",
197-
"\u001b[36mFile \u001b[39m\u001b[32m~/dev/DesignSafe/Dapi-Tapis/dapi/dapi/files.py:557\u001b[39m, in \u001b[36mlist_files\u001b[39m\u001b[34m(t, remote_uri, limit, offset)\u001b[39m\n\u001b[32m 555\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m FileOperationError(\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[33mRemote path not found at \u001b[39m\u001b[33m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mremote_uri\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m'\u001b[39m\u001b[33m\"\u001b[39m) \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01me\u001b[39;00m\n\u001b[32m 556\u001b[39m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[32m--> \u001b[39m\u001b[32m557\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m FileOperationError(\n\u001b[32m 558\u001b[39m \u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[33mTapis file listing failed for \u001b[39m\u001b[33m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mremote_uri\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m'\u001b[39m\u001b[33m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00me\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m\"\u001b[39m\n\u001b[32m 559\u001b[39m ) \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01me\u001b[39;00m\n\u001b[32m 560\u001b[39m \u001b[38;5;28;01mexcept\u001b[39;00m (\u001b[38;5;167;01mValueError\u001b[39;00m, \u001b[38;5;167;01mException\u001b[39;00m) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[32m 561\u001b[39m \u001b[38;5;28;01mraise\u001b[39;00m FileOperationError(\u001b[33mf\u001b[39m\u001b[33m\"\u001b[39m\u001b[33mFailed to list files at \u001b[39m\u001b[33m'\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mremote_uri\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m'\u001b[39m\u001b[33m: \u001b[39m\u001b[38;5;132;01m{\u001b[39;00me\u001b[38;5;132;01m}\u001b[39;00m\u001b[33m\"\u001b[39m) \u001b[38;5;28;01mfrom\u001b[39;00m\u001b[38;5;250m \u001b[39m\u001b[34;01me\u001b[39;00m\n",
198-
"\u001b[31mFileOperationError\u001b[39m: Tapis file listing failed for 'tapis://designsafe.storage.community/': message: path is a required argument and cannot be None."
237+
"name": "stdout",
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"output_type": "stream",
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"text": [
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"Found 30 items.\n",
241+
"- READ ME - How to contribute to Community Data dir\n",
242+
".Trash dir\n",
243+
"app_examples dir\n",
244+
"CERA dir\n",
245+
"COSMOS_WCEE_2024_competition dir\n",
246+
"dapi dir\n",
247+
"DesignSafe_QuakeCoRE CI Workshop dir\n",
248+
"Education Resources dir\n",
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"geoclaw dir\n",
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"GIS_workshop dir\n"
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]
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}
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],
@@ -210,14 +262,27 @@
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{
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"cell_type": "code",
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"execution_count": 8,
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"metadata": {},
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:58.996165Z",
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"iopub.status.busy": "2026-04-02T11:23:58.995871Z",
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"iopub.status.idle": "2026-04-02T11:23:59.845844Z",
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"shell.execute_reply": "2026-04-02T11:23:59.844371Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Translated '/MyProjects/PRJ-1305/Training/' to 'tapis://project-7997906542076432871-242ac11c-0001-012/Training/'\n",
220-
"Listing files in system 'project-7997906542076432871-242ac11c-0001-012' at path 'Training/'...\n",
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"Listing files in system 'project-7997906542076432871-242ac11c-0001-012' at path 'Training/'...\n"
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]
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},
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"Found 26 items.\n",
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"2023-NHERI-Academy dir\n",
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"2024-NHERI-AI-Academy dir\n",
@@ -250,7 +315,14 @@
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{
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"cell_type": "code",
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"execution_count": 9,
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"metadata": {},
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:59.850600Z",
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"iopub.status.busy": "2026-04-02T11:23:59.850244Z",
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"iopub.status.idle": "2026-04-02T11:23:59.854968Z",
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"shell.execute_reply": "2026-04-02T11:23:59.854337Z"
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}
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},
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"outputs": [
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{
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"name": "stdout",
@@ -280,8 +352,15 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"execution_count": 10,
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"metadata": {
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"execution": {
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"iopub.execute_input": "2026-04-02T11:23:59.857123Z",
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"iopub.status.busy": "2026-04-02T11:23:59.856957Z",
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"iopub.status.idle": "2026-04-02T11:23:59.859021Z",
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"shell.execute_reply": "2026-04-02T11:23:59.858672Z"
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}
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},
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"outputs": [],
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"source": [
287366
"# Upload a file to MyData\n",

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