From c4a3a9b295cbbe268a8c086e9dc30385ee1b6046 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Wed, 13 May 2020 09:08:07 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../0308e2c322734725b07608fbaf75dca6.cwl | 120 +++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 3 +
runs/download-covidtracking-data.runs.ipynb | 144 +++++++++---------
4 files changed, 197 insertions(+), 74 deletions(-)
create mode 100644 .renku/workflow/0308e2c322734725b07608fbaf75dca6.cwl
create mode 100644 data/covidtracking/states-metadata.json
diff --git a/.renku/workflow/0308e2c322734725b07608fbaf75dca6.cwl b/.renku/workflow/0308e2c322734725b07608fbaf75dca6.cwl
new file mode 100644
index 000000000..308b84ab3
--- /dev/null
+++ b/.renku/workflow/0308e2c322734725b07608fbaf75dca6.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: out_folder
+ streamable: false
+ type: string
+ input_2:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_3:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_4:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_5:
+ default: states-metadata.json
+ streamable: false
+ type: string
+ input_6:
+ default: states-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+ output_2:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: input_4
+ out:
+ - output_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_2:
+ in:
+ filename: input_5
+ input_directory: step_1/output_1
+ out:
+ - output_file
+ run:
+ arguments: []
+ baseCommand:
+ - 'true'
+ class: CommandLineTool
+ cwlVersion: v1.0
+ hints: []
+ inputs:
+ filename:
+ default: states-metadata.json
+ streamable: false
+ type: string
+ input_directory:
+ streamable: false
+ type: Directory
+ outputs:
+ output_file:
+ outputBinding:
+ glob: $(inputs.filename)
+ streamable: false
+ type: File
+ permanentFailCodes: []
+ requirements:
+ - &id001
+ class: InlineJavascriptRequirement
+ - &id002
+ class: InitialWorkDirRequirement
+ listing: $(inputs.input_directory.listing)
+ successCodes: []
+ temporaryFailCodes: []
+ step_3:
+ in:
+ filename: input_6
+ input_directory: step_1/output_1
+ out:
+ - output_file
+ run:
+ arguments: []
+ baseCommand:
+ - 'true'
+ class: CommandLineTool
+ cwlVersion: v1.0
+ hints: []
+ inputs:
+ filename:
+ default: states-daily.json
+ streamable: false
+ type: string
+ input_directory:
+ streamable: false
+ type: Directory
+ outputs:
+ output_file:
+ outputBinding:
+ glob: $(inputs.filename)
+ streamable: false
+ type: File
+ permanentFailCodes: []
+ requirements:
+ - *id001
+ - *id002
+ successCodes: []
+ temporaryFailCodes: []
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 1d6060de3..7201bef25 100644
--- a/data/covidtracking/states-daily.json
+++ b/data/covidtracking/states-daily.json
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:8559ed3a981bb365de2dbd4f0293ec03b39c5b1a4754a94d59e45cafce4123b2
-size 2214065
+oid sha256:43eecd43e6c46a74e6de15982cf36b3fc0e0787ce12ddd061ecf3ee143d3e31c
+size 2247094
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
new file mode 100644
index 000000000..d1f619dad
--- /dev/null
+++ b/data/covidtracking/states-metadata.json
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:b48c0fd54e43b491a56fd0b2f36c4d683e742940b5172b07e53b622191b93eee
+size 30913
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 4a3e31b8a..b9e8c12bc 100644
--- a/runs/download-covidtracking-data.runs.ipynb
+++ b/runs/download-covidtracking-data.runs.ipynb
@@ -5,10 +5,10 @@
"execution_count": 1,
"metadata": {
"papermill": {
- "duration": 4.308881,
- "end_time": "2020-05-12T07:26:15.161447",
+ "duration": 4.361081,
+ "end_time": "2020-05-13T09:08:01.086604",
"exception": false,
- "start_time": "2020-05-12T07:26:10.852566",
+ "start_time": "2020-05-13T09:07:56.725523",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.019705,
- "end_time": "2020-05-12T07:26:15.195521",
+ "duration": 0.018596,
+ "end_time": "2020-05-13T09:08:01.115959",
"exception": false,
- "start_time": "2020-05-12T07:26:15.175816",
+ "start_time": "2020-05-13T09:08:01.097363",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019669,
- "end_time": "2020-05-12T07:26:15.223947",
+ "duration": 0.022521,
+ "end_time": "2020-05-13T09:08:01.146502",
"exception": false,
- "start_time": "2020-05-12T07:26:15.204278",
+ "start_time": "2020-05-13T09:08:01.123981",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/osodv0vi/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/x8u9p2lc/notebooks/process/download-covidtracking-data.ipynb\"\n",
"PAPERMILL_OUTPUT_PATH = \"runs/download-covidtracking-data.runs.ipynb\"\n",
"out_folder = \"data/covidtracking\"\n"
]
@@ -68,10 +68,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007462,
- "end_time": "2020-05-12T07:26:15.240736",
+ "duration": 0.007505,
+ "end_time": "2020-05-13T09:08:01.165512",
"exception": false,
- "start_time": "2020-05-12T07:26:15.233274",
+ "start_time": "2020-05-13T09:08:01.158007",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.681241,
- "end_time": "2020-05-12T07:26:15.929292",
+ "duration": 0.732189,
+ "end_time": "2020-05-13T09:08:01.905618",
"exception": false,
- "start_time": "2020-05-12T07:26:15.248051",
+ "start_time": "2020-05-13T09:08:01.173429",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.026845,
- "end_time": "2020-05-12T07:26:15.969206",
+ "duration": 0.024547,
+ "end_time": "2020-05-13T09:08:01.945188",
"exception": false,
- "start_time": "2020-05-12T07:26:15.942361",
+ "start_time": "2020-05-13T09:08:01.920641",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.099138,
- "end_time": "2020-05-12T07:26:16.078578",
+ "duration": 0.077147,
+ "end_time": "2020-05-13T09:08:02.031640",
"exception": false,
- "start_time": "2020-05-12T07:26:15.979440",
+ "start_time": "2020-05-13T09:08:01.954493",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008504,
- "end_time": "2020-05-12T07:26:16.096531",
+ "duration": 0.007787,
+ "end_time": "2020-05-13T09:08:02.056581",
"exception": false,
- "start_time": "2020-05-12T07:26:16.088027",
+ "start_time": "2020-05-13T09:08:02.048794",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 4.274671,
- "end_time": "2020-05-12T07:26:20.379592",
+ "duration": 4.091394,
+ "end_time": "2020-05-13T09:08:06.155844",
"exception": false,
- "start_time": "2020-05-12T07:26:16.104921",
+ "start_time": "2020-05-13T09:08:02.064450",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.030263,
- "end_time": "2020-05-12T07:26:20.423251",
+ "duration": 0.027153,
+ "end_time": "2020-05-13T09:08:06.195769",
"exception": false,
- "start_time": "2020-05-12T07:26:20.392988",
+ "start_time": "2020-05-13T09:08:06.168616",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.156344,
- "end_time": "2020-05-12T07:26:20.592247",
+ "duration": 0.148828,
+ "end_time": "2020-05-13T09:08:06.353717",
"exception": false,
- "start_time": "2020-05-12T07:26:20.435903",
+ "start_time": "2020-05-13T09:08:06.204889",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "3769 data points\n"
+ "3825 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200511</td>\n",
+ " <td>20200512</td>\n",
" <td>AK</td>\n",
- " <td>381.0</td>\n",
- " <td>28299.0</td>\n",
+ " <td>383.0</td>\n",
+ " <td>29578.0</td>\n",
" <td>NaN</td>\n",
- " <td>7.0</td>\n",
+ " <td>10.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
" <td>NaN</td>\n",
- " <td>28680</td>\n",
- " <td>28680</td>\n",
- " <td>28680</td>\n",
+ " <td>29961</td>\n",
+ " <td>29961</td>\n",
+ " <td>29961</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
- " <td>1314.0</td>\n",
+ " <td>1279.0</td>\n",
" <td>2.0</td>\n",
- " <td>1316.0</td>\n",
+ " <td>1281.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200511</td>\n",
+ " <td>20200512</td>\n",
" <td>AL</td>\n",
- " <td>10009.0</td>\n",
- " <td>119435.0</td>\n",
+ " <td>10310.0</td>\n",
+ " <td>122908.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>1256.0</td>\n",
+ " <td>1287.0</td>\n",
" <td>NaN</td>\n",
- " <td>463.0</td>\n",
+ " <td>468.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>1256.0</td>\n",
- " <td>129444</td>\n",
- " <td>129444</td>\n",
- " <td>129444</td>\n",
+ " <td>1287.0</td>\n",
+ " <td>133218</td>\n",
+ " <td>133218</td>\n",
+ " <td>133218</td>\n",
" <td>1</td>\n",
- " <td>8.0</td>\n",
- " <td>16.0</td>\n",
- " <td>1791.0</td>\n",
- " <td>232.0</td>\n",
- " <td>2023.0</td>\n",
+ " <td>28.0</td>\n",
+ " <td>31.0</td>\n",
+ " <td>3473.0</td>\n",
+ " <td>301.0</td>\n",
+ " <td>3774.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200511 AK 381.0 28299.0 NaN 7.0 \n",
- "1 20200511 AL 10009.0 119435.0 NaN NaN \n",
+ "0 20200512 AK 383.0 29578.0 NaN 10.0 \n",
+ "1 20200512 AL 10310.0 122908.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 1256.0 NaN 463.0 \n",
+ "1 1287.0 NaN 468.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults posNeg \\\n",
- "0 NaN ... NaN 28680 28680 28680 \n",
- "1 NaN ... 1256.0 129444 129444 129444 \n",
+ "0 NaN ... NaN 29961 29961 29961 \n",
+ "1 NaN ... 1287.0 133218 133218 133218 \n",
"\n",
" fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 2 0.0 0.0 1314.0 \n",
- "1 1 8.0 16.0 1791.0 \n",
+ "0 2 0.0 0.0 1279.0 \n",
+ "1 1 28.0 31.0 3473.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 2.0 1316.0 \n",
- "1 232.0 2023.0 \n",
+ "0 2.0 1281.0 \n",
+ "1 301.0 3774.0 \n",
"\n",
"[2 rows x 27 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 11.757658,
- "end_time": "2020-05-12T07:26:20.913569",
+ "duration": 11.412102,
+ "end_time": "2020-05-13T09:08:06.675940",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/osodv0vi/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/x8u9p2lc/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/osodv0vi/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/x8u9p2lc/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-05-12T07:26:09.155911",
+ "start_time": "2020-05-13T09:07:55.263838",
"version": "1.1.0"
}
},
--
GitLab