From 42ed628b9ad13eb0f51d31682ef1022442f4a998 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Sun, 22 Nov 2020 07:37:29 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../65cb477295174a6281baf559bf997f10.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 136 +++++++++---------
4 files changed, 192 insertions(+), 72 deletions(-)
create mode 100644 .renku/workflow/65cb477295174a6281baf559bf997f10.cwl
diff --git a/.renku/workflow/65cb477295174a6281baf559bf997f10.cwl b/.renku/workflow/65cb477295174a6281baf559bf997f10.cwl
new file mode 100644
index 000000000..274898149
--- /dev/null
+++ b/.renku/workflow/65cb477295174a6281baf559bf997f10.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: states-daily.json
+ streamable: false
+ type: string
+ input_2:
+ default: out_folder
+ streamable: false
+ type: string
+ input_3:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_4:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_5:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_6:
+ default: states-metadata.json
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_2:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+requirements: []
+steps:
+ step_1:
+ in:
+ filename: input_1
+ input_directory: step_2/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
+ class: InlineJavascriptRequirement
+ - &id002
+ class: InitialWorkDirRequirement
+ listing: $(inputs.input_directory.listing)
+ successCodes: []
+ temporaryFailCodes: []
+ step_2:
+ in:
+ input_1: input_2
+ input_2: input_3
+ input_3: input_4
+ input_4: input_5
+ out:
+ - output_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_3:
+ in:
+ filename: input_6
+ input_directory: step_2/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
+ - *id002
+ successCodes: []
+ temporaryFailCodes: []
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 32934ba40..26f4a230a 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 sha256:7d3309abd61b9b22d466d78f61eb72f18f1deafb021f99284036397b655148fa
-size 20081678
+oid sha256:377b6af4da405530763928fe9f18f9d150508fc3944b69d69cbf7e005da51544
+size 20158771
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 9017958be..195efa7d8 100644
--- a/data/covidtracking/states-metadata.json
+++ b/data/covidtracking/states-metadata.json
@@ -1,3 +1,3 @@
version https://git-lfs.github.com/spec/v1
-oid sha256:5582f4bb85af8899ad6a9a70cee9aa8b00dfc9a0088fdb244bb9637a3f94ec59
-size 127025
+oid sha256:58c2665088124cd2c937a5f1c490c4450f3a8d1f0b85a4d0d9acbc91f1810384
+size 127946
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index ef83cb13b..9756296f2 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": 6.545257,
- "end_time": "2020-11-21T07:41:11.579354",
+ "duration": 4.749163,
+ "end_time": "2020-11-22T07:36:53.157405",
"exception": false,
- "start_time": "2020-11-21T07:41:05.034097",
+ "start_time": "2020-11-22T07:36:48.408242",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.023318,
- "end_time": "2020-11-21T07:41:11.612396",
+ "duration": 0.020819,
+ "end_time": "2020-11-22T07:36:53.191032",
"exception": false,
- "start_time": "2020-11-21T07:41:11.589078",
+ "start_time": "2020-11-22T07:36:53.170213",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.020231,
- "end_time": "2020-11-21T07:41:11.649536",
+ "duration": 0.018921,
+ "end_time": "2020-11-22T07:36:53.217437",
"exception": false,
- "start_time": "2020-11-21T07:41:11.629305",
+ "start_time": "2020-11-22T07:36:53.198516",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/qu6m417e/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/gwoumd9n/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": 0.008641,
- "end_time": "2020-11-21T07:41:11.668486",
+ "duration": 0.005065,
+ "end_time": "2020-11-22T07:36:53.228475",
"exception": false,
- "start_time": "2020-11-21T07:41:11.659845",
+ "start_time": "2020-11-22T07:36:53.223410",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.270076,
- "end_time": "2020-11-21T07:41:11.944530",
+ "duration": 0.988163,
+ "end_time": "2020-11-22T07:36:54.220939",
"exception": false,
- "start_time": "2020-11-21T07:41:11.674454",
+ "start_time": "2020-11-22T07:36:53.232776",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.017829,
- "end_time": "2020-11-21T07:41:11.977090",
+ "duration": 0.022572,
+ "end_time": "2020-11-22T07:36:54.255117",
"exception": false,
- "start_time": "2020-11-21T07:41:11.959261",
+ "start_time": "2020-11-22T07:36:54.232545",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.073701,
- "end_time": "2020-11-21T07:41:12.056774",
+ "duration": 0.07183,
+ "end_time": "2020-11-22T07:36:54.335970",
"exception": false,
- "start_time": "2020-11-21T07:41:11.983073",
+ "start_time": "2020-11-22T07:36:54.264140",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007285,
- "end_time": "2020-11-21T07:41:12.073365",
+ "duration": 0.006726,
+ "end_time": "2020-11-22T07:36:54.354334",
"exception": false,
- "start_time": "2020-11-21T07:41:12.066080",
+ "start_time": "2020-11-22T07:36:54.347608",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.486251,
- "end_time": "2020-11-21T07:41:12.567821",
+ "duration": 33.373785,
+ "end_time": "2020-11-22T07:37:27.734288",
"exception": false,
- "start_time": "2020-11-21T07:41:12.081570",
+ "start_time": "2020-11-22T07:36:54.360503",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.079999,
- "end_time": "2020-11-21T07:41:12.666722",
+ "duration": 0.051596,
+ "end_time": "2020-11-22T07:37:27.802794",
"exception": false,
- "start_time": "2020-11-21T07:41:12.586723",
+ "start_time": "2020-11-22T07:37:27.751198",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.775336,
- "end_time": "2020-11-21T07:41:13.460390",
+ "duration": 0.501441,
+ "end_time": "2020-11-22T07:37:28.316489",
"exception": false,
- "start_time": "2020-11-21T07:41:12.685054",
+ "start_time": "2020-11-22T07:37:27.815048",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "14729 data points\n"
+ "14785 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201120</td>\n",
+ " <td>20201121</td>\n",
" <td>AK</td>\n",
- " <td>25369.0</td>\n",
+ " <td>26044.0</td>\n",
" <td>NaN</td>\n",
- " <td>879343.0</td>\n",
+ " <td>892701.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>904712.0</td>\n",
- " <td>127.0</td>\n",
- " <td>606.0</td>\n",
+ " <td>918745.0</td>\n",
+ " <td>129.0</td>\n",
+ " <td>612.0</td>\n",
" <td>...</td>\n",
- " <td>904712</td>\n",
- " <td>0</td>\n",
- " <td>13</td>\n",
- " <td>69903ec40b2eb2629d77fa81ecaea343e862a768</td>\n",
+ " <td>918745</td>\n",
+ " <td>1</td>\n",
+ " <td>6</td>\n",
+ " <td>0d51b28ef5ce194e5dc76dcf4e15162d75123d17</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -430,21 +430,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20201120</td>\n",
+ " <td>20201121</td>\n",
" <td>AL</td>\n",
- " <td>228373.0</td>\n",
- " <td>36965.0</td>\n",
- " <td>1316804.0</td>\n",
+ " <td>230708.0</td>\n",
+ " <td>37613.0</td>\n",
+ " <td>1325091.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1508212.0</td>\n",
- " <td>1329.0</td>\n",
+ " <td>1518186.0</td>\n",
+ " <td>1300.0</td>\n",
" <td>23449.0</td>\n",
" <td>...</td>\n",
- " <td>1545177</td>\n",
- " <td>32</td>\n",
- " <td>154</td>\n",
- " <td>f80f4da63db3493044b482c48fbd160331904b94</td>\n",
+ " <td>1555799</td>\n",
+ " <td>6</td>\n",
+ " <td>0</td>\n",
+ " <td>659435bfb739cc4892ee95aef1a62ff35977768a</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -459,20 +459,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201120 AK 25369.0 NaN 879343.0 NaN \n",
- "1 20201120 AL 228373.0 36965.0 1316804.0 NaN \n",
+ "0 20201121 AK 26044.0 NaN 892701.0 NaN \n",
+ "1 20201121 AL 230708.0 37613.0 1325091.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 904712.0 127.0 \n",
- "1 totalTestsViral 1508212.0 1329.0 \n",
+ "0 totalTestsViral 918745.0 129.0 \n",
+ "1 totalTestsViral 1518186.0 1300.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 606.0 ... 904712 0 13 \n",
- "1 23449.0 ... 1545177 32 154 \n",
+ "0 612.0 ... 918745 1 6 \n",
+ "1 23449.0 ... 1555799 6 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 69903ec40b2eb2629d77fa81ecaea343e862a768 0 \n",
- "1 f80f4da63db3493044b482c48fbd160331904b94 0 \n",
+ "0 0d51b28ef5ce194e5dc76dcf4e15162d75123d17 0 \n",
+ "1 659435bfb739cc4892ee95aef1a62ff35977768a 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -512,18 +512,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 11.243961,
- "end_time": "2020-11-21T07:41:13.886011",
+ "duration": 41.94801,
+ "end_time": "2020-11-22T07:37:28.640711",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/qu6m417e/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/gwoumd9n/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/qu6m417e/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/gwoumd9n/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-11-21T07:41:02.642050",
+ "start_time": "2020-11-22T07:36:46.692701",
"version": "1.1.0"
}
},
--
GitLab