diff --git a/.renku/workflow/88764c64ec20413f9fe790b1dfd1dd87.cwl b/.renku/workflow/88764c64ec20413f9fe790b1dfd1dd87.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..cacd35c4a592c048d98a6ecf615ea774ca905c47
--- /dev/null
+++ b/.renku/workflow/88764c64ec20413f9fe790b1dfd1dd87.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: states-metadata.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-daily.json
+ streamable: false
+ type: string
+outputs:
+ output_0:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_1:
+ 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-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_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-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 6233cbf3a78a4505d6b847484014f515fdcd2f38..71f4aed23cdbb041211dbdef016bb654508d640e 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:e6086cb19690e6a1a340496a347395b5659b0d571e797e56fe75f22382cfe0de
-size 18253505
+oid sha256:621c2db64408ecf998235e836a602f6c6a428267262c19563696f02874c0d98d
+size 18350031
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 531ba2ba232bcb533d06058af5477d1d5d9f08a1..22c5f5f3c2d6c09aca2c88e8cb5051aa673b90dd 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 sha256:2a42c427de85fd5f0b2dca4993f4ec06a324f092e0b703bcded87c50defc65b7
-size 104080
+oid sha256:a90c02b00607993b7b37368d4e79437d9d58b24ed000a36668e4fe39d718def8
+size 107425
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 38226a095b7648d1ba32e851fa06d24c436d1617..8f5a19e97b24ebd7cc76379cfd36f9c007ea79ea 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": 4.537249,
- "end_time": "2020-10-29T07:39:06.222092",
+ "duration": 4.322888,
+ "end_time": "2020-10-30T07:38:40.349844",
"exception": false,
- "start_time": "2020-10-29T07:39:01.684843",
+ "start_time": "2020-10-30T07:38:36.026956",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.021881,
- "end_time": "2020-10-29T07:39:06.258241",
+ "duration": 0.021903,
+ "end_time": "2020-10-30T07:38:40.384648",
"exception": false,
- "start_time": "2020-10-29T07:39:06.236360",
+ "start_time": "2020-10-30T07:38:40.362745",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.027575,
- "end_time": "2020-10-29T07:39:06.297922",
+ "duration": 0.022912,
+ "end_time": "2020-10-30T07:38:40.415858",
"exception": false,
- "start_time": "2020-10-29T07:39:06.270347",
+ "start_time": "2020-10-30T07:38:40.392946",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/42lwuooh/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/it23r6lx/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": 0.007823,
- "end_time": "2020-10-29T07:39:06.317748",
+ "duration": 0.008181,
+ "end_time": "2020-10-30T07:38:40.434413",
"exception": false,
- "start_time": "2020-10-29T07:39:06.309925",
+ "start_time": "2020-10-30T07:38:40.426232",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.384563,
- "end_time": "2020-10-29T07:39:06.710425",
+ "duration": 0.570667,
+ "end_time": "2020-10-30T07:38:41.013127",
"exception": false,
- "start_time": "2020-10-29T07:39:06.325862",
+ "start_time": "2020-10-30T07:38:40.442460",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.023132,
- "end_time": "2020-10-29T07:39:06.744099",
+ "duration": 0.025008,
+ "end_time": "2020-10-30T07:38:41.047633",
"exception": false,
- "start_time": "2020-10-29T07:39:06.720967",
+ "start_time": "2020-10-30T07:38:41.022625",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.110546,
- "end_time": "2020-10-29T07:39:06.864298",
+ "duration": 0.077261,
+ "end_time": "2020-10-30T07:38:41.133806",
"exception": false,
- "start_time": "2020-10-29T07:39:06.753752",
+ "start_time": "2020-10-30T07:38:41.056545",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.009476,
- "end_time": "2020-10-29T07:39:06.883639",
+ "duration": 0.008744,
+ "end_time": "2020-10-30T07:38:41.155983",
"exception": false,
- "start_time": "2020-10-29T07:39:06.874163",
+ "start_time": "2020-10-30T07:38:41.147239",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 30.429905,
- "end_time": "2020-10-29T07:39:37.322953",
+ "duration": 30.457404,
+ "end_time": "2020-10-30T07:39:11.621966",
"exception": false,
- "start_time": "2020-10-29T07:39:06.893048",
+ "start_time": "2020-10-30T07:38:41.164562",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.053599,
- "end_time": "2020-10-29T07:39:37.390618",
+ "duration": 0.053966,
+ "end_time": "2020-10-30T07:39:11.689178",
"exception": false,
- "start_time": "2020-10-29T07:39:37.337019",
+ "start_time": "2020-10-30T07:39:11.635212",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.701681,
- "end_time": "2020-10-29T07:39:38.103517",
+ "duration": 0.692648,
+ "end_time": "2020-10-30T07:39:12.392023",
"exception": false,
- "start_time": "2020-10-29T07:39:37.401836",
+ "start_time": "2020-10-30T07:39:11.699375",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "13416 data points\n"
+ "13476 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201028</td>\n",
+ " <td>20201029</td>\n",
" <td>AK</td>\n",
- " <td>15155.0</td>\n",
+ " <td>15522.0</td>\n",
" <td>NaN</td>\n",
- " <td>565444.0</td>\n",
+ " <td>568746.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>580599.0</td>\n",
- " <td>80.0</td>\n",
+ " <td>584268.0</td>\n",
+ " <td>89.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>580599</td>\n",
- " <td>1</td>\n",
+ " <td>584268</td>\n",
+ " <td>6</td>\n",
" <td>0</td>\n",
- " <td>f0f48cae1ff48cce0b1dfa2a67c30709261bf7f5</td>\n",
+ " <td>01d32bd4e56cdbdb3ce1f28f13f4d195e46fc6af</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -426,21 +426,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20201028</td>\n",
+ " <td>20201029</td>\n",
" <td>AL</td>\n",
- " <td>187706.0</td>\n",
- " <td>27326.0</td>\n",
- " <td>1159926.0</td>\n",
+ " <td>189149.0</td>\n",
+ " <td>27612.0</td>\n",
+ " <td>1165898.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1320306.0</td>\n",
+ " <td>1327435.0</td>\n",
" <td>1013.0</td>\n",
- " <td>20116.0</td>\n",
+ " <td>20246.0</td>\n",
" <td>...</td>\n",
- " <td>1347632</td>\n",
- " <td>19</td>\n",
- " <td>142</td>\n",
- " <td>c713ea2c14a2c1435e7c7cbada7a09af31a376a6</td>\n",
+ " <td>1355047</td>\n",
+ " <td>3</td>\n",
+ " <td>130</td>\n",
+ " <td>cbe87bb193799153fdc2dd806e04fe810f982227</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -455,20 +455,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201028 AK 15155.0 NaN 565444.0 NaN \n",
- "1 20201028 AL 187706.0 27326.0 1159926.0 NaN \n",
+ "0 20201029 AK 15522.0 NaN 568746.0 NaN \n",
+ "1 20201029 AL 189149.0 27612.0 1165898.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 580599.0 80.0 \n",
- "1 totalTestsViral 1320306.0 1013.0 \n",
+ "0 totalTestsViral 584268.0 89.0 \n",
+ "1 totalTestsViral 1327435.0 1013.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 580599 1 0 \n",
- "1 20116.0 ... 1347632 19 142 \n",
+ "0 NaN ... 584268 6 0 \n",
+ "1 20246.0 ... 1355047 3 130 \n",
"\n",
" hash commercialScore \\\n",
- "0 f0f48cae1ff48cce0b1dfa2a67c30709261bf7f5 0 \n",
- "1 c713ea2c14a2c1435e7c7cbada7a09af31a376a6 0 \n",
+ "0 01d32bd4e56cdbdb3ce1f28f13f4d195e46fc6af 0 \n",
+ "1 cbe87bb193799153fdc2dd806e04fe810f982227 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -508,18 +508,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 39.630647,
- "end_time": "2020-10-29T07:39:38.423262",
+ "duration": 38.511335,
+ "end_time": "2020-10-30T07:39:12.714574",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/42lwuooh/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/it23r6lx/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/42lwuooh/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/it23r6lx/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-29T07:38:58.792615",
+ "start_time": "2020-10-30T07:38:34.203239",
"version": "1.1.0"
}
},