diff --git a/.renku/workflow/d6b47617f0be44b9b30d3dadf36ecbb5.cwl b/.renku/workflow/d6b47617f0be44b9b30d3dadf36ecbb5.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..f5144208b36236c200738058d75107082967a37a
--- /dev/null
+++ b/.renku/workflow/d6b47617f0be44b9b30d3dadf36ecbb5.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: states-metadata.json
+ streamable: false
+ type: string
+ input_3:
+ default: out_folder
+ streamable: false
+ type: string
+ input_4:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_5:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_6:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+outputs:
+ output_1:
+ outputSource: step_3/output_1
+ streamable: false
+ type: Directory
+ output_2:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+requirements: []
+steps:
+ step_1:
+ in:
+ filename: input_1
+ input_directory: step_3/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:
+ filename: input_2
+ input_directory: step_3/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: []
+ step_3:
+ in:
+ input_1: input_3
+ input_2: input_4
+ input_3: input_5
+ input_4: input_6
+ out:
+ - output_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 313b4dcd8ba026393bf8d856e6f3ed39fb0fbff2..79108d0ddc56b64fd90e76fe08bc702e9649c7cc 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 sha256:3e3f573dfadd19add61f23f173c691376a9e7314f675c8c95d4d6587250003de
-size 20320781
+oid sha256:bdad962f55521d67f534b2aeb1badaf6b703e76057653c269428a9e327f46b25
+size 20485516
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 338e4649aefc02038004ea48c352bed36bd9c059..3ae8e969bb56dd18b12fb5df9fea5fbbe6b8694b 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:ae36642b16f7dc2df25eba3634adfd5772731de2874d7bd625fe1b87d8a8bed7
-size 129621
+oid sha256:1d3ae035cdae441dea198f8a30c79af627e67e76952a06595f266a56428c44cc
+size 132306
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 5e9efabf370f5c19464dfb67b3ed22b72c8639fb..b71ede25110f09d17878b684980a6aac9770fc2f 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": 5.255276,
- "end_time": "2020-11-24T07:44:49.459961",
+ "duration": 6.475913,
+ "end_time": "2020-11-26T07:58:35.675162",
"exception": false,
- "start_time": "2020-11-24T07:44:44.204685",
+ "start_time": "2020-11-26T07:58:29.199249",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.023889,
- "end_time": "2020-11-24T07:44:49.499512",
+ "duration": 0.020822,
+ "end_time": "2020-11-26T07:58:35.708619",
"exception": false,
- "start_time": "2020-11-24T07:44:49.475623",
+ "start_time": "2020-11-26T07:58:35.687797",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.010921,
- "end_time": "2020-11-24T07:44:49.516597",
+ "duration": 0.017946,
+ "end_time": "2020-11-26T07:58:35.734541",
"exception": false,
- "start_time": "2020-11-24T07:44:49.505676",
+ "start_time": "2020-11-26T07:58:35.716595",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/t0y_essg/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/p4r5vl68/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": 0.004343,
- "end_time": "2020-11-24T07:44:49.525362",
+ "duration": 0.005967,
+ "end_time": "2020-11-26T07:58:35.746416",
"exception": false,
- "start_time": "2020-11-24T07:44:49.521019",
+ "start_time": "2020-11-26T07:58:35.740449",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 10.391367,
- "end_time": "2020-11-24T07:44:59.920943",
+ "duration": 10.821161,
+ "end_time": "2020-11-26T07:58:46.572554",
"exception": false,
- "start_time": "2020-11-24T07:44:49.529576",
+ "start_time": "2020-11-26T07:58:35.751393",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.024074,
- "end_time": "2020-11-24T07:44:59.957871",
+ "duration": 0.029661,
+ "end_time": "2020-11-26T07:58:46.614568",
"exception": false,
- "start_time": "2020-11-24T07:44:59.933797",
+ "start_time": "2020-11-26T07:58:46.584907",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.066306,
- "end_time": "2020-11-24T07:45:00.032836",
+ "duration": 0.063953,
+ "end_time": "2020-11-26T07:58:46.690388",
"exception": false,
- "start_time": "2020-11-24T07:44:59.966530",
+ "start_time": "2020-11-26T07:58:46.626435",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007437,
- "end_time": "2020-11-24T07:45:00.052559",
+ "duration": 0.00631,
+ "end_time": "2020-11-26T07:58:46.707816",
"exception": false,
- "start_time": "2020-11-24T07:45:00.045122",
+ "start_time": "2020-11-26T07:58:46.701506",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 10.634454,
- "end_time": "2020-11-24T07:45:10.693263",
+ "duration": 10.615746,
+ "end_time": "2020-11-26T07:58:57.330443",
"exception": false,
- "start_time": "2020-11-24T07:45:00.058809",
+ "start_time": "2020-11-26T07:58:46.714697",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.047788,
- "end_time": "2020-11-24T07:45:10.754629",
+ "duration": 0.035601,
+ "end_time": "2020-11-26T07:58:57.378913",
"exception": false,
- "start_time": "2020-11-24T07:45:10.706841",
+ "start_time": "2020-11-26T07:58:57.343312",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.55723,
- "end_time": "2020-11-24T07:45:11.324807",
+ "duration": 0.515161,
+ "end_time": "2020-11-26T07:58:57.904857",
"exception": false,
- "start_time": "2020-11-24T07:45:10.767577",
+ "start_time": "2020-11-26T07:58:57.389696",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "14899 data points\n"
+ "15017 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201123</td>\n",
+ " <td>20201125</td>\n",
" <td>AK</td>\n",
- " <td>27085.0</td>\n",
+ " <td>28339.0</td>\n",
" <td>NaN</td>\n",
- " <td>905931.0</td>\n",
+ " <td>925937.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>933016.0</td>\n",
- " <td>146.0</td>\n",
- " <td>617.0</td>\n",
+ " <td>954276.0</td>\n",
+ " <td>145.0</td>\n",
+ " <td>663.0</td>\n",
" <td>...</td>\n",
- " <td>933016</td>\n",
+ " <td>954276</td>\n",
" <td>0</td>\n",
- " <td>5</td>\n",
- " <td>cbbe56430899e87f4ea8a0336bdc01fdb3b34998</td>\n",
+ " <td>32</td>\n",
+ " <td>e4015d41f79fe8f9552517702ee27996c0d86b6a</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>20201123</td>\n",
+ " <td>20201125</td>\n",
" <td>AL</td>\n",
- " <td>234080.0</td>\n",
- " <td>38193.0</td>\n",
- " <td>1337741.0</td>\n",
+ " <td>239318.0</td>\n",
+ " <td>39692.0</td>\n",
+ " <td>1353961.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1533628.0</td>\n",
- " <td>1427.0</td>\n",
- " <td>23942.0</td>\n",
+ " <td>1553587.0</td>\n",
+ " <td>1483.0</td>\n",
+ " <td>24376.0</td>\n",
" <td>...</td>\n",
- " <td>1571821</td>\n",
- " <td>2</td>\n",
- " <td>493</td>\n",
- " <td>064b957eb226a47780acf699e8e184c49ced247b</td>\n",
+ " <td>1593279</td>\n",
+ " <td>60</td>\n",
+ " <td>216</td>\n",
+ " <td>cfbf3932514b39bd3f684d0fc235d8daa8009616</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 20201123 AK 27085.0 NaN 905931.0 NaN \n",
- "1 20201123 AL 234080.0 38193.0 1337741.0 NaN \n",
+ "0 20201125 AK 28339.0 NaN 925937.0 NaN \n",
+ "1 20201125 AL 239318.0 39692.0 1353961.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 933016.0 146.0 \n",
- "1 totalTestsViral 1533628.0 1427.0 \n",
+ "0 totalTestsViral 954276.0 145.0 \n",
+ "1 totalTestsViral 1553587.0 1483.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 617.0 ... 933016 0 5 \n",
- "1 23942.0 ... 1571821 2 493 \n",
+ "0 663.0 ... 954276 0 32 \n",
+ "1 24376.0 ... 1593279 60 216 \n",
"\n",
" hash commercialScore \\\n",
- "0 cbbe56430899e87f4ea8a0336bdc01fdb3b34998 0 \n",
- "1 064b957eb226a47780acf699e8e184c49ced247b 0 \n",
+ "0 e4015d41f79fe8f9552517702ee27996c0d86b6a 0 \n",
+ "1 cfbf3932514b39bd3f684d0fc235d8daa8009616 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": 29.443362,
- "end_time": "2020-11-24T07:45:11.646275",
+ "duration": 31.109234,
+ "end_time": "2020-11-26T07:58:58.230145",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/t0y_essg/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/p4r5vl68/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/t0y_essg/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/p4r5vl68/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-11-24T07:44:42.202913",
+ "start_time": "2020-11-26T07:58:27.120911",
"version": "1.1.0"
}
},