diff --git a/.renku/workflow/28bc0cc31893437cab56c61748db62c8.cwl b/.renku/workflow/28bc0cc31893437cab56c61748db62c8.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..cacfa38e3aed120889f49fc9a1f78a3341a9bc64
--- /dev/null
+++ b/.renku/workflow/28bc0cc31893437cab56c61748db62c8.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_2:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+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 938bc093ebfcc2e4d368fd74070c8470c86b71a4..adbd858f26c78dc150ca76147d74b38eecf4a15a 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 sha256:1dd314d75ff4c809171c2437438c9295165f38d153afc790f2502eb8488991c7
-size 16036594
+oid sha256:5af26320abdb32731e189d5ed01bf9f46a09841335b3afca822d83dd6dcb8317
+size 16363980
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index e0c29e3754ed54e3ce8f938e543944acc8163079..f27fe2ba87c6cfe58cf3f0c2311cdccdc61f5369 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 sha256:7208f9c3859bb5f6fabec7937db54dbe516642a1ac272bc236ec47637d7cadf6
-size 88769
+oid sha256:2eec03d97a289e047e6a901a66182a2102d1ef31b80441be1dcf03ca23ee531c
+size 88814
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index b3a5dc6079e2ca8ca6ce3e30440fcf4bf961bbc1..46bcf828d14026e01df79043f87d7822c2767334 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": 3.944179,
- "end_time": "2020-10-05T07:37:18.124257",
+ "duration": 6.011567,
+ "end_time": "2020-10-06T07:35:57.380380",
"exception": false,
- "start_time": "2020-10-05T07:37:14.180078",
+ "start_time": "2020-10-06T07:35:51.368813",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.029625,
- "end_time": "2020-10-05T07:37:18.168127",
+ "duration": 0.024071,
+ "end_time": "2020-10-06T07:35:57.420161",
"exception": false,
- "start_time": "2020-10-05T07:37:18.138502",
+ "start_time": "2020-10-06T07:35:57.396090",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.024459,
- "end_time": "2020-10-05T07:37:18.205933",
+ "duration": 0.021094,
+ "end_time": "2020-10-06T07:35:57.452270",
"exception": false,
- "start_time": "2020-10-05T07:37:18.181474",
+ "start_time": "2020-10-06T07:35:57.431176",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/c_ekx4yo/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/yrdslkae/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": 0.00705,
- "end_time": "2020-10-05T07:37:18.221433",
+ "duration": 0.005907,
+ "end_time": "2020-10-06T07:35:57.465749",
"exception": false,
- "start_time": "2020-10-05T07:37:18.214383",
+ "start_time": "2020-10-06T07:35:57.459842",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.966198,
- "end_time": "2020-10-05T07:37:19.193755",
+ "duration": 0.851667,
+ "end_time": "2020-10-06T07:35:58.323073",
"exception": false,
- "start_time": "2020-10-05T07:37:18.227557",
+ "start_time": "2020-10-06T07:35:57.471406",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.037265,
- "end_time": "2020-10-05T07:37:19.244465",
+ "duration": 0.028465,
+ "end_time": "2020-10-06T07:35:58.360536",
"exception": false,
- "start_time": "2020-10-05T07:37:19.207200",
+ "start_time": "2020-10-06T07:35:58.332071",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.106637,
- "end_time": "2020-10-05T07:37:19.359169",
+ "duration": 0.218574,
+ "end_time": "2020-10-06T07:35:58.595397",
"exception": false,
- "start_time": "2020-10-05T07:37:19.252532",
+ "start_time": "2020-10-06T07:35:58.376823",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008661,
- "end_time": "2020-10-05T07:37:19.381916",
+ "duration": 0.008019,
+ "end_time": "2020-10-06T07:35:58.617883",
"exception": false,
- "start_time": "2020-10-05T07:37:19.373255",
+ "start_time": "2020-10-06T07:35:58.609864",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.579767,
- "end_time": "2020-10-05T07:37:19.968147",
+ "duration": 27.315918,
+ "end_time": "2020-10-06T07:36:25.940528",
"exception": false,
- "start_time": "2020-10-05T07:37:19.388380",
+ "start_time": "2020-10-06T07:35:58.624610",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.04722,
- "end_time": "2020-10-05T07:37:20.034407",
+ "duration": 0.075191,
+ "end_time": "2020-10-06T07:36:26.035475",
"exception": false,
- "start_time": "2020-10-05T07:37:19.987187",
+ "start_time": "2020-10-06T07:36:25.960284",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.584158,
- "end_time": "2020-10-05T07:37:20.633990",
+ "duration": 0.53003,
+ "end_time": "2020-10-06T07:36:26.577471",
"exception": false,
- "start_time": "2020-10-05T07:37:20.049832",
+ "start_time": "2020-10-06T07:36:26.047441",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "12026 data points\n"
+ "12082 data points\n"
]
},
{
@@ -379,13 +379,13 @@
" <th>date</th>\n",
" <th>state</th>\n",
" <th>positive</th>\n",
+ " <th>probableCases</th>\n",
" <th>negative</th>\n",
" <th>pending</th>\n",
" <th>totalTestResults</th>\n",
" <th>hospitalizedCurrently</th>\n",
" <th>hospitalizedCumulative</th>\n",
" <th>inIcuCurrently</th>\n",
- " <th>inIcuCumulative</th>\n",
" <th>...</th>\n",
" <th>posNeg</th>\n",
" <th>deathIncrease</th>\n",
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201004</td>\n",
+ " <td>20201005</td>\n",
" <td>AK</td>\n",
- " <td>9376.0</td>\n",
- " <td>467442.0</td>\n",
+ " <td>9587.0</td>\n",
" <td>NaN</td>\n",
- " <td>476818.0</td>\n",
- " <td>51.0</td>\n",
+ " <td>469787.0</td>\n",
" <td>NaN</td>\n",
+ " <td>479374.0</td>\n",
+ " <td>45.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>476818</td>\n",
+ " <td>479374</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>d10acf299a4fff49e734775bc42aeaebfbe9776a</td>\n",
+ " <td>f9b74c2d6aff526dd04b6faa52faa6e5719eed19</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>20201004</td>\n",
+ " <td>20201005</td>\n",
" <td>AL</td>\n",
- " <td>159169.0</td>\n",
- " <td>1022073.0</td>\n",
+ " <td>159713.0</td>\n",
+ " <td>18791.0</td>\n",
+ " <td>1026591.0</td>\n",
" <td>NaN</td>\n",
- " <td>1162518.0</td>\n",
- " <td>757.0</td>\n",
- " <td>17420.0</td>\n",
+ " <td>1167513.0</td>\n",
+ " <td>791.0</td>\n",
+ " <td>17699.0</td>\n",
" <td>NaN</td>\n",
- " <td>1845.0</td>\n",
" <td>...</td>\n",
- " <td>1181242</td>\n",
- " <td>0</td>\n",
- " <td>0</td>\n",
- " <td>8b4f0135c1c94f579c47b8ec993ab4f2ed59114c</td>\n",
+ " <td>1186304</td>\n",
+ " <td>1</td>\n",
+ " <td>279</td>\n",
+ " <td>61b0ad490d1cbcfba06b4dc3a0355d0778530cc4</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -450,31 +450,31 @@
" </tr>\n",
" </tbody>\n",
"</table>\n",
- "<p>2 rows × 54 columns</p>\n",
+ "<p>2 rows × 55 columns</p>\n",
"</div>"
],
"text/plain": [
- " date state positive negative pending totalTestResults \\\n",
- "0 20201004 AK 9376.0 467442.0 NaN 476818.0 \n",
- "1 20201004 AL 159169.0 1022073.0 NaN 1162518.0 \n",
+ " date state positive probableCases negative pending \\\n",
+ "0 20201005 AK 9587.0 NaN 469787.0 NaN \n",
+ "1 20201005 AL 159713.0 18791.0 1026591.0 NaN \n",
"\n",
- " hospitalizedCurrently hospitalizedCumulative inIcuCurrently \\\n",
- "0 51.0 NaN NaN \n",
- "1 757.0 17420.0 NaN \n",
+ " totalTestResults hospitalizedCurrently hospitalizedCumulative \\\n",
+ "0 479374.0 45.0 NaN \n",
+ "1 1167513.0 791.0 17699.0 \n",
"\n",
- " inIcuCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 476818 0 0 \n",
- "1 1845.0 ... 1181242 0 0 \n",
+ " inIcuCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
+ "0 NaN ... 479374 0 0 \n",
+ "1 NaN ... 1186304 1 279 \n",
"\n",
" hash commercialScore \\\n",
- "0 d10acf299a4fff49e734775bc42aeaebfbe9776a 0 \n",
- "1 8b4f0135c1c94f579c47b8ec993ab4f2ed59114c 0 \n",
+ "0 f9b74c2d6aff526dd04b6faa52faa6e5719eed19 0 \n",
+ "1 61b0ad490d1cbcfba06b4dc3a0355d0778530cc4 0 \n",
"\n",
- " negativeRegularScore negativeScore positiveScore score grade \n",
- "0 0 0 0 0 \n",
- "1 0 0 0 0 \n",
+ " negativeRegularScore negativeScore positiveScore score grade \n",
+ "0 0 0 0 0 \n",
+ "1 0 0 0 0 \n",
"\n",
- "[2 rows x 54 columns]"
+ "[2 rows x 55 columns]"
]
},
"execution_count": 9,
@@ -508,18 +508,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 8.117604,
- "end_time": "2020-10-05T07:37:21.066814",
+ "duration": 37.917862,
+ "end_time": "2020-10-06T07:36:27.007239",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/c_ekx4yo/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/yrdslkae/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/c_ekx4yo/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/yrdslkae/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-05T07:37:12.949210",
+ "start_time": "2020-10-06T07:35:49.089377",
"version": "1.1.0"
}
},