diff --git a/.renku/workflow/a97f3a1ea634476ba0056fdd0b027528.cwl b/.renku/workflow/a97f3a1ea634476ba0056fdd0b027528.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..0c4ffa04b46c90814d6c80c4f76124a60ad21cc8
--- /dev/null
+++ b/.renku/workflow/a97f3a1ea634476ba0056fdd0b027528.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: states-daily.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_0:
+ 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-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:
+ 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-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: []
+ step_3:
+ in:
+ input_1: input_3
+ input_2: input_4
+ input_3: input_5
+ input_4: input_6
+ out:
+ - output_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index 1075cc3f443cc14029bda3433ea3c838baba380e..0055f84dfafcb87700f4a2ce3729a46e73bd3847 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:c80b65820b6241c370620a8583e079f6acafd8d9b421e5add6fc9d78220528d6
-size 1203304
+oid sha256:98f82a5b65d02f0a717ed6030c45888d1684f9a25887ff1b1b3510b3b5e29424
+size 1234525
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 8d90d68c4f7400ff9ed02bf524bde5ce8ad2448a..74d937fcc2700fe78ab60c44c5fa8c03b13dbaf8 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:a2e45292b5796ff458d826f6d1f26e8914d89ff5d87d78a5fb91c78f61237cc7
-size 27705
+oid sha256:71e330ddff6f2314bcdda80dd2311315c1cad1dcd22dc534c5f35de31dbec8a3
+size 28275
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index b4cc7c18d3d49f7aada623e842f4508bd69b3cf5..628587f24e616e24be282f6049856f909ddfcf83 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": 5.671212,
- "end_time": "2020-04-19T19:56:23.928932",
+ "duration": 0.670971,
+ "end_time": "2020-04-20T09:46:45.215508",
"exception": false,
- "start_time": "2020-04-19T19:56:18.257720",
+ "start_time": "2020-04-20T09:46:44.544537",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.018453,
- "end_time": "2020-04-19T19:56:23.958250",
+ "duration": 0.017354,
+ "end_time": "2020-04-20T09:46:45.242288",
"exception": false,
- "start_time": "2020-04-19T19:56:23.939797",
+ "start_time": "2020-04-20T09:46:45.224934",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019133,
- "end_time": "2020-04-19T19:56:23.986818",
+ "duration": 0.017449,
+ "end_time": "2020-04-20T09:46:45.268250",
"exception": false,
- "start_time": "2020-04-19T19:56:23.967685",
+ "start_time": "2020-04-20T09:46:45.250801",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/_uzn4el5/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/ukjvdt8w/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": 0.007776,
- "end_time": "2020-04-19T19:56:24.002340",
+ "duration": 0.007493,
+ "end_time": "2020-04-20T09:46:45.284450",
"exception": false,
- "start_time": "2020-04-19T19:56:23.994564",
+ "start_time": "2020-04-20T09:46:45.276957",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.160899,
- "end_time": "2020-04-19T19:56:24.171242",
+ "duration": 0.698636,
+ "end_time": "2020-04-20T09:46:45.990193",
"exception": false,
- "start_time": "2020-04-19T19:56:24.010343",
+ "start_time": "2020-04-20T09:46:45.291557",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.019485,
- "end_time": "2020-04-19T19:56:24.199510",
+ "duration": 0.022706,
+ "end_time": "2020-04-20T09:46:46.025249",
"exception": false,
- "start_time": "2020-04-19T19:56:24.180025",
+ "start_time": "2020-04-20T09:46:46.002543",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.085508,
- "end_time": "2020-04-19T19:56:24.292339",
+ "duration": 0.065726,
+ "end_time": "2020-04-20T09:46:46.100845",
"exception": false,
- "start_time": "2020-04-19T19:56:24.206831",
+ "start_time": "2020-04-20T09:46:46.035119",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008133,
- "end_time": "2020-04-19T19:56:24.309427",
+ "duration": 0.008043,
+ "end_time": "2020-04-20T09:46:46.120804",
"exception": false,
- "start_time": "2020-04-19T19:56:24.301294",
+ "start_time": "2020-04-20T09:46:46.112761",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.35078,
- "end_time": "2020-04-19T19:56:24.668340",
+ "duration": 0.16965,
+ "end_time": "2020-04-20T09:46:46.298759",
"exception": false,
- "start_time": "2020-04-19T19:56:24.317560",
+ "start_time": "2020-04-20T09:46:46.129109",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.022744,
- "end_time": "2020-04-19T19:56:24.700667",
+ "duration": 0.027576,
+ "end_time": "2020-04-20T09:46:46.338007",
"exception": false,
- "start_time": "2020-04-19T19:56:24.677923",
+ "start_time": "2020-04-20T09:46:46.310431",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.110746,
- "end_time": "2020-04-19T19:56:24.819861",
+ "duration": 0.116367,
+ "end_time": "2020-04-20T09:46:46.465702",
"exception": false,
- "start_time": "2020-04-19T19:56:24.709115",
+ "start_time": "2020-04-20T09:46:46.349335",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "2452 data points\n"
+ "2508 data points\n"
]
},
{
@@ -368,51 +368,51 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200418</td>\n",
+ " <td>20200419</td>\n",
" <td>AK</td>\n",
- " <td>314.0</td>\n",
- " <td>9341.0</td>\n",
+ " <td>319.0</td>\n",
+ " <td>9576.0</td>\n",
" <td>NaN</td>\n",
- " <td>39.0</td>\n",
+ " <td>37.0</td>\n",
" <td>36.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
" <td>36.0</td>\n",
- " <td>9655.0</td>\n",
- " <td>9655.0</td>\n",
- " <td>9655.0</td>\n",
+ " <td>9895.0</td>\n",
+ " <td>9895.0</td>\n",
+ " <td>9895.0</td>\n",
" <td>2</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
- " <td>200.0</td>\n",
+ " <td>235.0</td>\n",
" <td>5.0</td>\n",
- " <td>205.0</td>\n",
+ " <td>240.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200418</td>\n",
+ " <td>20200419</td>\n",
" <td>AL</td>\n",
- " <td>4655.0</td>\n",
- " <td>37883.0</td>\n",
+ " <td>4837.0</td>\n",
+ " <td>40875.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>620.0</td>\n",
+ " <td>641.0</td>\n",
" <td>NaN</td>\n",
- " <td>247.0</td>\n",
+ " <td>260.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>620.0</td>\n",
- " <td>42538.0</td>\n",
- " <td>42538.0</td>\n",
- " <td>42538.0</td>\n",
+ " <td>641.0</td>\n",
+ " <td>45712.0</td>\n",
+ " <td>45712.0</td>\n",
+ " <td>45712.0</td>\n",
" <td>1</td>\n",
- " <td>2.0</td>\n",
- " <td>26.0</td>\n",
- " <td>4565.0</td>\n",
- " <td>125.0</td>\n",
- " <td>4690.0</td>\n",
+ " <td>8.0</td>\n",
+ " <td>21.0</td>\n",
+ " <td>2992.0</td>\n",
+ " <td>182.0</td>\n",
+ " <td>3174.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -421,24 +421,24 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200418 AK 314.0 9341.0 NaN 39.0 \n",
- "1 20200418 AL 4655.0 37883.0 NaN NaN \n",
+ "0 20200419 AK 319.0 9576.0 NaN 37.0 \n",
+ "1 20200419 AL 4837.0 40875.0 NaN NaN \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 36.0 NaN NaN \n",
- "1 620.0 NaN 247.0 \n",
+ "1 641.0 NaN 260.0 \n",
"\n",
" onVentilatorCurrently ... hospitalized total totalTestResults \\\n",
- "0 NaN ... 36.0 9655.0 9655.0 \n",
- "1 NaN ... 620.0 42538.0 42538.0 \n",
+ "0 NaN ... 36.0 9895.0 9895.0 \n",
+ "1 NaN ... 641.0 45712.0 45712.0 \n",
"\n",
" posNeg fips deathIncrease hospitalizedIncrease negativeIncrease \\\n",
- "0 9655.0 2 0.0 0.0 200.0 \n",
- "1 42538.0 1 2.0 26.0 4565.0 \n",
+ "0 9895.0 2 0.0 0.0 235.0 \n",
+ "1 45712.0 1 8.0 21.0 2992.0 \n",
"\n",
" positiveIncrease totalTestResultsIncrease \n",
- "0 5.0 205.0 \n",
- "1 125.0 4690.0 \n",
+ "0 5.0 240.0 \n",
+ "1 182.0 3174.0 \n",
"\n",
"[2 rows x 25 columns]"
]
@@ -474,18 +474,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 8.208523,
- "end_time": "2020-04-19T19:56:25.142083",
+ "duration": 3.15694,
+ "end_time": "2020-04-20T09:46:46.789934",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/_uzn4el5/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/ukjvdt8w/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/_uzn4el5/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/ukjvdt8w/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-04-19T19:56:16.933560",
+ "start_time": "2020-04-20T09:46:43.632994",
"version": "1.1.0"
}
},