diff --git a/.renku/workflow/1e225dfd73f14eefa9a98769403b2963.cwl b/.renku/workflow/1e225dfd73f14eefa9a98769403b2963.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..4105b2e4b7864a8c984c0fb6a1ce3eb1cd63e3e3
--- /dev/null
+++ b/.renku/workflow/1e225dfd73f14eefa9a98769403b2963.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_1:
+ 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-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_0
+ - output_1
+ 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 c39e7cb93cd9b2e8dabda54c0e28ac5900c24a01..551a9727a6090c9f3a304341d39ab87bd8fa1400 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 sha256:620d7a5960bd2efd7502001d04f38d2cf630a5937e9b5b30ee59edecab5b7a3a
-size 451064
+oid sha256:801b058f6d058226e08bf7199653a1684747727adcb9c15864858faf6d76ad09
+size 471445
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index f3ede08085838e9f0060fc88168e3e6a24620316..ce67df1e5fe13b40b7edb398717f42f91edfd7f5 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 sha256:9ee2bb71091d1976a748e75088484a079c32f959736aefb777262beef24b71d5
-size 25321
+oid sha256:306bc64b6fee54d73398efe54f01497474cbf76b0c2ddbd38a86f5a4652f8f46
+size 25348
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index f64569502a12438646fd6e18212f3b4bb56a8b2c..1f78abb390d756bce4b657a3f175d0da8733171d 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": 0.466467,
- "end_time": "2020-03-29T08:22:31.907089",
+ "duration": 0.492815,
+ "end_time": "2020-03-30T08:27:40.229411",
"exception": false,
- "start_time": "2020-03-29T08:22:31.440622",
+ "start_time": "2020-03-30T08:27:39.736596",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.018031,
- "end_time": "2020-03-29T08:22:31.938653",
+ "duration": 0.021021,
+ "end_time": "2020-03-30T08:27:40.266638",
"exception": false,
- "start_time": "2020-03-29T08:22:31.920622",
+ "start_time": "2020-03-30T08:27:40.245617",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.018359,
- "end_time": "2020-03-29T08:22:31.964788",
+ "duration": 0.021844,
+ "end_time": "2020-03-30T08:27:40.297532",
"exception": false,
- "start_time": "2020-03-29T08:22:31.946429",
+ "start_time": "2020-03-30T08:27:40.275688",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/bdf81mi5/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/d1j8kx27/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": 0.008065,
- "end_time": "2020-03-29T08:22:31.981763",
+ "duration": 0.00787,
+ "end_time": "2020-03-30T08:27:40.314046",
"exception": false,
- "start_time": "2020-03-29T08:22:31.973698",
+ "start_time": "2020-03-30T08:27:40.306176",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.063028,
- "end_time": "2020-03-29T08:22:32.052258",
+ "duration": 0.203713,
+ "end_time": "2020-03-30T08:27:40.523793",
"exception": false,
- "start_time": "2020-03-29T08:22:31.989230",
+ "start_time": "2020-03-30T08:27:40.320080",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.020595,
- "end_time": "2020-03-29T08:22:32.084858",
+ "duration": 0.027624,
+ "end_time": "2020-03-30T08:27:40.565900",
"exception": false,
- "start_time": "2020-03-29T08:22:32.064263",
+ "start_time": "2020-03-30T08:27:40.538276",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.062439,
- "end_time": "2020-03-29T08:22:32.156029",
+ "duration": 0.06934,
+ "end_time": "2020-03-30T08:27:40.645200",
"exception": false,
- "start_time": "2020-03-29T08:22:32.093590",
+ "start_time": "2020-03-30T08:27:40.575860",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007936,
- "end_time": "2020-03-29T08:22:32.175985",
+ "duration": 0.008708,
+ "end_time": "2020-03-30T08:27:40.669585",
"exception": false,
- "start_time": "2020-03-29T08:22:32.168049",
+ "start_time": "2020-03-30T08:27:40.660877",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.16391,
- "end_time": "2020-03-29T08:22:32.348092",
+ "duration": 0.189596,
+ "end_time": "2020-03-30T08:27:40.865837",
"exception": false,
- "start_time": "2020-03-29T08:22:32.184182",
+ "start_time": "2020-03-30T08:27:40.676241",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.021284,
- "end_time": "2020-03-29T08:22:32.380284",
+ "duration": 0.028367,
+ "end_time": "2020-03-30T08:27:40.910685",
"exception": false,
- "start_time": "2020-03-29T08:22:32.359000",
+ "start_time": "2020-03-30T08:27:40.882318",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.076359,
- "end_time": "2020-03-29T08:22:32.467959",
+ "duration": 0.077961,
+ "end_time": "2020-03-30T08:27:40.998256",
"exception": false,
- "start_time": "2020-03-29T08:22:32.391600",
+ "start_time": "2020-03-30T08:27:40.920295",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "1261 data points\n"
+ "1317 data points\n"
]
},
{
@@ -364,43 +364,43 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200328</td>\n",
+ " <td>20200329</td>\n",
" <td>AK</td>\n",
- " <td>85.0</td>\n",
- " <td>2836.0</td>\n",
+ " <td>102.0</td>\n",
+ " <td>3232.0</td>\n",
" <td>NaN</td>\n",
- " <td>5.0</td>\n",
+ " <td>6.0</td>\n",
" <td>2.0</td>\n",
- " <td>2921</td>\n",
- " <td>edb7e6bcde715f8bbea31547e99aa8b4712ea5fb</td>\n",
- " <td>2020-03-28T20:00:00Z</td>\n",
- " <td>2921</td>\n",
+ " <td>3334</td>\n",
+ " <td>d4c0789e67f59e98176a9ea96200ed348161c6d4</td>\n",
+ " <td>2020-03-29T20:00:00Z</td>\n",
+ " <td>3334</td>\n",
" <td>2</td>\n",
+ " <td>0.0</td>\n",
" <td>1.0</td>\n",
- " <td>2.0</td>\n",
- " <td>517.0</td>\n",
- " <td>16.0</td>\n",
- " <td>533.0</td>\n",
+ " <td>396.0</td>\n",
+ " <td>17.0</td>\n",
+ " <td>413.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200328</td>\n",
+ " <td>20200329</td>\n",
" <td>AL</td>\n",
- " <td>696.0</td>\n",
+ " <td>806.0</td>\n",
" <td>4184.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>3.0</td>\n",
- " <td>4880</td>\n",
- " <td>c9986a845bd2f8f9c9a4294a8e5d66a01ee6aadf</td>\n",
- " <td>2020-03-28T20:00:00Z</td>\n",
- " <td>4880</td>\n",
+ " <td>4.0</td>\n",
+ " <td>4990</td>\n",
+ " <td>9dbf0b598d35897b1f6857899d0a834990f4ec51</td>\n",
+ " <td>2020-03-29T20:00:00Z</td>\n",
+ " <td>4990</td>\n",
" <td>1</td>\n",
+ " <td>1.0</td>\n",
" <td>0.0</td>\n",
" <td>0.0</td>\n",
- " <td>0.0</td>\n",
- " <td>109.0</td>\n",
- " <td>109.0</td>\n",
+ " <td>110.0</td>\n",
+ " <td>110.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -408,20 +408,20 @@
],
"text/plain": [
" date state positive negative pending hospitalized death total \\\n",
- "0 20200328 AK 85.0 2836.0 NaN 5.0 2.0 2921 \n",
- "1 20200328 AL 696.0 4184.0 NaN NaN 3.0 4880 \n",
+ "0 20200329 AK 102.0 3232.0 NaN 6.0 2.0 3334 \n",
+ "1 20200329 AL 806.0 4184.0 NaN NaN 4.0 4990 \n",
"\n",
" hash dateChecked \\\n",
- "0 edb7e6bcde715f8bbea31547e99aa8b4712ea5fb 2020-03-28T20:00:00Z \n",
- "1 c9986a845bd2f8f9c9a4294a8e5d66a01ee6aadf 2020-03-28T20:00:00Z \n",
+ "0 d4c0789e67f59e98176a9ea96200ed348161c6d4 2020-03-29T20:00:00Z \n",
+ "1 9dbf0b598d35897b1f6857899d0a834990f4ec51 2020-03-29T20:00:00Z \n",
"\n",
" totalTestResults fips deathIncrease hospitalizedIncrease \\\n",
- "0 2921 2 1.0 2.0 \n",
- "1 4880 1 0.0 0.0 \n",
+ "0 3334 2 0.0 1.0 \n",
+ "1 4990 1 1.0 0.0 \n",
"\n",
" negativeIncrease positiveIncrease totalTestResultsIncrease \n",
- "0 517.0 16.0 533.0 \n",
- "1 0.0 109.0 109.0 "
+ "0 396.0 17.0 413.0 \n",
+ "1 0.0 110.0 110.0 "
]
},
"execution_count": 9,
@@ -455,18 +455,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 2.185859,
- "end_time": "2020-03-29T08:22:32.791063",
+ "duration": 2.53769,
+ "end_time": "2020-03-30T08:27:41.335247",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/bdf81mi5/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/d1j8kx27/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/bdf81mi5/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/d1j8kx27/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-03-29T08:22:30.605204",
+ "start_time": "2020-03-30T08:27:38.797557",
"version": "1.1.0"
}
},