diff --git a/.renku/workflow/044798d41dd4416b8d5c9355e16d551a.cwl b/.renku/workflow/044798d41dd4416b8d5c9355e16d551a.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..fde0deca2576a4283f0bc4ad475ba0a2c8b46edd
--- /dev/null
+++ b/.renku/workflow/044798d41dd4416b8d5c9355e16d551a.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_0:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+ output_2:
+ outputSource: step_3/output_1
+ streamable: false
+ type: Directory
+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_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index f6d605a83690cde7d628276bc3b8c4915fe3b1fe..fbc87dfdb96042130c44350efc976e4b0c5782d8 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 sha256:56ac30fed3a75c442559f4d888dadb545890e7ac864db45a1eb466a31ad4090f
-size 491877
+oid sha256:1b4cf0b6b4063633188335e2ac325c164482417d490642fd7bc2d28c999c0a16
+size 512308
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 464bdcf241c2e20b932f5ab998cf20d18b400c50..5ea208db896ce30ce126d6be413f55538bae9d2b 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:d7100b6f41ef1cfea9a6a995dc202bcb62aa8110ff6b5605c05e7ba1fd721794
-size 25296
+oid sha256:162a1e7cff5c197e79e0efcbfe69bd4c94d8872d0b7c143fe9286680489fa5a9
+size 25370
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 4f842f2090c7b93cd9893169c8a79ed031ab7316..0ca3b1c28caa3bb4b2a5d989a7431a3e229162d4 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": 0.471733,
- "end_time": "2020-03-31T08:24:30.934689",
+ "duration": 0.486177,
+ "end_time": "2020-04-01T11:24:57.200104",
"exception": false,
- "start_time": "2020-03-31T08:24:30.462956",
+ "start_time": "2020-04-01T11:24:56.713927",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.026018,
- "end_time": "2020-03-31T08:24:30.978110",
+ "duration": 0.019035,
+ "end_time": "2020-04-01T11:24:57.231060",
"exception": false,
- "start_time": "2020-03-31T08:24:30.952092",
+ "start_time": "2020-04-01T11:24:57.212025",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.023835,
- "end_time": "2020-03-31T08:24:31.015903",
+ "duration": 0.023334,
+ "end_time": "2020-04-01T11:24:57.261409",
"exception": false,
- "start_time": "2020-03-31T08:24:30.992068",
+ "start_time": "2020-04-01T11:24:57.238075",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/anascddl/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/v_x6sgie/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": 0.005891,
- "end_time": "2020-03-31T08:24:31.031893",
+ "duration": 0.007865,
+ "end_time": "2020-04-01T11:24:57.279101",
"exception": false,
- "start_time": "2020-03-31T08:24:31.026002",
+ "start_time": "2020-04-01T11:24:57.271236",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.748106,
- "end_time": "2020-03-31T08:24:31.785977",
+ "duration": 0.195872,
+ "end_time": "2020-04-01T11:24:57.481715",
"exception": false,
- "start_time": "2020-03-31T08:24:31.037871",
+ "start_time": "2020-04-01T11:24:57.285843",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.025387,
- "end_time": "2020-03-31T08:24:31.825517",
+ "duration": 0.024992,
+ "end_time": "2020-04-01T11:24:57.512245",
"exception": false,
- "start_time": "2020-03-31T08:24:31.800130",
+ "start_time": "2020-04-01T11:24:57.487253",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.072397,
- "end_time": "2020-03-31T08:24:31.905584",
+ "duration": 0.0607,
+ "end_time": "2020-04-01T11:24:57.580990",
"exception": false,
- "start_time": "2020-03-31T08:24:31.833187",
+ "start_time": "2020-04-01T11:24:57.520290",
"status": "completed"
},
"tags": []
@@ -246,10 +246,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.00763,
- "end_time": "2020-03-31T08:24:31.927988",
+ "duration": 0.007609,
+ "end_time": "2020-04-01T11:24:57.607059",
"exception": false,
- "start_time": "2020-03-31T08:24:31.920358",
+ "start_time": "2020-04-01T11:24:57.599450",
"status": "completed"
},
"tags": []
@@ -263,10 +263,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.330782,
- "end_time": "2020-03-31T08:24:32.265799",
+ "duration": 0.199119,
+ "end_time": "2020-04-01T11:24:57.812781",
"exception": false,
- "start_time": "2020-03-31T08:24:31.935017",
+ "start_time": "2020-04-01T11:24:57.613662",
"status": "completed"
},
"tags": []
@@ -283,10 +283,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.029205,
- "end_time": "2020-03-31T08:24:32.310572",
+ "duration": 0.027022,
+ "end_time": "2020-04-01T11:24:57.854471",
"exception": false,
- "start_time": "2020-03-31T08:24:32.281367",
+ "start_time": "2020-04-01T11:24:57.827449",
"status": "completed"
},
"tags": []
@@ -305,10 +305,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.07432,
- "end_time": "2020-03-31T08:24:32.406024",
+ "duration": 0.082088,
+ "end_time": "2020-04-01T11:24:57.946250",
"exception": false,
- "start_time": "2020-03-31T08:24:32.331704",
+ "start_time": "2020-04-01T11:24:57.864162",
"status": "completed"
},
"tags": []
@@ -318,7 +318,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "1373 data points\n"
+ "1429 data points\n"
]
},
{
@@ -364,43 +364,43 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200330</td>\n",
+ " <td>20200331</td>\n",
" <td>AK</td>\n",
- " <td>114.0</td>\n",
- " <td>3540.0</td>\n",
+ " <td>119.0</td>\n",
+ " <td>3594.0</td>\n",
" <td>NaN</td>\n",
" <td>7.0</td>\n",
" <td>3.0</td>\n",
- " <td>3654</td>\n",
- " <td>01a1c96fd2ed214d8747ab778c2fec7203c8cd2f</td>\n",
- " <td>2020-03-30T20:00:00Z</td>\n",
- " <td>3654</td>\n",
+ " <td>3713</td>\n",
+ " <td>5339d73f78797a2174fe32109c081c80915f8378</td>\n",
+ " <td>2020-03-31T20:00:00Z</td>\n",
+ " <td>3713</td>\n",
" <td>2</td>\n",
- " <td>1.0</td>\n",
- " <td>1.0</td>\n",
- " <td>308.0</td>\n",
- " <td>12.0</td>\n",
- " <td>320.0</td>\n",
+ " <td>0.0</td>\n",
+ " <td>0.0</td>\n",
+ " <td>54.0</td>\n",
+ " <td>5.0</td>\n",
+ " <td>59.0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200330</td>\n",
+ " <td>20200331</td>\n",
" <td>AL</td>\n",
- " <td>859.0</td>\n",
- " <td>5694.0</td>\n",
+ " <td>981.0</td>\n",
+ " <td>6298.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>6.0</td>\n",
- " <td>6553</td>\n",
- " <td>1ced1dbd9879f8bbc4b1f7b7876b82611895d58e</td>\n",
- " <td>2020-03-30T20:00:00Z</td>\n",
- " <td>6553</td>\n",
+ " <td>13.0</td>\n",
+ " <td>7279</td>\n",
+ " <td>06fc31f03af09c0f09f4c5bc18fac9daa63e94f8</td>\n",
+ " <td>2020-03-31T20:00:00Z</td>\n",
+ " <td>7279</td>\n",
" <td>1</td>\n",
- " <td>2.0</td>\n",
+ " <td>7.0</td>\n",
" <td>0.0</td>\n",
- " <td>1510.0</td>\n",
- " <td>53.0</td>\n",
- " <td>1563.0</td>\n",
+ " <td>604.0</td>\n",
+ " <td>122.0</td>\n",
+ " <td>726.0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
@@ -408,20 +408,20 @@
],
"text/plain": [
" date state positive negative pending hospitalized death total \\\n",
- "0 20200330 AK 114.0 3540.0 NaN 7.0 3.0 3654 \n",
- "1 20200330 AL 859.0 5694.0 NaN NaN 6.0 6553 \n",
+ "0 20200331 AK 119.0 3594.0 NaN 7.0 3.0 3713 \n",
+ "1 20200331 AL 981.0 6298.0 NaN NaN 13.0 7279 \n",
"\n",
" hash dateChecked \\\n",
- "0 01a1c96fd2ed214d8747ab778c2fec7203c8cd2f 2020-03-30T20:00:00Z \n",
- "1 1ced1dbd9879f8bbc4b1f7b7876b82611895d58e 2020-03-30T20:00:00Z \n",
+ "0 5339d73f78797a2174fe32109c081c80915f8378 2020-03-31T20:00:00Z \n",
+ "1 06fc31f03af09c0f09f4c5bc18fac9daa63e94f8 2020-03-31T20:00:00Z \n",
"\n",
" totalTestResults fips deathIncrease hospitalizedIncrease \\\n",
- "0 3654 2 1.0 1.0 \n",
- "1 6553 1 2.0 0.0 \n",
+ "0 3713 2 0.0 0.0 \n",
+ "1 7279 1 7.0 0.0 \n",
"\n",
" negativeIncrease positiveIncrease totalTestResultsIncrease \n",
- "0 308.0 12.0 320.0 \n",
- "1 1510.0 53.0 1563.0 "
+ "0 54.0 5.0 59.0 \n",
+ "1 604.0 122.0 726.0 "
]
},
"execution_count": 9,
@@ -455,18 +455,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 3.290092,
- "end_time": "2020-03-31T08:24:32.748032",
+ "duration": 2.364995,
+ "end_time": "2020-04-01T11:24:58.291712",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/anascddl/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/v_x6sgie/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/anascddl/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/v_x6sgie/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-03-31T08:24:29.457940",
+ "start_time": "2020-04-01T11:24:55.926717",
"version": "1.1.0"
}
},