diff --git a/.renku/workflow/dbdecdb499f04eee86d54e69d32cba44.cwl b/.renku/workflow/dbdecdb499f04eee86d54e69d32cba44.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..bf3d45b32b4d5c704c364f99318a2acf1fdc743e
--- /dev/null
+++ b/.renku/workflow/dbdecdb499f04eee86d54e69d32cba44.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_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-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 cdfc89c699dc3163797eef25bed7389d6857db86..4599fa881e3862839816aed69d5d622295aebd92 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 sha256:9efebd725653a363e81e3ce23049783f07a69fc11c7baf53b4180832e074c705
-size 16904054
+oid sha256:f3e6ca4a0e573fb7c61646da3830e19767e4d6e572dabf41d2e37d455f7e62d2
+size 16980722
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 4275d0d934b67741c1962b4c44329caaa0194b56..86b2da912a1b8e618b9c1c732bf2b3892a7a360f 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 sha256:221fe0ffc46c51469e093fee5b79437b97dcefde8de4dac5b4e2ec4415aa8953
-size 95250
+oid sha256:819cc5dfeac04b86836b9fab05a39b13a545e06e9cd3fb5b9b300438608bad29
+size 95977
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index b248fdc78bbc61ce0043041399d27df23ded3314..5afe8f82bc12ed407dedc3734ba30d99f63de87d 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": 4.367513,
- "end_time": "2020-10-13T07:37:36.058414",
+ "duration": 2.358472,
+ "end_time": "2020-10-14T07:36:57.770956",
"exception": false,
- "start_time": "2020-10-13T07:37:31.690901",
+ "start_time": "2020-10-14T07:36:55.412484",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.024929,
- "end_time": "2020-10-13T07:37:36.100157",
+ "duration": 0.024658,
+ "end_time": "2020-10-14T07:36:57.811834",
"exception": false,
- "start_time": "2020-10-13T07:37:36.075228",
+ "start_time": "2020-10-14T07:36:57.787176",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.022783,
- "end_time": "2020-10-13T07:37:36.135278",
+ "duration": 0.021832,
+ "end_time": "2020-10-14T07:36:57.845563",
"exception": false,
- "start_time": "2020-10-13T07:37:36.112495",
+ "start_time": "2020-10-14T07:36:57.823731",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/0u0vlt9d/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/wkiajyw0/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": 0.005511,
- "end_time": "2020-10-13T07:37:36.148935",
+ "duration": 0.005956,
+ "end_time": "2020-10-14T07:36:57.859365",
"exception": false,
- "start_time": "2020-10-13T07:37:36.143424",
+ "start_time": "2020-10-14T07:36:57.853409",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.783371,
- "end_time": "2020-10-13T07:37:36.939210",
+ "duration": 0.961671,
+ "end_time": "2020-10-14T07:36:58.826923",
"exception": false,
- "start_time": "2020-10-13T07:37:36.155839",
+ "start_time": "2020-10-14T07:36:57.865252",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.027963,
- "end_time": "2020-10-13T07:37:36.980895",
+ "duration": 0.024675,
+ "end_time": "2020-10-14T07:36:58.867816",
"exception": false,
- "start_time": "2020-10-13T07:37:36.952932",
+ "start_time": "2020-10-14T07:36:58.843141",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.08441,
- "end_time": "2020-10-13T07:37:37.077147",
+ "duration": 0.116794,
+ "end_time": "2020-10-14T07:36:58.992950",
"exception": false,
- "start_time": "2020-10-13T07:37:36.992737",
+ "start_time": "2020-10-14T07:36:58.876156",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008393,
- "end_time": "2020-10-13T07:37:37.099679",
+ "duration": 0.008136,
+ "end_time": "2020-10-14T07:36:59.013531",
"exception": false,
- "start_time": "2020-10-13T07:37:37.091286",
+ "start_time": "2020-10-14T07:36:59.005395",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 27.922089,
- "end_time": "2020-10-13T07:38:05.028680",
+ "duration": 28.308817,
+ "end_time": "2020-10-14T07:37:27.328847",
"exception": false,
- "start_time": "2020-10-13T07:37:37.106591",
+ "start_time": "2020-10-14T07:36:59.020030",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.054229,
- "end_time": "2020-10-13T07:38:05.101847",
+ "duration": 0.032088,
+ "end_time": "2020-10-14T07:37:27.369420",
"exception": false,
- "start_time": "2020-10-13T07:38:05.047618",
+ "start_time": "2020-10-14T07:37:27.337332",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.602416,
- "end_time": "2020-10-13T07:38:05.720664",
+ "duration": 0.568302,
+ "end_time": "2020-10-14T07:37:27.944447",
"exception": false,
- "start_time": "2020-10-13T07:38:05.118248",
+ "start_time": "2020-10-14T07:37:27.376145",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "12477 data points\n"
+ "12533 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201012</td>\n",
+ " <td>20201013</td>\n",
" <td>AK</td>\n",
- " <td>10884.0</td>\n",
+ " <td>11039.0</td>\n",
" <td>NaN</td>\n",
- " <td>495043.0</td>\n",
+ " <td>503750.0</td>\n",
" <td>NaN</td>\n",
- " <td>505927.0</td>\n",
- " <td>50.0</td>\n",
+ " <td>514789.0</td>\n",
+ " <td>59.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>505927</td>\n",
+ " <td>514789</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>1d12a6644f8d97132e890998a17090d44e70d4e1</td>\n",
+ " <td>881fbdb23caeb53c47e5007c8599ec1624e1c68d</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>20201012</td>\n",
+ " <td>20201013</td>\n",
" <td>AL</td>\n",
- " <td>166076.0</td>\n",
- " <td>19853.0</td>\n",
- " <td>1068387.0</td>\n",
+ " <td>167193.0</td>\n",
+ " <td>20110.0</td>\n",
+ " <td>1074124.0</td>\n",
" <td>NaN</td>\n",
- " <td>1214610.0</td>\n",
- " <td>856.0</td>\n",
- " <td>18179.0</td>\n",
+ " <td>1221207.0</td>\n",
+ " <td>823.0</td>\n",
+ " <td>18440.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>1234463</td>\n",
- " <td>1</td>\n",
+ " <td>1241317</td>\n",
" <td>0</td>\n",
- " <td>feb6ff2653368253706dc08cae65080d91c5d680</td>\n",
+ " <td>261</td>\n",
+ " <td>19ea68f7f6d374d276ce094b7473ceb24e9e0cae</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -455,20 +455,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201012 AK 10884.0 NaN 495043.0 NaN \n",
- "1 20201012 AL 166076.0 19853.0 1068387.0 NaN \n",
+ "0 20201013 AK 11039.0 NaN 503750.0 NaN \n",
+ "1 20201013 AL 167193.0 20110.0 1074124.0 NaN \n",
"\n",
" totalTestResults hospitalizedCurrently hospitalizedCumulative \\\n",
- "0 505927.0 50.0 NaN \n",
- "1 1214610.0 856.0 18179.0 \n",
+ "0 514789.0 59.0 NaN \n",
+ "1 1221207.0 823.0 18440.0 \n",
"\n",
" inIcuCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 505927 0 0 \n",
- "1 NaN ... 1234463 1 0 \n",
+ "0 NaN ... 514789 0 0 \n",
+ "1 NaN ... 1241317 0 261 \n",
"\n",
" hash commercialScore \\\n",
- "0 1d12a6644f8d97132e890998a17090d44e70d4e1 0 \n",
- "1 feb6ff2653368253706dc08cae65080d91c5d680 0 \n",
+ "0 881fbdb23caeb53c47e5007c8599ec1624e1c68d 0 \n",
+ "1 19ea68f7f6d374d276ce094b7473ceb24e9e0cae 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -508,18 +508,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 36.408658,
- "end_time": "2020-10-13T07:38:06.155114",
+ "duration": 34.640425,
+ "end_time": "2020-10-14T07:37:28.363129",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/0u0vlt9d/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/wkiajyw0/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/0u0vlt9d/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/wkiajyw0/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-13T07:37:29.746456",
+ "start_time": "2020-10-14T07:36:53.722704",
"version": "1.1.0"
}
},