diff --git a/.renku/workflow/8da137e532e245ab9b4eec02a551f756.cwl b/.renku/workflow/8da137e532e245ab9b4eec02a551f756.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..a282305da7d1840f2b9bdbd9a9d7b649221ef14c
--- /dev/null
+++ b/.renku/workflow/8da137e532e245ab9b4eec02a551f756.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_0:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_2:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+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_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-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 99d721ed2bb48353d1b37776794212205bd6dc5d..d26ad32fdd684cb80a899cff9b7ab9f51609d694 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:df4a48da05c6878a61511c2021a5d411742ae4073d16763f803115cf8900784d
-size 15810522
+oid sha256:8ebad7d955d752aceb574fc1350ef6a762ee12ab5c260ab3c6dd4afec3d49f5c
+size 15885953
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 77e163455bff354a0cb4b4fb0b377271170fabfa..0c501462c1b934af65e781c2be8da86c8a436be5 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 sha256:2868a9d42f7c9acf305bbb3fb7b2cb1bc8da99abdeb0414c9ab0bfaf1d7e03c3
-size 88112
+oid sha256:332734a3fad7b29d49cbc3275b1a653f2a41fb67abc9cb4916d4923e6c826ceb
+size 88234
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 1961076cc5bb56c6465cb1040dfc1a8bff986b3f..9f40ab1cca538923e249ec6f660c18e8ceb9a0d5 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": 4.046085,
- "end_time": "2020-10-02T07:38:06.758857",
+ "duration": 5.253052,
+ "end_time": "2020-10-03T07:35:25.026066",
"exception": false,
- "start_time": "2020-10-02T07:38:02.712772",
+ "start_time": "2020-10-03T07:35:19.773014",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.025391,
- "end_time": "2020-10-02T07:38:06.803555",
+ "duration": 0.022596,
+ "end_time": "2020-10-03T07:35:25.064552",
"exception": false,
- "start_time": "2020-10-02T07:38:06.778164",
+ "start_time": "2020-10-03T07:35:25.041956",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.02627,
- "end_time": "2020-10-02T07:38:06.839437",
+ "duration": 0.020122,
+ "end_time": "2020-10-03T07:35:25.093667",
"exception": false,
- "start_time": "2020-10-02T07:38:06.813167",
+ "start_time": "2020-10-03T07:35:25.073545",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/el6ip4bh/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/zy0hkj0c/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": 0.008354,
- "end_time": "2020-10-02T07:38:06.861958",
+ "duration": 0.006778,
+ "end_time": "2020-10-03T07:35:25.108259",
"exception": false,
- "start_time": "2020-10-02T07:38:06.853604",
+ "start_time": "2020-10-03T07:35:25.101481",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.758127,
- "end_time": "2020-10-02T07:38:07.627135",
+ "duration": 0.532189,
+ "end_time": "2020-10-03T07:35:25.645896",
"exception": false,
- "start_time": "2020-10-02T07:38:06.869008",
+ "start_time": "2020-10-03T07:35:25.113707",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.02875,
- "end_time": "2020-10-02T07:38:07.669426",
+ "duration": 0.022618,
+ "end_time": "2020-10-03T07:35:25.681256",
"exception": false,
- "start_time": "2020-10-02T07:38:07.640676",
+ "start_time": "2020-10-03T07:35:25.658638",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.109723,
- "end_time": "2020-10-02T07:38:07.793523",
+ "duration": 0.091493,
+ "end_time": "2020-10-03T07:35:25.780175",
"exception": false,
- "start_time": "2020-10-02T07:38:07.683800",
+ "start_time": "2020-10-03T07:35:25.688682",
"status": "completed"
},
"tags": []
@@ -280,10 +280,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007719,
- "end_time": "2020-10-02T07:38:07.814061",
+ "duration": 0.006967,
+ "end_time": "2020-10-03T07:35:25.803168",
"exception": false,
- "start_time": "2020-10-02T07:38:07.806342",
+ "start_time": "2020-10-03T07:35:25.796201",
"status": "completed"
},
"tags": []
@@ -297,10 +297,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 26.639647,
- "end_time": "2020-10-02T07:38:34.460276",
+ "duration": 26.252126,
+ "end_time": "2020-10-03T07:35:52.061529",
"exception": false,
- "start_time": "2020-10-02T07:38:07.820629",
+ "start_time": "2020-10-03T07:35:25.809403",
"status": "completed"
},
"tags": []
@@ -317,10 +317,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.045923,
- "end_time": "2020-10-02T07:38:34.525196",
+ "duration": 0.06406,
+ "end_time": "2020-10-03T07:35:52.143430",
"exception": false,
- "start_time": "2020-10-02T07:38:34.479273",
+ "start_time": "2020-10-03T07:35:52.079370",
"status": "completed"
},
"tags": []
@@ -339,10 +339,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.702638,
- "end_time": "2020-10-02T07:38:35.242651",
+ "duration": 0.575261,
+ "end_time": "2020-10-03T07:35:52.733021",
"exception": false,
- "start_time": "2020-10-02T07:38:34.540013",
+ "start_time": "2020-10-03T07:35:52.157760",
"status": "completed"
},
"tags": []
@@ -352,7 +352,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "11858 data points\n"
+ "11914 data points\n"
]
},
{
@@ -402,21 +402,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201001</td>\n",
+ " <td>20201002</td>\n",
" <td>AK</td>\n",
- " <td>8912.0</td>\n",
- " <td>453411.0</td>\n",
+ " <td>9040.0</td>\n",
+ " <td>460250.0</td>\n",
" <td>NaN</td>\n",
- " <td>462323.0</td>\n",
- " <td>42.0</td>\n",
+ " <td>469290.0</td>\n",
+ " <td>41.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>462323</td>\n",
- " <td>1</td>\n",
+ " <td>469290</td>\n",
+ " <td>0</td>\n",
" <td>0</td>\n",
- " <td>6fce5edde2805fba8ccfabc0232b39bb079a0c0a</td>\n",
+ " <td>77ea689d232f21d7c3e86721a92703f37b818df6</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>20201001</td>\n",
+ " <td>20201002</td>\n",
" <td>AL</td>\n",
- " <td>155744.0</td>\n",
- " <td>1000570.0</td>\n",
+ " <td>156698.0</td>\n",
+ " <td>1006612.0</td>\n",
" <td>NaN</td>\n",
- " <td>1138732.0</td>\n",
- " <td>760.0</td>\n",
- " <td>17257.0</td>\n",
+ " <td>1145601.0</td>\n",
+ " <td>752.0</td>\n",
+ " <td>17420.0</td>\n",
" <td>NaN</td>\n",
- " <td>1832.0</td>\n",
+ " <td>1840.0</td>\n",
" <td>...</td>\n",
- " <td>1156314</td>\n",
- " <td>8</td>\n",
- " <td>0</td>\n",
- " <td>d7277459136bf4c2075ceaea9cd64c6a193a9e80</td>\n",
+ " <td>1163310</td>\n",
+ " <td>2</td>\n",
+ " <td>163</td>\n",
+ " <td>38da52ec54bc8d9114fc1ef392985f137e8c9e1f</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -455,20 +455,20 @@
],
"text/plain": [
" date state positive negative pending totalTestResults \\\n",
- "0 20201001 AK 8912.0 453411.0 NaN 462323.0 \n",
- "1 20201001 AL 155744.0 1000570.0 NaN 1138732.0 \n",
+ "0 20201002 AK 9040.0 460250.0 NaN 469290.0 \n",
+ "1 20201002 AL 156698.0 1006612.0 NaN 1145601.0 \n",
"\n",
" hospitalizedCurrently hospitalizedCumulative inIcuCurrently \\\n",
- "0 42.0 NaN NaN \n",
- "1 760.0 17257.0 NaN \n",
+ "0 41.0 NaN NaN \n",
+ "1 752.0 17420.0 NaN \n",
"\n",
" inIcuCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 NaN ... 462323 1 0 \n",
- "1 1832.0 ... 1156314 8 0 \n",
+ "0 NaN ... 469290 0 0 \n",
+ "1 1840.0 ... 1163310 2 163 \n",
"\n",
" hash commercialScore \\\n",
- "0 6fce5edde2805fba8ccfabc0232b39bb079a0c0a 0 \n",
- "1 d7277459136bf4c2075ceaea9cd64c6a193a9e80 0 \n",
+ "0 77ea689d232f21d7c3e86721a92703f37b818df6 0 \n",
+ "1 38da52ec54bc8d9114fc1ef392985f137e8c9e1f 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": 34.808625,
- "end_time": "2020-10-02T07:38:35.670354",
+ "duration": 36.095374,
+ "end_time": "2020-10-03T07:35:53.164442",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/el6ip4bh/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/zy0hkj0c/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/el6ip4bh/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/zy0hkj0c/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-10-02T07:38:00.861729",
+ "start_time": "2020-10-03T07:35:17.069068",
"version": "1.1.0"
}
},