From 201df7a068a49bd211e04ac6bf4e917efdee7fb2 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Wed, 29 Jul 2020 07:32:53 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../a31dda8820e245c6af116fee39caaeba.cwl | 120 ++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 128 +++++++++---------
4 files changed, 188 insertions(+), 68 deletions(-)
create mode 100644 .renku/workflow/a31dda8820e245c6af116fee39caaeba.cwl
diff --git a/.renku/workflow/a31dda8820e245c6af116fee39caaeba.cwl b/.renku/workflow/a31dda8820e245c6af116fee39caaeba.cwl
new file mode 100644
index 000000000..764b082e4
--- /dev/null
+++ b/.renku/workflow/a31dda8820e245c6af116fee39caaeba.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_2:
+ outputSource: step_3/output_0
+ streamable: false
+ type: File
+ output_3:
+ 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-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_0
+ - output_1
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
diff --git a/data/covidtracking/states-daily.json b/data/covidtracking/states-daily.json
index cdba449b4..1555ddfcf 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 sha256:516201d9016280980a6ee820c53937dbf7240419c40a76cef885c806668d569b
-size 7501954
+oid sha256:f7073509fa6668976fd62235a4e4b6bf0da964fb1656fff9738e99f4ea6c69b3
+size 7554680
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 09d0cab52..2160d9b58 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 sha256:44e29bf4c35ce79572343dd09de46c8730020a0703289e8e8996dd5ca125bc7e
-size 54647
+oid sha256:c00124de21c434a218eed723fb751d1b2b6c4dd294118e95836ff189ebdbc9cd
+size 55384
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 937352e5a..4a91fa1c3 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": 4.721152,
- "end_time": "2020-07-28T07:33:19.919400",
+ "duration": 1.634067,
+ "end_time": "2020-07-29T07:32:51.603280",
"exception": false,
- "start_time": "2020-07-28T07:33:15.198248",
+ "start_time": "2020-07-29T07:32:49.969213",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.022697,
- "end_time": "2020-07-28T07:33:19.955433",
+ "duration": 0.027599,
+ "end_time": "2020-07-29T07:32:51.645061",
"exception": false,
- "start_time": "2020-07-28T07:33:19.932736",
+ "start_time": "2020-07-29T07:32:51.617462",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.018764,
- "end_time": "2020-07-28T07:33:19.983298",
+ "duration": 0.022819,
+ "end_time": "2020-07-29T07:32:51.676504",
"exception": false,
- "start_time": "2020-07-28T07:33:19.964534",
+ "start_time": "2020-07-29T07:32:51.653685",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/zzp5_gpn/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/0mrm7jst/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": 0.008371,
- "end_time": "2020-07-28T07:33:19.999719",
+ "duration": 0.009235,
+ "end_time": "2020-07-29T07:32:51.700436",
"exception": false,
- "start_time": "2020-07-28T07:33:19.991348",
+ "start_time": "2020-07-29T07:32:51.691201",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.106491,
- "end_time": "2020-07-28T07:33:20.113724",
+ "duration": 0.082633,
+ "end_time": "2020-07-29T07:32:51.789179",
"exception": false,
- "start_time": "2020-07-28T07:33:20.007233",
+ "start_time": "2020-07-29T07:32:51.706546",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.024516,
- "end_time": "2020-07-28T07:33:20.150633",
+ "duration": 0.026774,
+ "end_time": "2020-07-29T07:32:51.838420",
"exception": false,
- "start_time": "2020-07-28T07:33:20.126117",
+ "start_time": "2020-07-29T07:32:51.811646",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.074387,
- "end_time": "2020-07-28T07:33:20.234935",
+ "duration": 0.09229,
+ "end_time": "2020-07-29T07:32:51.941010",
"exception": false,
- "start_time": "2020-07-28T07:33:20.160548",
+ "start_time": "2020-07-29T07:32:51.848720",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.008074,
- "end_time": "2020-07-28T07:33:20.251748",
+ "duration": 0.007278,
+ "end_time": "2020-07-29T07:32:51.960099",
"exception": false,
- "start_time": "2020-07-28T07:33:20.243674",
+ "start_time": "2020-07-29T07:32:51.952821",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.238079,
- "end_time": "2020-07-28T07:33:20.498065",
+ "duration": 0.313721,
+ "end_time": "2020-07-29T07:32:52.281007",
"exception": false,
- "start_time": "2020-07-28T07:33:20.259986",
+ "start_time": "2020-07-29T07:32:51.967286",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.030914,
- "end_time": "2020-07-28T07:33:20.543729",
+ "duration": 0.035029,
+ "end_time": "2020-07-29T07:32:52.331598",
"exception": false,
- "start_time": "2020-07-28T07:33:20.512815",
+ "start_time": "2020-07-29T07:32:52.296569",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.314232,
- "end_time": "2020-07-28T07:33:20.868187",
+ "duration": 0.368739,
+ "end_time": "2020-07-29T07:32:52.713521",
"exception": false,
- "start_time": "2020-07-28T07:33:20.553955",
+ "start_time": "2020-07-29T07:32:52.344782",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "8081 data points\n"
+ "8137 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200727</td>\n",
+ " <td>20200728</td>\n",
" <td>AK</td>\n",
- " <td>3206.0</td>\n",
- " <td>204162.0</td>\n",
+ " <td>3350.0</td>\n",
+ " <td>210525.0</td>\n",
" <td>NaN</td>\n",
- " <td>38.0</td>\n",
+ " <td>44.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>3.0</td>\n",
+ " <td>4.0</td>\n",
" <td>...</td>\n",
- " <td>207368</td>\n",
+ " <td>213875</td>\n",
" <td>1</td>\n",
" <td>0</td>\n",
- " <td>de28ff6d7d2874c791219904c2fa81f83142a78f</td>\n",
+ " <td>ae5f917caa2078779c9ac0c581af0b3740885be7</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -395,21 +395,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20200727</td>\n",
+ " <td>20200728</td>\n",
" <td>AL</td>\n",
- " <td>81115.0</td>\n",
- " <td>576844.0</td>\n",
+ " <td>82366.0</td>\n",
+ " <td>583033.0</td>\n",
" <td>NaN</td>\n",
- " <td>1599.0</td>\n",
- " <td>9694.0</td>\n",
+ " <td>1598.0</td>\n",
+ " <td>9893.0</td>\n",
" <td>NaN</td>\n",
- " <td>1081.0</td>\n",
+ " <td>1094.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>657959</td>\n",
- " <td>18</td>\n",
- " <td>537</td>\n",
- " <td>906fddfa88864f88bdf0d2bcb19cf267a406f2e6</td>\n",
+ " <td>665399</td>\n",
+ " <td>0</td>\n",
+ " <td>199</td>\n",
+ " <td>c1a5bd8f18d98fc9530cd541a50772d21cbfb38a</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -424,20 +424,20 @@
],
"text/plain": [
" date state positive negative pending hospitalizedCurrently \\\n",
- "0 20200727 AK 3206.0 204162.0 NaN 38.0 \n",
- "1 20200727 AL 81115.0 576844.0 NaN 1599.0 \n",
+ "0 20200728 AK 3350.0 210525.0 NaN 44.0 \n",
+ "1 20200728 AL 82366.0 583033.0 NaN 1598.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 9694.0 NaN 1081.0 \n",
+ "1 9893.0 NaN 1094.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 3.0 ... 207368 1 0 \n",
- "1 NaN ... 657959 18 537 \n",
+ "0 4.0 ... 213875 1 0 \n",
+ "1 NaN ... 665399 0 199 \n",
"\n",
" hash commercialScore \\\n",
- "0 de28ff6d7d2874c791219904c2fa81f83142a78f 0 \n",
- "1 906fddfa88864f88bdf0d2bcb19cf267a406f2e6 0 \n",
+ "0 ae5f917caa2078779c9ac0c581af0b3740885be7 0 \n",
+ "1 c1a5bd8f18d98fc9530cd541a50772d21cbfb38a 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -477,18 +477,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 7.539678,
- "end_time": "2020-07-28T07:33:21.188443",
+ "duration": 4.508495,
+ "end_time": "2020-07-29T07:32:53.140366",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/zzp5_gpn/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/0mrm7jst/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/zzp5_gpn/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/0mrm7jst/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-07-28T07:33:13.648765",
+ "start_time": "2020-07-29T07:32:48.631871",
"version": "1.1.0"
}
},
--
GitLab