From 8354f13fc30adf55753da072e7d6342ef5fcba84 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Thu, 30 Jul 2020 07:31:19 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../812230b2beb242f38b032a29e4483a9f.cwl | 120 +++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 124 +++++++++---------
4 files changed, 186 insertions(+), 66 deletions(-)
create mode 100644 .renku/workflow/812230b2beb242f38b032a29e4483a9f.cwl
diff --git a/.renku/workflow/812230b2beb242f38b032a29e4483a9f.cwl b/.renku/workflow/812230b2beb242f38b032a29e4483a9f.cwl
new file mode 100644
index 000000000..0e74f62c2
--- /dev/null
+++ b/.renku/workflow/812230b2beb242f38b032a29e4483a9f.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_0:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+ output_2:
+ 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 1555ddfcf..d6c801a24 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:f7073509fa6668976fd62235a4e4b6bf0da964fb1656fff9738e99f4ea6c69b3
-size 7554680
+oid sha256:97c134a06483128db08e938cf71875392cbea85979fbd26c74781fce36af065d
+size 7607316
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 2160d9b58..3884a502a 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:c00124de21c434a218eed723fb751d1b2b6c4dd294118e95836ff189ebdbc9cd
-size 55384
+oid sha256:05e5ccb1f970e3a175428e24ab590fb9617b6758099708f6e6059a48e6140aa9
+size 56087
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 4a91fa1c3..e5b552504 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": 1.634067,
- "end_time": "2020-07-29T07:32:51.603280",
+ "duration": 4.245417,
+ "end_time": "2020-07-30T07:31:17.545891",
"exception": false,
- "start_time": "2020-07-29T07:32:49.969213",
+ "start_time": "2020-07-30T07:31:13.300474",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.027599,
- "end_time": "2020-07-29T07:32:51.645061",
+ "duration": 0.017034,
+ "end_time": "2020-07-30T07:31:17.576851",
"exception": false,
- "start_time": "2020-07-29T07:32:51.617462",
+ "start_time": "2020-07-30T07:31:17.559817",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.022819,
- "end_time": "2020-07-29T07:32:51.676504",
+ "duration": 0.020583,
+ "end_time": "2020-07-30T07:31:17.604547",
"exception": false,
- "start_time": "2020-07-29T07:32:51.653685",
+ "start_time": "2020-07-30T07:31:17.583964",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/0mrm7jst/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/vg71jqgt/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": 0.009235,
- "end_time": "2020-07-29T07:32:51.700436",
+ "duration": 0.007165,
+ "end_time": "2020-07-30T07:31:17.621588",
"exception": false,
- "start_time": "2020-07-29T07:32:51.691201",
+ "start_time": "2020-07-30T07:31:17.614423",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.082633,
- "end_time": "2020-07-29T07:32:51.789179",
+ "duration": 0.172965,
+ "end_time": "2020-07-30T07:31:17.801988",
"exception": false,
- "start_time": "2020-07-29T07:32:51.706546",
+ "start_time": "2020-07-30T07:31:17.629023",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.026774,
- "end_time": "2020-07-29T07:32:51.838420",
+ "duration": 0.019319,
+ "end_time": "2020-07-30T07:31:17.833009",
"exception": false,
- "start_time": "2020-07-29T07:32:51.811646",
+ "start_time": "2020-07-30T07:31:17.813690",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.09229,
- "end_time": "2020-07-29T07:32:51.941010",
+ "duration": 0.066186,
+ "end_time": "2020-07-30T07:31:17.908024",
"exception": false,
- "start_time": "2020-07-29T07:32:51.848720",
+ "start_time": "2020-07-30T07:31:17.841838",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007278,
- "end_time": "2020-07-29T07:32:51.960099",
+ "duration": 0.008214,
+ "end_time": "2020-07-30T07:31:17.927031",
"exception": false,
- "start_time": "2020-07-29T07:32:51.952821",
+ "start_time": "2020-07-30T07:31:17.918817",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.313721,
- "end_time": "2020-07-29T07:32:52.281007",
+ "duration": 0.326219,
+ "end_time": "2020-07-30T07:31:18.261696",
"exception": false,
- "start_time": "2020-07-29T07:32:51.967286",
+ "start_time": "2020-07-30T07:31:17.935477",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.035029,
- "end_time": "2020-07-29T07:32:52.331598",
+ "duration": 0.025568,
+ "end_time": "2020-07-30T07:31:18.299253",
"exception": false,
- "start_time": "2020-07-29T07:32:52.296569",
+ "start_time": "2020-07-30T07:31:18.273685",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.368739,
- "end_time": "2020-07-29T07:32:52.713521",
+ "duration": 0.331916,
+ "end_time": "2020-07-30T07:31:18.639298",
"exception": false,
- "start_time": "2020-07-29T07:32:52.344782",
+ "start_time": "2020-07-30T07:31:18.307382",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "8137 data points\n"
+ "8193 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200728</td>\n",
+ " <td>20200729</td>\n",
" <td>AK</td>\n",
- " <td>3350.0</td>\n",
- " <td>210525.0</td>\n",
+ " <td>3442.0</td>\n",
+ " <td>220222.0</td>\n",
" <td>NaN</td>\n",
- " <td>44.0</td>\n",
+ " <td>45.0</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
" <td>NaN</td>\n",
- " <td>4.0</td>\n",
+ " <td>3.0</td>\n",
" <td>...</td>\n",
- " <td>213875</td>\n",
- " <td>1</td>\n",
+ " <td>223664</td>\n",
+ " <td>0</td>\n",
" <td>0</td>\n",
- " <td>ae5f917caa2078779c9ac0c581af0b3740885be7</td>\n",
+ " <td>e3c05df1cf92b9c80941cec8daaf723905e7a0dd</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>20200728</td>\n",
+ " <td>20200729</td>\n",
" <td>AL</td>\n",
- " <td>82366.0</td>\n",
- " <td>583033.0</td>\n",
+ " <td>83782.0</td>\n",
+ " <td>584493.0</td>\n",
" <td>NaN</td>\n",
" <td>1598.0</td>\n",
" <td>9893.0</td>\n",
" <td>NaN</td>\n",
- " <td>1094.0</td>\n",
+ " <td>1109.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>665399</td>\n",
+ " <td>668275</td>\n",
+ " <td>47</td>\n",
" <td>0</td>\n",
- " <td>199</td>\n",
- " <td>c1a5bd8f18d98fc9530cd541a50772d21cbfb38a</td>\n",
+ " <td>a7b049cfd14780e56e6ef98fb2aba9f82fe89838</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 20200728 AK 3350.0 210525.0 NaN 44.0 \n",
- "1 20200728 AL 82366.0 583033.0 NaN 1598.0 \n",
+ "0 20200729 AK 3442.0 220222.0 NaN 45.0 \n",
+ "1 20200729 AL 83782.0 584493.0 NaN 1598.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 9893.0 NaN 1094.0 \n",
+ "1 9893.0 NaN 1109.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 4.0 ... 213875 1 0 \n",
- "1 NaN ... 665399 0 199 \n",
+ "0 3.0 ... 223664 0 0 \n",
+ "1 NaN ... 668275 47 0 \n",
"\n",
" hash commercialScore \\\n",
- "0 ae5f917caa2078779c9ac0c581af0b3740885be7 0 \n",
- "1 c1a5bd8f18d98fc9530cd541a50772d21cbfb38a 0 \n",
+ "0 e3c05df1cf92b9c80941cec8daaf723905e7a0dd 0 \n",
+ "1 a7b049cfd14780e56e6ef98fb2aba9f82fe89838 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": 4.508495,
- "end_time": "2020-07-29T07:32:53.140366",
+ "duration": 7.336817,
+ "end_time": "2020-07-30T07:31:18.963931",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/0mrm7jst/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/vg71jqgt/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/0mrm7jst/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/vg71jqgt/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-07-29T07:32:48.631871",
+ "start_time": "2020-07-30T07:31:11.627114",
"version": "1.1.0"
}
},
--
GitLab