From 50366b9b64638d1b345340e6d5db85e4126b45ce Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Fri, 31 Jul 2020 07:31:40 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../af5dfb58f2b24a47982f53bc439eb361.cwl | 120 +++++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 126 +++++++++---------
4 files changed, 187 insertions(+), 67 deletions(-)
create mode 100644 .renku/workflow/af5dfb58f2b24a47982f53bc439eb361.cwl
diff --git a/.renku/workflow/af5dfb58f2b24a47982f53bc439eb361.cwl b/.renku/workflow/af5dfb58f2b24a47982f53bc439eb361.cwl
new file mode 100644
index 000000000..6ce8c67ad
--- /dev/null
+++ b/.renku/workflow/af5dfb58f2b24a47982f53bc439eb361.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_2:
+ outputSource: step_2/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ 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 d6c801a24..451bde44e 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 sha256:97c134a06483128db08e938cf71875392cbea85979fbd26c74781fce36af065d
-size 7607316
+oid sha256:0e93551218f4f81392d24f6ff17007b5121303ee9eb8dbc1559da7bec33c93b2
+size 7659954
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 3884a502a..e561fa962 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 sha256:05e5ccb1f970e3a175428e24ab590fb9617b6758099708f6e6059a48e6140aa9
-size 56087
+oid sha256:97f32e3b08ceb5019605543e0a90d8b53c0933ad0950677c58fd868943bd2f38
+size 56338
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index c8da48431..9d0290c1e 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": 0.907046,
- "end_time": "2020-07-30T14:24:08.534068",
+ "duration": 0.636339,
+ "end_time": "2020-07-31T07:31:38.916840",
"exception": false,
- "start_time": "2020-07-30T14:24:07.627022",
+ "start_time": "2020-07-31T07:31:38.280501",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.017285,
- "end_time": "2020-07-30T14:24:08.564468",
+ "duration": 0.017811,
+ "end_time": "2020-07-31T07:31:38.947335",
"exception": false,
- "start_time": "2020-07-30T14:24:08.547183",
+ "start_time": "2020-07-31T07:31:38.929524",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.019325,
- "end_time": "2020-07-30T14:24:08.591665",
+ "duration": 0.019772,
+ "end_time": "2020-07-31T07:31:38.974996",
"exception": false,
- "start_time": "2020-07-30T14:24:08.572340",
+ "start_time": "2020-07-31T07:31:38.955224",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/fjybgsvd/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/z_m8yogb/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": 0.009349,
- "end_time": "2020-07-30T14:24:08.610870",
+ "duration": 0.006274,
+ "end_time": "2020-07-31T07:31:38.988972",
"exception": false,
- "start_time": "2020-07-30T14:24:08.601521",
+ "start_time": "2020-07-31T07:31:38.982698",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.204592,
- "end_time": "2020-07-30T14:24:08.822751",
+ "duration": 0.31111,
+ "end_time": "2020-07-31T07:31:39.306628",
"exception": false,
- "start_time": "2020-07-30T14:24:08.618159",
+ "start_time": "2020-07-31T07:31:38.995518",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.020289,
- "end_time": "2020-07-30T14:24:08.853913",
+ "duration": 0.019968,
+ "end_time": "2020-07-31T07:31:39.336696",
"exception": false,
- "start_time": "2020-07-30T14:24:08.833624",
+ "start_time": "2020-07-31T07:31:39.316728",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.062187,
- "end_time": "2020-07-30T14:24:08.924813",
+ "duration": 0.058807,
+ "end_time": "2020-07-31T07:31:39.403115",
"exception": false,
- "start_time": "2020-07-30T14:24:08.862626",
+ "start_time": "2020-07-31T07:31:39.344308",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.0084,
- "end_time": "2020-07-30T14:24:08.943709",
+ "duration": 0.007059,
+ "end_time": "2020-07-31T07:31:39.417766",
"exception": false,
- "start_time": "2020-07-30T14:24:08.935309",
+ "start_time": "2020-07-31T07:31:39.410707",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.227722,
- "end_time": "2020-07-30T14:24:09.179458",
+ "duration": 0.234612,
+ "end_time": "2020-07-31T07:31:39.659826",
"exception": false,
- "start_time": "2020-07-30T14:24:08.951736",
+ "start_time": "2020-07-31T07:31:39.425214",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.027108,
- "end_time": "2020-07-30T14:24:09.220333",
+ "duration": 0.029778,
+ "end_time": "2020-07-31T07:31:39.701277",
"exception": false,
- "start_time": "2020-07-30T14:24:09.193225",
+ "start_time": "2020-07-31T07:31:39.671499",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.309148,
- "end_time": "2020-07-30T14:24:09.540890",
+ "duration": 0.346106,
+ "end_time": "2020-07-31T07:31:40.058722",
"exception": false,
- "start_time": "2020-07-30T14:24:09.231742",
+ "start_time": "2020-07-31T07:31:39.712616",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "8193 data points\n"
+ "8249 data points\n"
]
},
{
@@ -371,10 +371,10 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200729</td>\n",
+ " <td>20200730</td>\n",
" <td>AK</td>\n",
- " <td>3442.0</td>\n",
- " <td>220222.0</td>\n",
+ " <td>3559.0</td>\n",
+ " <td>221498.0</td>\n",
" <td>NaN</td>\n",
" <td>45.0</td>\n",
" <td>NaN</td>\n",
@@ -382,10 +382,10 @@
" <td>NaN</td>\n",
" <td>3.0</td>\n",
" <td>...</td>\n",
- " <td>223664</td>\n",
- " <td>0</td>\n",
+ " <td>225057</td>\n",
+ " <td>1</td>\n",
" <td>0</td>\n",
- " <td>e3c05df1cf92b9c80941cec8daaf723905e7a0dd</td>\n",
+ " <td>d66445af73028a02a5d6713580a4c470cc603322</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>20200729</td>\n",
+ " <td>20200730</td>\n",
" <td>AL</td>\n",
- " <td>83782.0</td>\n",
- " <td>584493.0</td>\n",
+ " <td>85762.0</td>\n",
+ " <td>594346.0</td>\n",
" <td>NaN</td>\n",
- " <td>1598.0</td>\n",
- " <td>9893.0</td>\n",
+ " <td>1595.0</td>\n",
+ " <td>10070.0</td>\n",
" <td>NaN</td>\n",
- " <td>1109.0</td>\n",
+ " <td>1129.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>668275</td>\n",
- " <td>47</td>\n",
- " <td>0</td>\n",
- " <td>a7b049cfd14780e56e6ef98fb2aba9f82fe89838</td>\n",
+ " <td>680108</td>\n",
+ " <td>27</td>\n",
+ " <td>177</td>\n",
+ " <td>5776f9724a3452e48705a9b2c73f52d3e631229d</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 20200729 AK 3442.0 220222.0 NaN 45.0 \n",
- "1 20200729 AL 83782.0 584493.0 NaN 1598.0 \n",
+ "0 20200730 AK 3559.0 221498.0 NaN 45.0 \n",
+ "1 20200730 AL 85762.0 594346.0 NaN 1595.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 9893.0 NaN 1109.0 \n",
+ "1 10070.0 NaN 1129.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 3.0 ... 223664 0 0 \n",
- "1 NaN ... 668275 47 0 \n",
+ "0 3.0 ... 225057 1 0 \n",
+ "1 NaN ... 680108 27 177 \n",
"\n",
" hash commercialScore \\\n",
- "0 e3c05df1cf92b9c80941cec8daaf723905e7a0dd 0 \n",
- "1 a7b049cfd14780e56e6ef98fb2aba9f82fe89838 0 \n",
+ "0 d66445af73028a02a5d6713580a4c470cc603322 0 \n",
+ "1 5776f9724a3452e48705a9b2c73f52d3e631229d 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": 3.334052,
- "end_time": "2020-07-30T14:24:09.864496",
+ "duration": 3.000062,
+ "end_time": "2020-07-31T07:31:40.379070",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/fjybgsvd/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/z_m8yogb/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/fjybgsvd/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/z_m8yogb/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-07-30T14:24:06.530444",
+ "start_time": "2020-07-31T07:31:37.379008",
"version": "1.1.0"
}
},
--
GitLab