From 812a4a3c6f29e2462c55fff604f5e5b6644d9326 Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Fri, 12 Jun 2020 07:28:01 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../4d4fd4a4bd4143109c05a9a4cf6100c6.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/4d4fd4a4bd4143109c05a9a4cf6100c6.cwl
diff --git a/.renku/workflow/4d4fd4a4bd4143109c05a9a4cf6100c6.cwl b/.renku/workflow/4d4fd4a4bd4143109c05a9a4cf6100c6.cwl
new file mode 100644
index 000000000..75a9e4293
--- /dev/null
+++ b/.renku/workflow/4d4fd4a4bd4143109c05a9a4cf6100c6.cwl
@@ -0,0 +1,120 @@
+class: Workflow
+cwlVersion: v1.0
+hints: []
+inputs:
+ input_1:
+ default: out_folder
+ streamable: false
+ type: string
+ input_2:
+ default: data/covidtracking
+ streamable: false
+ type: string
+ input_3:
+ default:
+ class: File
+ path: ../../notebooks/process/download-covidtracking-data.ipynb
+ streamable: false
+ type: File
+ input_4:
+ default: runs/download-covidtracking-data.runs.ipynb
+ streamable: false
+ type: string
+ input_5:
+ default: states-daily.json
+ streamable: false
+ type: string
+ input_6:
+ default: states-metadata.json
+ streamable: false
+ type: string
+outputs:
+ output_2:
+ outputSource: step_1/output_1
+ streamable: false
+ type: Directory
+ output_3:
+ outputSource: step_1/output_0
+ streamable: false
+ type: File
+requirements: []
+steps:
+ step_1:
+ in:
+ input_1: input_1
+ input_2: input_2
+ input_3: input_3
+ input_4: input_4
+ out:
+ - output_1
+ - output_0
+ run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
+ step_2:
+ in:
+ filename: input_5
+ input_directory: step_1/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_3:
+ in:
+ filename: input_6
+ input_directory: step_1/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 60fc7bacc..0088ba7b9 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:f267857f071efbd257d39a8e53597a33766547cafe42a33c8fe223186c40a1af
-size 4803258
+oid sha256:c094d0a006dab360e7a6e145993c356d376491c000065cb56bcccad90615f88b
+size 4853561
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index 4cdbf31f5..35d1920c5 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:b7f6ed28bdb6086871fec5a39085c151ec8b06e4e74304f4a6dac28966e241d1
-size 37118
+oid sha256:de4dc030edf206a7230a45472b7f29ecc2df492951ebf966a134a316a932b54f
+size 37594
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 69e7931ba..5e1967d20 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": 0.487122,
- "end_time": "2020-06-11T07:27:32.572137",
+ "duration": 2.865511,
+ "end_time": "2020-06-12T07:27:59.346077",
"exception": false,
- "start_time": "2020-06-11T07:27:32.085015",
+ "start_time": "2020-06-12T07:27:56.480566",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.021695,
- "end_time": "2020-06-11T07:27:32.609291",
+ "duration": 0.02443,
+ "end_time": "2020-06-12T07:27:59.385536",
"exception": false,
- "start_time": "2020-06-11T07:27:32.587596",
+ "start_time": "2020-06-12T07:27:59.361106",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.021591,
- "end_time": "2020-06-11T07:27:32.641347",
+ "duration": 0.023488,
+ "end_time": "2020-06-12T07:27:59.423778",
"exception": false,
- "start_time": "2020-06-11T07:27:32.619756",
+ "start_time": "2020-06-12T07:27:59.400290",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/iyyjg3ga/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/ns7xs7kt/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": 0.006855,
- "end_time": "2020-06-11T07:27:32.657727",
+ "duration": 0.007475,
+ "end_time": "2020-06-12T07:27:59.442200",
"exception": false,
- "start_time": "2020-06-11T07:27:32.650872",
+ "start_time": "2020-06-12T07:27:59.434725",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.171513,
- "end_time": "2020-06-11T07:27:32.835574",
+ "duration": 0.21893,
+ "end_time": "2020-06-12T07:27:59.667840",
"exception": false,
- "start_time": "2020-06-11T07:27:32.664061",
+ "start_time": "2020-06-12T07:27:59.448910",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.026162,
- "end_time": "2020-06-11T07:27:32.876893",
+ "duration": 0.025752,
+ "end_time": "2020-06-12T07:27:59.708723",
"exception": false,
- "start_time": "2020-06-11T07:27:32.850731",
+ "start_time": "2020-06-12T07:27:59.682971",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.074292,
- "end_time": "2020-06-11T07:27:32.960997",
+ "duration": 0.074061,
+ "end_time": "2020-06-12T07:27:59.794796",
"exception": false,
- "start_time": "2020-06-11T07:27:32.886705",
+ "start_time": "2020-06-12T07:27:59.720735",
"status": "completed"
},
"tags": []
@@ -249,10 +249,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.007967,
- "end_time": "2020-06-11T07:27:32.983385",
+ "duration": 0.00787,
+ "end_time": "2020-06-12T07:27:59.816778",
"exception": false,
- "start_time": "2020-06-11T07:27:32.975418",
+ "start_time": "2020-06-12T07:27:59.808908",
"status": "completed"
},
"tags": []
@@ -266,10 +266,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.191262,
- "end_time": "2020-06-11T07:27:33.181607",
+ "duration": 0.203847,
+ "end_time": "2020-06-12T07:28:00.027355",
"exception": false,
- "start_time": "2020-06-11T07:27:32.990345",
+ "start_time": "2020-06-12T07:27:59.823508",
"status": "completed"
},
"tags": []
@@ -286,10 +286,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.033195,
- "end_time": "2020-06-11T07:27:33.231102",
+ "duration": 0.033323,
+ "end_time": "2020-06-12T07:28:00.078483",
"exception": false,
- "start_time": "2020-06-11T07:27:33.197907",
+ "start_time": "2020-06-12T07:28:00.045160",
"status": "completed"
},
"tags": []
@@ -308,10 +308,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.210495,
- "end_time": "2020-06-11T07:27:33.456670",
+ "duration": 0.212287,
+ "end_time": "2020-06-12T07:28:00.306197",
"exception": false,
- "start_time": "2020-06-11T07:27:33.246175",
+ "start_time": "2020-06-12T07:28:00.093910",
"status": "completed"
},
"tags": []
@@ -321,7 +321,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "5449 data points\n"
+ "5505 data points\n"
]
},
{
@@ -371,21 +371,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20200610</td>\n",
+ " <td>20200611</td>\n",
" <td>AK</td>\n",
- " <td>593.0</td>\n",
- " <td>67127.0</td>\n",
+ " <td>611.0</td>\n",
+ " <td>68400.0</td>\n",
" <td>NaN</td>\n",
- " <td>22.0</td>\n",
+ " <td>18.0</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>67720</td>\n",
+ " <td>69011</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
- " <td>c9486e6829e118950bb3df693089884e90df1761</td>\n",
+ " <td>81be29c53674efe5eb683d80c80ed7b7a012f113</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>20200610</td>\n",
+ " <td>20200611</td>\n",
" <td>AL</td>\n",
- " <td>21989.0</td>\n",
- " <td>251068.0</td>\n",
+ " <td>22845.0</td>\n",
+ " <td>255981.0</td>\n",
" <td>NaN</td>\n",
- " <td>629.0</td>\n",
- " <td>2129.0</td>\n",
+ " <td>647.0</td>\n",
+ " <td>2165.0</td>\n",
" <td>NaN</td>\n",
- " <td>646.0</td>\n",
+ " <td>650.0</td>\n",
" <td>NaN</td>\n",
" <td>...</td>\n",
- " <td>273057</td>\n",
- " <td>15</td>\n",
- " <td>42</td>\n",
- " <td>19414d6567b3415847b4d4d5d4c191f2b954647f</td>\n",
+ " <td>278826</td>\n",
+ " <td>11</td>\n",
+ " <td>36</td>\n",
+ " <td>14deff225758b20ec967e765c4fb230342d28c70</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 20200610 AK 593.0 67127.0 NaN 22.0 \n",
- "1 20200610 AL 21989.0 251068.0 NaN 629.0 \n",
+ "0 20200611 AK 611.0 68400.0 NaN 18.0 \n",
+ "1 20200611 AL 22845.0 255981.0 NaN 647.0 \n",
"\n",
" hospitalizedCumulative inIcuCurrently inIcuCumulative \\\n",
"0 NaN NaN NaN \n",
- "1 2129.0 NaN 646.0 \n",
+ "1 2165.0 NaN 650.0 \n",
"\n",
" onVentilatorCurrently ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 3.0 ... 67720 0 0 \n",
- "1 NaN ... 273057 15 42 \n",
+ "0 4.0 ... 69011 0 0 \n",
+ "1 NaN ... 278826 11 36 \n",
"\n",
" hash commercialScore \\\n",
- "0 c9486e6829e118950bb3df693089884e90df1761 0 \n",
- "1 19414d6567b3415847b4d4d5d4c191f2b954647f 0 \n",
+ "0 81be29c53674efe5eb683d80c80ed7b7a012f113 0 \n",
+ "1 14deff225758b20ec967e765c4fb230342d28c70 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": 2.546059,
- "end_time": "2020-06-11T07:27:33.780969",
+ "duration": 5.690537,
+ "end_time": "2020-06-12T07:28:00.738243",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/iyyjg3ga/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/ns7xs7kt/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/iyyjg3ga/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/ns7xs7kt/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-06-11T07:27:31.234910",
+ "start_time": "2020-06-12T07:27:55.047706",
"version": "1.1.0"
}
},
--
GitLab