From 46e3de8333eb35561a51d197fc399394280641ef Mon Sep 17 00:00:00 2001
From: "CR (covid cron)" <beepbop@example.com>
Date: Fri, 4 Dec 2020 07:37:09 +0000
Subject: [PATCH] renku rerun data/covidtracking/states-metadata.json
data/covidtracking/states-daily.json
---
.../fee2db68809c45de96163347d55b9425.cwl | 120 +++++++++++++++
data/covidtracking/states-daily.json | 4 +-
data/covidtracking/states-metadata.json | 4 +-
runs/download-covidtracking-data.runs.ipynb | 138 +++++++++---------
4 files changed, 193 insertions(+), 73 deletions(-)
create mode 100644 .renku/workflow/fee2db68809c45de96163347d55b9425.cwl
diff --git a/.renku/workflow/fee2db68809c45de96163347d55b9425.cwl b/.renku/workflow/fee2db68809c45de96163347d55b9425.cwl
new file mode 100644
index 000000000..7e18cfca8
--- /dev/null
+++ b/.renku/workflow/fee2db68809c45de96163347d55b9425.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_2:
+ outputSource: step_2/output_0
+ streamable: false
+ type: File
+ output_3:
+ 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 7ffcf1bcc..c0c399f22 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:c180ff6d02061f0792e2ae53cc4a47b78340a48405898e385a3fcdb11dbc9045
-size 21027260
+oid sha256:662e369e343e09636e98549770cf2070c4f1d1b44b3ad0fb199e26762e993149
+size 21104582
diff --git a/data/covidtracking/states-metadata.json b/data/covidtracking/states-metadata.json
index a7a7489b3..6a8a0a5c3 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 sha256:8e57dac38e089a26811c85796f13c80ec2df5ac7e2a2dfa69c7e25fc57f3dd8d
-size 143804
+oid sha256:4c0175b1b16a001928a55df9de49217460b254e09c141aafb61ba8725dfb624c
+size 143951
diff --git a/runs/download-covidtracking-data.runs.ipynb b/runs/download-covidtracking-data.runs.ipynb
index 6b36dbd4a..e9a5c9415 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": 4.788875,
- "end_time": "2020-12-03T07:38:28.465846",
+ "duration": 4.531192,
+ "end_time": "2020-12-04T07:37:06.722979",
"exception": false,
- "start_time": "2020-12-03T07:38:23.676971",
+ "start_time": "2020-12-04T07:37:02.191787",
"status": "completed"
},
"tags": []
@@ -25,10 +25,10 @@
"execution_count": 2,
"metadata": {
"papermill": {
- "duration": 0.019484,
- "end_time": "2020-12-03T07:38:28.499005",
+ "duration": 0.020784,
+ "end_time": "2020-12-04T07:37:06.757030",
"exception": false,
- "start_time": "2020-12-03T07:38:28.479521",
+ "start_time": "2020-12-04T07:37:06.736246",
"status": "completed"
},
"tags": [
@@ -46,10 +46,10 @@
"execution_count": 3,
"metadata": {
"papermill": {
- "duration": 0.011148,
- "end_time": "2020-12-03T07:38:28.517058",
+ "duration": 0.021,
+ "end_time": "2020-12-04T07:37:06.785589",
"exception": false,
- "start_time": "2020-12-03T07:38:28.505910",
+ "start_time": "2020-12-04T07:37:06.764589",
"status": "completed"
},
"tags": [
@@ -59,7 +59,7 @@
"outputs": [],
"source": [
"# Parameters\n",
- "PAPERMILL_INPUT_PATH = \"/tmp/18hdod4w/notebooks/process/download-covidtracking-data.ipynb\"\n",
+ "PAPERMILL_INPUT_PATH = \"/tmp/4jh789g5/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": 0.004225,
- "end_time": "2020-12-03T07:38:28.525806",
+ "duration": 0.007858,
+ "end_time": "2020-12-04T07:37:06.804981",
"exception": false,
- "start_time": "2020-12-03T07:38:28.521581",
+ "start_time": "2020-12-04T07:37:06.797123",
"status": "completed"
},
"tags": []
@@ -87,10 +87,10 @@
"execution_count": 4,
"metadata": {
"papermill": {
- "duration": 0.355297,
- "end_time": "2020-12-03T07:38:28.885395",
+ "duration": 0.443813,
+ "end_time": "2020-12-04T07:37:07.254800",
"exception": false,
- "start_time": "2020-12-03T07:38:28.530098",
+ "start_time": "2020-12-04T07:37:06.810987",
"status": "completed"
},
"tags": []
@@ -107,10 +107,10 @@
"execution_count": 5,
"metadata": {
"papermill": {
- "duration": 0.014069,
- "end_time": "2020-12-03T07:38:28.908662",
+ "duration": 0.023261,
+ "end_time": "2020-12-04T07:37:07.291923",
"exception": false,
- "start_time": "2020-12-03T07:38:28.894593",
+ "start_time": "2020-12-04T07:37:07.268662",
"status": "completed"
},
"tags": []
@@ -129,10 +129,10 @@
"execution_count": 6,
"metadata": {
"papermill": {
- "duration": 0.057278,
- "end_time": "2020-12-03T07:38:28.970747",
+ "duration": 0.06675,
+ "end_time": "2020-12-04T07:37:07.366359",
"exception": false,
- "start_time": "2020-12-03T07:38:28.913469",
+ "start_time": "2020-12-04T07:37:07.299609",
"status": "completed"
},
"tags": []
@@ -284,10 +284,10 @@
"cell_type": "markdown",
"metadata": {
"papermill": {
- "duration": 0.004708,
- "end_time": "2020-12-03T07:38:28.981128",
+ "duration": 0.007091,
+ "end_time": "2020-12-04T07:37:07.384941",
"exception": false,
- "start_time": "2020-12-03T07:38:28.976420",
+ "start_time": "2020-12-04T07:37:07.377850",
"status": "completed"
},
"tags": []
@@ -301,10 +301,10 @@
"execution_count": 7,
"metadata": {
"papermill": {
- "duration": 0.611817,
- "end_time": "2020-12-03T07:38:29.597559",
+ "duration": 0.642862,
+ "end_time": "2020-12-04T07:37:08.033860",
"exception": false,
- "start_time": "2020-12-03T07:38:28.985742",
+ "start_time": "2020-12-04T07:37:07.390998",
"status": "completed"
},
"tags": []
@@ -321,10 +321,10 @@
"execution_count": 8,
"metadata": {
"papermill": {
- "duration": 0.050611,
- "end_time": "2020-12-03T07:38:29.662663",
+ "duration": 0.058701,
+ "end_time": "2020-12-04T07:37:08.109308",
"exception": false,
- "start_time": "2020-12-03T07:38:29.612052",
+ "start_time": "2020-12-04T07:37:08.050607",
"status": "completed"
},
"tags": []
@@ -343,10 +343,10 @@
"execution_count": 9,
"metadata": {
"papermill": {
- "duration": 0.583797,
- "end_time": "2020-12-03T07:38:30.259718",
+ "duration": 0.506741,
+ "end_time": "2020-12-04T07:37:08.629737",
"exception": false,
- "start_time": "2020-12-03T07:38:29.675921",
+ "start_time": "2020-12-04T07:37:08.122996",
"status": "completed"
},
"tags": []
@@ -356,7 +356,7 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "15409 data points\n"
+ "15465 data points\n"
]
},
{
@@ -406,21 +406,21 @@
" <tbody>\n",
" <tr>\n",
" <th>0</th>\n",
- " <td>20201202</td>\n",
+ " <td>20201203</td>\n",
" <td>AK</td>\n",
- " <td>32531.0</td>\n",
+ " <td>33291.0</td>\n",
" <td>NaN</td>\n",
- " <td>992112.0</td>\n",
+ " <td>1007214.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsViral</td>\n",
- " <td>1024643.0</td>\n",
- " <td>164.0</td>\n",
- " <td>768.0</td>\n",
+ " <td>1040505.0</td>\n",
+ " <td>157.0</td>\n",
+ " <td>783.0</td>\n",
" <td>...</td>\n",
- " <td>1024643</td>\n",
- " <td>0</td>\n",
- " <td>19</td>\n",
- " <td>a67835c9975e7a741cbe7511d7b8014f238f7381</td>\n",
+ " <td>1040505</td>\n",
+ " <td>8</td>\n",
+ " <td>15</td>\n",
+ " <td>2681286b4959bcec2a503789d53119c645f4b0c6</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -430,21 +430,21 @@
" </tr>\n",
" <tr>\n",
" <th>1</th>\n",
- " <td>20201202</td>\n",
+ " <td>20201203</td>\n",
" <td>AL</td>\n",
- " <td>256828.0</td>\n",
- " <td>43656.0</td>\n",
- " <td>1390351.0</td>\n",
+ " <td>260359.0</td>\n",
+ " <td>44421.0</td>\n",
+ " <td>1400010.0</td>\n",
" <td>NaN</td>\n",
" <td>totalTestsPeopleViral</td>\n",
- " <td>1603523.0</td>\n",
- " <td>1801.0</td>\n",
- " <td>25821.0</td>\n",
+ " <td>1615948.0</td>\n",
+ " <td>1827.0</td>\n",
+ " <td>26062.0</td>\n",
" <td>...</td>\n",
- " <td>1647179</td>\n",
- " <td>73</td>\n",
- " <td>211</td>\n",
- " <td>4aa82c6006d2babec8c2e4268bc0d73e2681fe76</td>\n",
+ " <td>1660369</td>\n",
+ " <td>65</td>\n",
+ " <td>241</td>\n",
+ " <td>d333019ec43ddf9c5c4ec262bc5ed78ee214f19b</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
" <td>0</td>\n",
@@ -459,20 +459,20 @@
],
"text/plain": [
" date state positive probableCases negative pending \\\n",
- "0 20201202 AK 32531.0 NaN 992112.0 NaN \n",
- "1 20201202 AL 256828.0 43656.0 1390351.0 NaN \n",
+ "0 20201203 AK 33291.0 NaN 1007214.0 NaN \n",
+ "1 20201203 AL 260359.0 44421.0 1400010.0 NaN \n",
"\n",
" totalTestResultsSource totalTestResults hospitalizedCurrently \\\n",
- "0 totalTestsViral 1024643.0 164.0 \n",
- "1 totalTestsPeopleViral 1603523.0 1801.0 \n",
+ "0 totalTestsViral 1040505.0 157.0 \n",
+ "1 totalTestsPeopleViral 1615948.0 1827.0 \n",
"\n",
" hospitalizedCumulative ... posNeg deathIncrease hospitalizedIncrease \\\n",
- "0 768.0 ... 1024643 0 19 \n",
- "1 25821.0 ... 1647179 73 211 \n",
+ "0 783.0 ... 1040505 8 15 \n",
+ "1 26062.0 ... 1660369 65 241 \n",
"\n",
" hash commercialScore \\\n",
- "0 a67835c9975e7a741cbe7511d7b8014f238f7381 0 \n",
- "1 4aa82c6006d2babec8c2e4268bc0d73e2681fe76 0 \n",
+ "0 2681286b4959bcec2a503789d53119c645f4b0c6 0 \n",
+ "1 d333019ec43ddf9c5c4ec262bc5ed78ee214f19b 0 \n",
"\n",
" negativeRegularScore negativeScore positiveScore score grade \n",
"0 0 0 0 0 \n",
@@ -512,18 +512,18 @@
"version": "3.7.3"
},
"papermill": {
- "duration": 8.673797,
- "end_time": "2020-12-03T07:38:30.582322",
+ "duration": 8.083653,
+ "end_time": "2020-12-04T07:37:08.951693",
"environment_variables": {},
"exception": null,
- "input_path": "/tmp/18hdod4w/notebooks/process/download-covidtracking-data.ipynb",
+ "input_path": "/tmp/4jh789g5/notebooks/process/download-covidtracking-data.ipynb",
"output_path": "runs/download-covidtracking-data.runs.ipynb",
"parameters": {
- "PAPERMILL_INPUT_PATH": "/tmp/18hdod4w/notebooks/process/download-covidtracking-data.ipynb",
+ "PAPERMILL_INPUT_PATH": "/tmp/4jh789g5/notebooks/process/download-covidtracking-data.ipynb",
"PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
"out_folder": "data/covidtracking"
},
- "start_time": "2020-12-03T07:38:21.908525",
+ "start_time": "2020-12-04T07:37:00.868040",
"version": "1.1.0"
}
},
--
GitLab