renku rerun data/covidtracking/states-metadata.json data/covidtracking/states-daily.json

4597cd96 · CI-bot · renku 0.10.4 · 4ca95a8c · 4597cd96 · 4597cd96
Commit 4597cd96 authored 4 years ago by CI-bot Committed by renku 0.10.4 4 years ago
--- a/.renku/workflow/faf9a75a6e43415bb1c5b9b002e51f78.cwl
+++ b/.renku/workflow/faf9a75a6e43415bb1c5b9b002e51f78.cwl
+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_0:
+    outputSource: step_3/output_1
+    streamable: false
+    type: Directory
+  output_2:
+    outputSource: step_3/output_0
+    streamable: false
+    type: File
+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_1
+    - output_0
+    run: a17d560c41a54f5aa307ce5f3c5effe5_papermill.cwl
--- a/data/covidtracking/states-daily.json
+++ b/data/covidtracking/states-daily.json
--- a/data/covidtracking/states-metadata.json
+++ b/data/covidtracking/states-metadata.json
--- a/runs/download-covidtracking-data.runs.ipynb
+++ b/runs/download-covidtracking-data.runs.ipynb
@@ -5,10 +5,10 @@
   "execution_count": 1,
   "metadata": {
    "papermill": {
-     "duration": 4.627897,
+     "duration": 1.081365,
-     "end_time": "2020-06-04T08:28:04.985732",
+     "end_time": "2020-06-05T07:26:40.376216",
     "exception": false,
-     "start_time": "2020-06-04T08:28:00.357835",
+     "start_time": "2020-06-05T07:26:39.294851",
     "status": "completed"
    },
    "tags": []
@@ -25,10 +25,10 @@
   "execution_count": 2,
   "metadata": {
    "papermill": {
-     "duration": 0.022291,
+     "duration": 0.026604,
-     "end_time": "2020-06-04T08:28:05.020399",
+     "end_time": "2020-06-05T07:26:40.419396",
     "exception": false,
-     "start_time": "2020-06-04T08:28:04.998108",
+     "start_time": "2020-06-05T07:26:40.392792",
     "status": "completed"
    },
    "tags": [
@@ -46,10 +46,10 @@
   "execution_count": 3,
   "metadata": {
    "papermill": {
-     "duration": 0.022545,
+     "duration": 0.023283,
-     "end_time": "2020-06-04T08:28:05.052282",
+     "end_time": "2020-06-05T07:26:40.455880",
     "exception": false,
-     "start_time": "2020-06-04T08:28:05.029737",
+     "start_time": "2020-06-05T07:26:40.432597",
     "status": "completed"
    },
    "tags": [
@@ -59,7 +59,7 @@
   "outputs": [],
   "source": [
    "# Parameters\n",
-    "PAPERMILL_INPUT_PATH = \"/tmp/m_83rm_4/notebooks/process/download-covidtracking-data.ipynb\"\n",
+    "PAPERMILL_INPUT_PATH = \"/tmp/nhlov4s_/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": 0.007006,
+     "duration": 0.007144,
-     "end_time": "2020-06-04T08:28:05.068409",
+     "end_time": "2020-06-05T07:26:40.473105",
     "exception": false,
-     "start_time": "2020-06-04T08:28:05.061403",
+     "start_time": "2020-06-05T07:26:40.465961",
     "status": "completed"
    },
    "tags": []
@@ -87,10 +87,10 @@
   "execution_count": 4,
   "metadata": {
    "papermill": {
-     "duration": 0.381514,
+     "duration": 0.174501,
-     "end_time": "2020-06-04T08:28:05.457090",
+     "end_time": "2020-06-05T07:26:40.653764",
     "exception": false,
-     "start_time": "2020-06-04T08:28:05.075576",
+     "start_time": "2020-06-05T07:26:40.479263",
     "status": "completed"
    },
    "tags": []
@@ -107,10 +107,10 @@
   "execution_count": 5,
   "metadata": {
    "papermill": {
-     "duration": 0.027088,
+     "duration": 0.025897,
-     "end_time": "2020-06-04T08:28:05.496958",
+     "end_time": "2020-06-05T07:26:40.695095",
     "exception": false,
-     "start_time": "2020-06-04T08:28:05.469870",
+     "start_time": "2020-06-05T07:26:40.669198",
     "status": "completed"
    },
    "tags": []
@@ -129,10 +129,10 @@
   "execution_count": 6,
   "metadata": {
    "papermill": {
-     "duration": 0.072587,
+     "duration": 0.073474,
-     "end_time": "2020-06-04T08:28:05.580434",
+     "end_time": "2020-06-05T07:26:40.778005",
     "exception": false,
-     "start_time": "2020-06-04T08:28:05.507847",
+     "start_time": "2020-06-05T07:26:40.704531",
     "status": "completed"
    },
    "tags": []
@@ -242,10 +242,10 @@
   "cell_type": "markdown",
   "metadata": {
    "papermill": {
-     "duration": 0.008248,
+     "duration": 0.00772,
-     "end_time": "2020-06-04T08:28:05.598828",
+     "end_time": "2020-06-05T07:26:40.798117",
     "exception": false,
-     "start_time": "2020-06-04T08:28:05.590580",
+     "start_time": "2020-06-05T07:26:40.790397",
     "status": "completed"
    },
    "tags": []
@@ -259,10 +259,10 @@
   "execution_count": 7,
   "metadata": {
    "papermill": {
-     "duration": 0.154111,
+     "duration": 0.209878,
-     "end_time": "2020-06-04T08:28:05.761833",
+     "end_time": "2020-06-05T07:26:41.014535",
     "exception": false,
-     "start_time": "2020-06-04T08:28:05.607722",
+     "start_time": "2020-06-05T07:26:40.804657",
     "status": "completed"
    },
    "tags": []
@@ -279,10 +279,10 @@
   "execution_count": 8,
   "metadata": {
    "papermill": {
-     "duration": 0.029699,
+     "duration": 0.033848,
-     "end_time": "2020-06-04T08:28:05.803127",
+     "end_time": "2020-06-05T07:26:41.066030",
     "exception": false,
-     "start_time": "2020-06-04T08:28:05.773428",
+     "start_time": "2020-06-05T07:26:41.032182",
     "status": "completed"
    },
    "tags": []
@@ -301,10 +301,10 @@
   "execution_count": 9,
   "metadata": {
    "papermill": {
-     "duration": 0.20856,
+     "duration": 0.195065,
-     "end_time": "2020-06-04T08:28:06.022260",
+     "end_time": "2020-06-05T07:26:41.272416",
     "exception": false,
-     "start_time": "2020-06-04T08:28:05.813700",
+     "start_time": "2020-06-05T07:26:41.077351",
     "status": "completed"
    },
    "tags": []
@@ -314,7 +314,7 @@
     "name": "stdout",
     "output_type": "stream",
     "text": [
-      "5057 data points\n"
+      "5113 data points\n"
     ]
    },
    {
@@ -364,21 +364,21 @@
       "  <tbody>\n",
       "    <tr>\n",
       "      <th>0</th>\n",
-       "      <td>20200603</td>\n",
+       "      <td>20200604</td>\n",
       "      <td>AK</td>\n",
-       "      <td>505.0</td>\n",
+       "      <td>513.0</td>\n",
-       "      <td>57677.0</td>\n",
+       "      <td>59584.0</td>\n",
       "      <td>NaN</td>\n",
-       "      <td>11.0</td>\n",
+       "      <td>13.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
-       "      <td>0.0</td>\n",
+       "      <td>1.0</td>\n",
       "      <td>...</td>\n",
-       "      <td>58182</td>\n",
+       "      <td>60097</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
-       "      <td>02548c93014e510ca02e0fc92122c299e4aa8e78</td>\n",
+       "      <td>c1046011af7271cbe2e6698526714c6cb5b92748</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
@@ -388,21 +388,21 @@
       "    </tr>\n",
       "    <tr>\n",
       "      <th>1</th>\n",
-       "      <td>20200603</td>\n",
+       "      <td>20200604</td>\n",
       "      <td>AL</td>\n",
-       "      <td>18851.0</td>\n",
+       "      <td>19072.0</td>\n",
-       "      <td>212743.0</td>\n",
+       "      <td>216227.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>NaN</td>\n",
-       "      <td>1900.0</td>\n",
+       "      <td>1929.0</td>\n",
       "      <td>NaN</td>\n",
-       "      <td>591.0</td>\n",
+       "      <td>601.0</td>\n",
       "      <td>NaN</td>\n",
       "      <td>...</td>\n",
-       "      <td>231594</td>\n",
+       "      <td>235299</td>\n",
-       "      <td>2</td>\n",
+       "      <td>0</td>\n",
-       "      <td>21</td>\n",
+       "      <td>29</td>\n",
-       "      <td>fe5df10e9c8639e15d2ce02d16d678e16f6f6cc7</td>\n",
+       "      <td>bcbefdb36212ba2b97b5a354f4e45bf16648ee23</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
       "      <td>0</td>\n",
@@ -417,20 +417,20 @@
      ],
      "text/plain": [
       "       date state  positive  negative  pending  hospitalizedCurrently  \\\n",
-       "0  20200603    AK     505.0   57677.0      NaN                   11.0   \n",
+       "0  20200604    AK     513.0   59584.0      NaN                   13.0   \n",
-       "1  20200603    AL   18851.0  212743.0      NaN                    NaN   \n",
+       "1  20200604    AL   19072.0  216227.0      NaN                    NaN   \n",
       "\n",
       "   hospitalizedCumulative  inIcuCurrently  inIcuCumulative  \\\n",
       "0                     NaN             NaN              NaN   \n",
-       "1                  1900.0             NaN            591.0   \n",
+       "1                  1929.0             NaN            601.0   \n",
       "\n",
       "   onVentilatorCurrently  ...  posNeg  deathIncrease hospitalizedIncrease  \\\n",
-       "0                    0.0  ...   58182              0                    0   \n",
+       "0                    1.0  ...   60097              0                    0   \n",
-       "1                    NaN  ...  231594              2                   21   \n",
+       "1                    NaN  ...  235299              0                   29   \n",
       "\n",
       "                                       hash commercialScore  \\\n",
-       "0  02548c93014e510ca02e0fc92122c299e4aa8e78               0   \n",
+       "0  c1046011af7271cbe2e6698526714c6cb5b92748               0   \n",
-       "1  fe5df10e9c8639e15d2ce02d16d678e16f6f6cc7               0   \n",
+       "1  bcbefdb36212ba2b97b5a354f4e45bf16648ee23               0   \n",
       "\n",
       "  negativeRegularScore  negativeScore  positiveScore score  grade  \n",
       "0                    0              0              0     0         \n",
@@ -470,18 +470,18 @@
   "version": "3.7.3"
  },
  "papermill": {
-   "duration": 7.919109,
+   "duration": 3.349554,
-   "end_time": "2020-06-04T08:28:06.447225",
+   "end_time": "2020-06-05T07:26:41.597056",
   "environment_variables": {},
   "exception": null,
-   "input_path": "/tmp/m_83rm_4/notebooks/process/download-covidtracking-data.ipynb",
+   "input_path": "/tmp/nhlov4s_/notebooks/process/download-covidtracking-data.ipynb",
   "output_path": "runs/download-covidtracking-data.runs.ipynb",
   "parameters": {
-    "PAPERMILL_INPUT_PATH": "/tmp/m_83rm_4/notebooks/process/download-covidtracking-data.ipynb",
+    "PAPERMILL_INPUT_PATH": "/tmp/nhlov4s_/notebooks/process/download-covidtracking-data.ipynb",
    "PAPERMILL_OUTPUT_PATH": "runs/download-covidtracking-data.runs.ipynb",
    "out_folder": "data/covidtracking"
   },
-   "start_time": "2020-06-04T08:27:58.528116",
+   "start_time": "2020-06-05T07:26:38.247502",
   "version": "1.1.0"
  }
 },

 %% Cell type:code id: tags:
 ``` python
 import requests
 import os
 import pandas as pd
 ```
 %% Cell type:code id: tags:parameters
 ``` python
 out_folder = "../data/covidtracking/"
 PAPERMILL_OUTPUT_PATH = None
 ```
 %% Cell type:code id: tags:injected-parameters
 ``` python
 # Parameters
-PAPERMILL_INPUT_PATH = "/tmp/m_83rm_4/notebooks/process/download-covidtracking-data.ipynb"
+PAPERMILL_INPUT_PATH = "/tmp/nhlov4s_/notebooks/process/download-covidtracking-data.ipynb"
 PAPERMILL_OUTPUT_PATH = "runs/download-covidtracking-data.runs.ipynb"
 out_folder = "data/covidtracking"
 ```
 %% Cell type:markdown id: tags:
 # Download state metadata
 Download a dataset of URLs for data for each US state and several territories. See [Google Doc](https://docs.google.com/spreadsheets/d/18oVRrHj3c183mHmq3m89_163yuYltLNlOmPerQ18E8w/htmlview?sle=true).
 %% Cell type:code id: tags:
 ``` python
 url = 'http://covidtracking.com/api/states/info'
 r = requests.get(url, allow_redirects=True)
 states_metadata_json = r.content
 ```
 %% Cell type:code id: tags:
 ``` python
 # save the result
 if PAPERMILL_OUTPUT_PATH:
    out_path = os.path.join(out_folder, 'states-metadata.json')
    with open(out_path, 'wb') as f:
        f.write(states_metadata_json)
 ```
 %% Cell type:code id: tags:
 ``` python
 metadata_df = pd.read_json(states_metadata_json)
 print(len(metadata_df), "states and territories have metadata")
 metadata_df.head(2)
 ```
 %% Output
    56 states and territories have metadata
      state                                              notes  \
    0    AK  Total tests are taken from the annotations on ...
    1    AL  Negatives = (Totals - Positives) \nPositives o...
                                             covid19Site  \
    0  http://dhss.alaska.gov/dph/Epi/id/Pages/COVID-...
    1  https://alpublichealth.maps.arcgis.com/apps/op...
                                    covid19SiteSecondary          twitter  \
    0  http://dhss.alaska.gov/dph/Epi/id/Pages/COVID-...     @Alaska_DHSS
    1            https://dph1.adph.state.al.us/covid-19/  @alpublichealth
                                          covid19SiteOld     name  fips pui    pum
    0  http://dhss.alaska.gov/dph/Epi/id/Pages/COVID-...   Alaska     2      False
    1  http://www.alabamapublichealth.gov/infectiousd...  Alabama     1      False
 %% Cell type:markdown id: tags:
 # Download daily state data
 %% Cell type:code id: tags:
 ``` python
 url = 'https://covidtracking.com/api/states/daily'
 r = requests.get(url, allow_redirects=True)
 states_daily_json = r.content
 ```
 %% Cell type:code id: tags:
 ``` python
 # save the result
 if PAPERMILL_OUTPUT_PATH:
    out_path = os.path.join(out_folder, 'states-daily.json')
    with open(out_path, 'wb') as f:
        f.write(states_daily_json)
 ```
 %% Cell type:code id: tags:
 ``` python
 data_df = pd.read_json(states_daily_json)
 print(len(data_df), "data points")
 data_df.head(2)
 ```
 %% Output
-    5057 data points
+    5113 data points
           date state  positive  negative  pending  hospitalizedCurrently  \
-    0  20200603    AK     505.0   57677.0      NaN                   11.0
+    0  20200604    AK     513.0   59584.0      NaN                   13.0
-    1  20200603    AL   18851.0  212743.0      NaN                    NaN
+    1  20200604    AL   19072.0  216227.0      NaN                    NaN
       hospitalizedCumulative  inIcuCurrently  inIcuCumulative  \
    0                     NaN             NaN              NaN
-    1                  1900.0             NaN            591.0
+    1                  1929.0             NaN            601.0
       onVentilatorCurrently  ...  posNeg  deathIncrease hospitalizedIncrease  \
-    0                    0.0  ...   58182              0                    0
+    0                    1.0  ...   60097              0                    0
-    1                    NaN  ...  231594              2                   21
+    1                    NaN  ...  235299              0                   29
                                           hash commercialScore  \
-    0  02548c93014e510ca02e0fc92122c299e4aa8e78               0
+    0  c1046011af7271cbe2e6698526714c6cb5b92748               0
-    1  fe5df10e9c8639e15d2ce02d16d678e16f6f6cc7               0
+    1  bcbefdb36212ba2b97b5a354f4e45bf16648ee23               0
      negativeRegularScore  negativeScore  positiveScore score  grade
    0                    0              0              0     0
    1                    0              0              0     0
    [2 rows x 35 columns]