Configuring github actions to run on live api

.github/workflows/python_live_tests.yml

@@ -0,0 +1,54 @@
+name: Python live API tests
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.11']
+    env:
+      GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+      GBIF_USER: ${{ secrets.GBIF_USER }}
+      GBIF_PWD: ${{ secrets.GBIF_PWD }}
+      GBIF_EMAIL: ${{ secrets.GBIF_EMAIL }}
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install system dependencies
+      run: |
+        sudo add-apt-repository ppa:ubuntugis/ppa
+        sudo apt-get update
+        sudo apt-get install -y libgeos-c1v5 libgeos-dev
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+
+    - name: Delete vcr cassettes so that it runs live tests
+      run: |
+        rm -rf test/vcr_cassettes/*
+        if [ "$(ls -A test/vcr_cassettes)" ]; then
+          echo "Directory is not empty"
+          exit 1
+        fi
+
+    - name: Tests
+      run: pytest
+
+    - name: Check if vcr cassettes were created today
+      run: |
+        for file in test/vcr_cassettes/*; do
+          file_date=$(stat -c %y "$file" | cut -d ' ' -f 1)
+          echo "File $file was created on $file_date"
+          current_date=$(date +%Y-%m-%d)
+          if [[ "$file_date" != "$current_date" ]]; then
+            echo "File $file was not created today"
+            exit 1
+          fi
+        done  
+

.vscode/settings.json

@@ -0,0 +1,4 @@
+{
+    "python.testing.unittestEnabled": false,
+    "python.testing.pytestEnabled": true
+}

pygbif/caching.py

@@ -83,7 +83,7 @@ def caching(
         requests_cache.install_cache(
             cache_name=CACHE_NAME, backend=backend, expire_after=expire_after
         )
-        requests_cache.delete(expired=True)
+        requests_cache.delete(expired=True)()
 
     cache_settings = {
         "cache": cache,

test/test-occurrences-count.py

@@ -4,15 +4,15 @@
 from pygbif import occurrences
 
 brecord_res = [
-    "LITERATURE",
-    "OBSERVATION",
-    "LIVING_SPECIMEN",
-    "UNKNOWN",
-    "MATERIAL_SAMPLE",
-    "PRESERVED_SPECIMEN",
-    "MACHINE_OBSERVATION",
     "HUMAN_OBSERVATION",
-    "FOSSIL_SPECIMEN",
+    "PRESERVED_SPECIMEN", 
+    "MATERIAL_SAMPLE", 
+    "OBSERVATION", 
+    "MACHINE_OBSERVATION", 
+    "OCCURRENCE", 
+    "FOSSIL_SPECIMEN", 
+    "MATERIAL_CITATION", 
+    "LIVING_SPECIMEN"
 ]
 
 year_res = [

test/test-occurrences-download_cancel.py

@@ -2,7 +2,6 @@
 from pygbif import occurrences as occ
 import vcr
 
-
 @vcr.use_cassette(
     "test/vcr_cassettes/test_download_cancel.yaml", filter_headers=["authorization"]
 )

test/test-occurrences-get.py

@@ -6,24 +6,24 @@
 @vcr.use_cassette("test/vcr_cassettes/test_get.yaml")
 def test_get():
     "occurrences.get - basic test"
-    res = occurrences.get(key=1248387548)
+    res = occurrences.get(key=1986620884)
     assert "dict" == res.__class__.__name__
     assert len(res) > 30
-    assert 1248387548 == res["key"]
+    assert 1986620884 == res["key"]
 
 
 @vcr.use_cassette("test/vcr_cassettes/test_get_verbatim.yaml")
 def test_get_verbatim():
     "occurrences.get_verbatim - basic test"
-    res = occurrences.get_verbatim(key=1248387548)
+    res = occurrences.get_verbatim(key=1986620884)
     assert "dict" == res.__class__.__name__
     assert len(res) > 20
-    assert 1248387548 == res["key"]
+    assert 1986620884 == res["key"]
 
 
 @vcr.use_cassette("test/vcr_cassettes/test_get_fragment.yaml")
 def test_get_fragment():
     "occurrences.get_fragment - basic test"
-    res = occurrences.get_fragment(key=1052909293)
+    res = occurrences.get_fragment(key=1986620884)
     assert "dict" == res.__class__.__name__
-    assert "humanobservation" == res["basisOfRecord"]
+    assert "HumanObservation" == res["basisOfRecord"]

test/test-registry-dataset_metrics.py

@@ -8,7 +8,7 @@ def test_dataset_metrics():
     "registry.dataset_metrics - basic test"
     res = registry.dataset_metrics(uuid="3f8a1297-3259-4700-91fc-acc4170b27ce")
     assert dict == res.__class__
-    assert 19 == len(res)
+    assert 18 == len(res)
 
 
 @vcr.use_cassette("test/vcr_cassettes/test_dataset_metrics_multiple_uuids.yaml")

test/test-registry-networks.py

@@ -9,7 +9,7 @@ def test_networks():
     res = registry.networks()
     assert dict == res.__class__
     assert 2 == len(res)
-    assert 4 == len(res["data"])
+    assert 11 == len(res["data"])
     assert ["data", "meta"] == sorted(res.keys())
 
 
@@ -18,7 +18,7 @@ def test_networks_limit():
     "registry.networks - limit param "
     res = registry.networks(limit=5)
     assert dict == res.__class__
-    assert 4 == len(res["data"])
+    assert 5 == len(res["data"])
 
 
 @vcr.use_cassette("test/vcr_cassettes/test_networks_uuid.yaml")

test/test-species-name_lookup.py

@@ -10,7 +10,7 @@ def test_name_lookup():
     assert dict == res.__class__
     assert 6 == len(res)
     assert 100 == len(res["results"])
-    assert "Mammalia" == res["results"][0]["canonicalName"]
+    assert "Mammaliaformes" == res["results"][0]["canonicalName"]
 
 
 @vcr.use_cassette("test/vcr_cassettes/test_name_lookup_paging.yaml")

test/vcr_cassettes/test_count.yaml

@@ -2,26 +2,51 @@ interactions:
 - request:
     body: null
     headers:
-      Accept: ['*/*']
-      Accept-Encoding: ['gzip, deflate']
-      Connection: [keep-alive]
-      user-agent: ['python-requests/2.22.0,pygbif/0.3.9']
+      Accept:
+      - '*/*'
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      user-agent:
+      - python-requests/2.31.0,pygbif/0.6.3
     method: GET
     uri: https://api.gbif.org/v1/occurrence/count?taxonKey=3329049
   response:
-    body: {string: '443'}
+    body:
+      string: '874'
     headers:
-      Accept-Ranges: [bytes]
-      Access-Control-Allow-Methods: ['HEAD, GET, POST, DELETE, PUT, OPTIONS']
-      Access-Control-Allow-Origin: ['*']
-      Age: ['648']
-      Cache-Control: ['public, max-age=600']
-      Connection: [keep-alive]
-      Content-Length: ['3']
-      Content-Type: [application/json]
-      Date: ['Wed, 20 Nov 2019 17:47:00 GMT']
-      Server: [Jetty(9.3.z-SNAPSHOT)]
-      Via: [1.1 varnish (Varnish/5.2)]
-      X-Varnish: [1003619963 1001194130]
-    status: {code: 200, message: OK}
+      Accept-Ranges:
+      - bytes
+      Age:
+      - '0'
+      Cache-Control:
+      - public, max-age=600
+      Connection:
+      - keep-alive
+      Content-Length:
+      - '3'
+      Content-Type:
+      - application/json
+      Date:
+      - Fri, 01 Mar 2024 08:32:14 GMT
+      Expires:
+      - '0'
+      Pragma:
+      - no-cache
+      Vary:
+      - Origin, Access-Control-Request-Method, Access-Control-Request-Headers
+      Via:
+      - 1.1 varnish (Varnish/6.0)
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - DENY
+      X-Varnish:
+      - '726239410'
+      X-XSS-Protection:
+      - 1; mode=block
+    status:
+      code: 200
+      message: OK
 version: 1

test/vcr_cassettes/test_count_basisofrecord.yaml

@@ -2,26 +2,51 @@ interactions:
 - request:
     body: null
     headers:
-      Accept: ['*/*']
-      Accept-Encoding: ['gzip, deflate']
-      Connection: [keep-alive]
-      user-agent: ['python-requests/2.22.0,pygbif/0.3.9']
+      Accept:
+      - '*/*'
+      Accept-Encoding:
+      - gzip, deflate
+      Connection:
+      - keep-alive
+      user-agent:
+      - python-requests/2.31.0,pygbif/0.6.3
     method: GET
     uri: https://api.gbif.org/v1/occurrence/counts/basisOfRecord
   response:
-    body: {string: '{"HUMAN_OBSERVATION":1105239040,"PRESERVED_SPECIMEN":166101035,"MATERIAL_SAMPLE":25326157,"OBSERVATION":19633469,"UNKNOWN":17292300,"MACHINE_OBSERVATION":11917524,"FOSSIL_SPECIMEN":8961546,"LIVING_SPECIMEN":1629229,"LITERATURE":219727}'}
+    body:
+      string: '{"HUMAN_OBSERVATION":2300698840,"PRESERVED_SPECIMEN":237830598,"MATERIAL_SAMPLE":55644452,"OBSERVATION":20774268,"MACHINE_OBSERVATION":20542140,"OCCURRENCE":19297806,"FOSSIL_SPECIMEN":10246202,"MATERIAL_CITATION":2664586,"LIVING_SPECIMEN":2000680}'
     headers:
-      Accept-Ranges: [bytes]
-      Access-Control-Allow-Methods: ['HEAD, GET, POST, DELETE, PUT, OPTIONS']
-      Access-Control-Allow-Origin: ['*']
-      Age: ['0']
-      Cache-Control: ['public, max-age=600']
-      Connection: [keep-alive]
-      Content-Length: ['235']
-      Content-Type: [application/json]
-      Date: ['Wed, 20 Nov 2019 17:57:49 GMT']
-      Server: [Jetty(9.3.z-SNAPSHOT)]
-      Via: [1.1 varnish (Varnish/5.2)]
-      X-Varnish: ['1006275396']
-    status: {code: 200, message: OK}
+      Accept-Ranges:
+      - bytes
+      Age:
+      - '657'
+      Cache-Control:
+      - public, max-age=600
+      Connection:
+      - keep-alive
+      Content-Length:
+      - '247'
+      Content-Type:
+      - application/json
+      Date:
+      - Fri, 01 Mar 2024 08:21:17 GMT
+      Expires:
+      - '0'
+      Pragma:
+      - no-cache
+      Vary:
+      - Origin, Access-Control-Request-Method, Access-Control-Request-Headers
+      Via:
+      - 1.1 varnish (Varnish/6.0)
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - DENY
+      X-Varnish:
+      - 704940086 710148283
+      X-XSS-Protection:
+      - 1; mode=block
+    status:
+      code: 200
+      message: OK
 version: 1