Merge branch 'main' into XSLT_Shiraz

.github/workflows/python-app.yml

@@ -37,4 +37,12 @@ jobs:
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
-        pytest
+        coverage run -m pytest
+        coverage report -m
+    - name: Test & publish code coverage
+      uses: paambaati/[email protected]
+      env:
+        CC_TEST_REPORTER_ID: ${{secrets.CC_TEST_REPORTER_ID}}
+      with:
+        coverageCommand: coverage xml
+        debug: true

README.md

@@ -1,7 +1,10 @@
 # python-zbMathRest2Oai
+
+[![DeepSource](https://app.deepsource.com/gh/MaRDI4NFDI/python-zbMathRest2Oai.svg/?label=resolved+issues&show_trend=true&token=SovMnB53sVw8-JcWeL8YRnsG)](https://app.deepsource.com/gh/MaRDI4NFDI/python-zbMathRest2Oai/) [![SWH](https://archive.softwareheritage.org/badge/origin/https://github.com/MaRDI4NFDI/python-zbMathRest2Oai/)](https://archive.softwareheritage.org/browse/origin/?origin_url=https://github.com/MaRDI4NFDI/python-zbMathRest2Oai) [![Maintainability](https://api.codeclimate.com/v1/badges/88fa012874c78bfeb8bf/maintainability)](https://codeclimate.com/github/MaRDI4NFDI/python-zbMathRest2Oai/maintainability) [![Test Coverage](https://api.codeclimate.com/v1/badges/88fa012874c78bfeb8bf/test_coverage)](https://codeclimate.com/github/MaRDI4NFDI/python-zbMathRest2Oai/test_coverage)
+
 Read data from the zbMATH Open API https://api.zbmath.org/docs and feed it to the OAI-PMH server https://oai.portal.mardi4nfdi.de/oai/
 
 Hint for a proper installation:
 
 _ point to the directory
-_ execute "pip install -e ."
+_ execute "pip install -e ."

codemeta.json

@@ -0,0 +1,79 @@
+{
+    "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
+    "@type": "SoftwareSourceCode",
+    "codeRepository": "https://github.com/MaRDI4NFDI/python-zbMathRest2Oai",
+    "contIntegration": "https://github.com/MaRDI4NFDI/python-zbMathRest2Oai/blob/main/.github/workflows/python-app.yml",
+    "dateCreated": "2024-02-13",
+    "datePublished": "2024-02-13",
+    "dateModified": "2024-02-13",
+    "downloadUrl": "https://github.com/MaRDI4NFDI/python-zbMathRest2Oai/archive/refs/heads/main.zip",
+    "issueTracker": "https://github.com/MaRDI4NFDI/python-zbMathRest2Oai/issues",
+    "name": "python-zbMathRest2Oai",
+    "version": "1.0.0",
+    "identifier": "swh:1:dir:de327a8f9f82353f91c8dbbdd3f54d1efb3ba04e",
+    "description": "Read data from the zbMATH Open API https://api.zbmath.org/docs and feed it to the OAI-PMH server https://oai.portal.mardi4nfdi.de/oai/",
+    "releaseNotes": "This is the first codemeta file we create, and should be considered as a prototype for the future beta integration in the faircore4eosc.",
+    "developmentStatus": "wip",
+    "isPartOf": "https://portal.mardi4nfdi.de/wiki/Portal",
+    "funder": {
+        "@type": "Organization",
+        "name": "FIZ Karlstruhe"
+    },
+    "keywords": [
+        "zbmath",
+        "swmath",
+        "EOSC",
+        "PIDGraph",
+        "RDGraph",
+        "RSAC"
+    ],
+    "programmingLanguage": [
+        "Python3",
+        "XSLT",
+        "shell"
+    ],
+    "operatingSystem": [
+        "Linux"
+    ],
+    "softwareRequirements": [
+        "Python 3.9"
+    ],
+    "relatedLink": [
+        "https://faircore4eosc.eu/"
+    ],
+    "author": [
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0000-0002-8710-9548",
+            "givenName": "Maxence",
+            "familyName": "Azzouz-Thuderoz",
+            "email": "[email protected]",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "Department of Mathematics, FIZ Karlsruhe"
+            }
+        },
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0009-0005-1697-3282",
+            "givenName": "Shiraz",
+            "familyName": "Malla Mohamad",
+            "email": "[email protected]",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "Department of Mathematics, FIZ Karlsruhe"
+            }
+        },
+        {
+            "@type": "Person",
+            "@id": "https://orcid.org/0000-0001-7141-4997",
+            "givenName": "Moritz",
+            "familyName": "Schubotz",
+            "email": "[email protected]",
+            "affiliation": {
+                "@type": "Organization",
+                "name": "Department of Mathematics, FIZ Karlsruhe"
+            }
+        }
+    ]
+}

formats/createFormats.sh

@@ -8,4 +8,8 @@ curl --noproxy '*' -X POST -H 'Content-Type: application/json' -H  "Authorizatio
 printf "\n\nCreate Format datacite\n\n"
 curl --noproxy '*' -X POST -H 'Content-Type: application/json' -H  "Authorization: Basic $AUTH" -i 'https://oai-input.portal.mardi4nfdi.de/oai-backend/format' --data '{"metadataPrefix":"oai_zb_preview","schemaLocation":"https://zbmath.org/OAI/2.0/oai_zb_preview/","schemaNamespace":"https://zbmath.org/zbmath/elements/1.0/","identifierXpath":""}'
 printf "\n\n Read all formats\n\n"
+curl --noproxy '*' -X POST -H 'Content-Type: application/json' -H  "Authorization: Basic $AUTH" -i 'https://oai-input.portal.mardi4nfdi.de/oai-backend/format' --data '{"metadataPrefix":"zbmath_rest_api","schemaLocation":"https://github.com/MaRDI4NFDI/python-zbMathRest2Oai/blob/main/tests/data/plain.xml","schemaNamespace":"https://github.com/MaRDI4NFDI/python-zbMathRest2Oai/blob/main/tests/data/","identifierXpath":""}'
+printf "\n\nCreate Format zbmath_rest_api\n\n"
+
+
 curl --noproxy '*' -X GET -H  "Authorization: Basic $AUTH"  'https://oai-input.portal.mardi4nfdi.de/oai-backend/format'

pyproject.toml

@@ -12,11 +12,11 @@ dynamic = ["version"]
 dependencies = [
     "dict2xml",
     "requests",
-    "swagger_client @ git+https://github.com/zbMATHOpen/zbRestApiClient.git"
 ]
 [project.optional-dependencies]
 test = [
     "black",
+    "coverage",
     "flake8",
     "isort",
     "pytest",
@@ -26,7 +26,8 @@ test = [
     "requests_mock",
     "python-dateutil",
     "pytest-coverage",
-    "xmldiff"
+    "xmldiff",
+    "lxml"
 ]
 
 [tool.setuptools]

src/zbmath_rest2oai/fake_dict_sw.py

@@ -0,0 +1,6 @@
+def fake_dict_sw():
+    with open('software.csv','w') as f:
+        return f.write("\n".join(map(str,list(range(2, 10)))))
+
+if __name__ == '__main__':
+    fake_dict_sw()

src/zbmath_rest2oai/getAsXml.py

@@ -2,25 +2,26 @@
 import requests
 
 
-def final_xml2(de):
+def final_xml2(de, api_source):
 
     headers = {'Accept': 'application/json'}
-
-    r = requests.get('https://api.zbmath.org/v1/document/' + de, headers=headers)
+    r = requests.get(api_source + de, headers=headers)
     if r.status_code != 200:
         raise Exception(f"Unexpected response with status code {r.status_code}: {r.text}")
     json = r.json()
     # Bugfix as the sates are lists of lists which has no canonical XML mapping
-    states = {}
-    for lst in json['result']['states']:
-        [k, v] = lst
-        states[k] = v
-    json['result']['states'] = states
+    if type(json['result'])==dict:
+
+        states = {}
+        for lst in json['result']['states']:
+            [k, v] = lst
+            states[k] = v
+        json['result']['states'] = states
     # End of fix
     return (
         dict2xml.Converter(wrap="root")
         .build(json, closed_tags_for=[
             # Bugfix for wired XML output such as the string None or </>
             [], '', [None], None
         ])
-    )
+    )