first prototype

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+

example_scicat.py

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+#!/usr/bin/env python3
+
+import urllib3
+
+urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
+
+
+from scilog import SciCat
+
+url = "https://dacat.psi.ch/api/v3/"
+cat = SciCat(url)
+
+props = cat.proposals
+nprops = len(props)
+print(f"got {nprops} proposals")
+print(props[0])
+
+
+

example_scilog.py

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+#!/usr/bin/env python3
+
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument("pgroup", help="Expected form: p12345")
+
+clargs = parser.parse_args()
+pgroup = clargs.pgroup
+
+
+import urllib3
+
+urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
+
+
+from scilog import SciLog
+
+url = "https://lnode2.psi.ch/api/v1"
+log = SciLog(url)
+#print(log.token)
+loc = log.get_snippets(title="location", ownerGroup="admin")
+
+assert len(loc) == 1
+loc_id = loc[0]["id"]
+print(loc_id)
+
+lb = log.get_snippets(snippetType="logbook", ownerGroup=pgroup)
+
+assert len(lb) == 1
+lb_id = lb[0]["id"]
+print(lb_id)
+
+res = log.post_snippet(snippetType="paragraph", ownerGroup=pgroup, parentId=lb_id, textcontent="<p>from python</p>")
+print(res)
+
+snips = log.get_snippets(snippetType="paragraph", ownerGroup=pgroup)
+print(snips)
+
+
+

scilog/__init__.py

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+
+from .scicat import SciCat
+from .scilog import SciLog
+
+

scilog/autherror.py

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+
+class AuthError(Exception):
+    pass
+
+

scilog/config.py

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+from pathlib import Path
+import json
+
+
+class Config(dict):
+
+    def __init__(self, fname, folder=None):
+        if folder is not None:
+            folder = Path(folder)
+        else:
+            folder = Path.home()
+        self.fname = folder / fname
+        content = self._load()
+        super().update(content)
+
+    def __setitem__(self, name, value):
+        self.update(**{name: value})
+
+    def update(self, **kwargs):
+        super().update(**kwargs)
+        self._save()
+
+    def _load(self):
+        fn = self.fname
+        if fn.exists():
+            return json_load(fn)
+        else:
+            return {}
+
+    def _save(self):
+        json_save(self, self.fname)
+
+
+
+def json_save(what, filename, *args, indent=4, sort_keys=True, **kwargs):
+    with open(filename, "w") as f:
+        json.dump(what, f, *args, indent=indent, sort_keys=sort_keys, **kwargs)
+
+def json_load(filename, *args, **kwargs):
+    with open(filename, "r") as f:
+        return json.load(f, *args, **kwargs)
+
+
+

scilog/mkfilt.py

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+import json
+
+
+def make_filter(**kwargs):
+    items = [{k: v} for k, v in kwargs.items()]
+    filt = {"where": {"and": items}}
+    filt = json.dumps(filt)
+    return {"filter": filt}
+
+
+

scilog/scicat.py

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+import getpass
+from .config import Config
+from .utils import post_request, get_request
+from .autherror import AuthError
+
+
+AUTH_HEADERS = {
+    "Content-type": "application/json",
+    "Accept":       "application/json"
+}
+
+
+class SciCat:
+
+    def __init__(self, address):
+        self.address = address.rstrip("/")
+        self._token = None
+        self.config = Config(".scicat-tokens")
+
+    def __repr__(self):
+        return f"SciCat @ {self.address}"
+
+    @property
+    def proposals(self):
+        url = self.address + "/proposals"
+        headers = self.auth_headers
+        return get_request(url, headers=headers)
+
+
+    @property
+    def auth_headers(self):
+        headers = AUTH_HEADERS.copy()
+        headers["Authorization"] = self.token
+        return headers
+
+    @property
+    def token(self):
+        username = getpass.getuser()
+        password = getpass.getpass(prompt=f"SciCat password for {username}: ")
+        token = self._token
+        if token is None:
+            try:
+                token = self.config[username]
+            except KeyError:
+                token = self.authenticate(username, password)
+        self.config[username] = self._token = token
+        return token
+
+    def authenticate(self, username, password):
+        url = self.address + "/users/login"
+        auth_payload = {
+            "username": username,
+            "password": password
+        }
+        res = post_request(url, auth_payload, AUTH_HEADERS)
+        try:
+            token = res["id"]
+        except KeyError as e:
+            raise SciCatAuthError(res) from e
+        else:
+            return token
+
+
+
+class SciCatAuthError(AuthError):
+    pass
+
+
+

scilog/scilog.py

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+import getpass
+from .config import Config
+from .utils import post_request, get_request
+from .autherror import AuthError
+from .mkfilt import make_filter
+
+
+AUTH_HEADERS = {
+    "Content-type": "application/json",
+    "Accept":       "application/json"
+}
+
+
+class SciLog:
+
+    def __init__(self, address):
+        self.address = address.rstrip("/")
+        self._token = None
+        self.config = Config(".scilog-tokens")
+
+    def __repr__(self):
+        return f"SciLog @ {self.address}"
+
+
+    def get_snippets(self, **kwargs):
+        url = self.address + "/basesnippets"
+        params = make_filter(**kwargs)
+        headers = self.auth_headers
+        return get_request(url, params=params, headers=headers)
+
+    def post_snippet(self, **kwargs):
+        url = self.address + "/basesnippets"
+        payload = kwargs
+        headers = self.auth_headers
+        return post_request(url, payload=payload, headers=headers)
+
+
+    @property
+    def auth_headers(self):
+        headers = AUTH_HEADERS.copy()
+        headers["Authorization"] = self.token
+        return headers
+
+    @property
+    def token(self):
+        username = getpass.getuser()
+        token = self._token
+        if token is None:
+            try:
+                token = self.config[username]
+            except KeyError:
+                password = getpass.getpass(prompt=f"SciLog password for {username}: ")
+                token = self.authenticate(username, password)
+        self.config[username] = self._token = token
+        return token
+
+    def authenticate(self, username, password):
+        url = self.address + "/users/login"
+        auth_payload = {
+            "principal": username,
+            "password":  password
+        }
+        res = post_request(url, auth_payload, AUTH_HEADERS)
+        try:
+            token = "Bearer " + res["token"]
+        except KeyError as e:
+            raise SciLogAuthError(res) from e
+        else:
+            return token
+
+
+
+class SciLogAuthError(AuthError):
+    pass
+
+
+

scilog/utils.py

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+import requests
+
+
+#TODO: add params/payload and response validation
+
+
+def get_request(url, params=None, headers=None, timeout=10):
+    response = requests.get(url, params=params, headers=headers, timeout=timeout, verify=False).json()
+    return response
+
+def post_request(url, payload=None, headers=None, timeout=10):
+    response = requests.post(url, json=payload, headers=headers, timeout=timeout, verify=False).json()
+    return response
+
+
+def typename(obj):
+    return type(obj).__name__
+
+
+

update_locations.py

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+#!/usr/bin/env python3
+
+import urllib3
+
+urllib3.disable_warnings(urllib3.exceptions.InsecureRequestWarning)
+
+
+from scicat import SciCat, SciLog
+
+
+def prepare_location_snippet(log):
+    snips = log.get_snippets(title="location", ownerGroup="admin")
+
+    if snips:
+        assert len(snips) == 1
+        loc_id = snips[0]["id"]
+        return loc_id
+
+    new_loc = {
+        "ownerGroup": "admin",
+        "accessGroups": ["customer"],
+        "isPrivate": True,
+        "title": "location",
+        "snippetType": "paragraph",
+    }
+
+    snip = log.post_snippet(**new_loc)
+    loc_id = snip["id"]
+    return loc_id
+
+
+def update_locations_and_proposals(log, loc_id, proposals):
+    _accessGroups, locations, proposalsStorage = _collect_data(proposals)
+    locationStorage = _update_locations(log, loc_id, locations)
+    _update_proposals(log, locationStorage, proposalsStorage)
+
+
+def _collect_data(proposals):
+    accessGroups = set()
+    locations = set()
+    proposalsStorage = []
+
+    for prop in proposals:
+        for ag in prop["accessGroups"]:
+            accessGroups.add(ag)
+
+        loc = prop["MeasurementPeriodList"][0]["instrument"]
+        locations.add(loc)
+
+        proposalsStorage.append({
+            "ownerGroup": prop["ownerGroup"],
+            "abstract": prop["abstract"],
+            "title": prop["title"],
+            "location": prop["MeasurementPeriodList"][0]["instrument"]
+        })
+
+    return accessGroups, locations, proposalsStorage
+
+
+def _update_locations(log, loc_id, locations):
+    locationStorage = dict()
+
+    for loc in locations:
+        #TODO: move this to the first loop?
+        if loc[:4] != "/PSI":
+            raise RuntimeError("Unexpected facility prefix")
+
+        snips = log.get_snippets(parentId=loc_id, location=loc)
+
+        if snips:
+            assert len(snips) == 1
+            snip = snips[0]
+            locationStorage[loc] = snip
+            continue
+
+        group = loc[5:].replace("/", "").lower()
+        new_snip = {
+            "ownerGroup": group,
+            "accessGroups": ["customer"],
+            "isPrivate": True,
+            "title": loc.split("/")[-1],
+            "location": loc,
+            "contact": group + "@psi.ch",
+            "snippetType": "image",
+            "parentId": loc_id,
+            "file": "files/default_logbook_icon.jpg"
+        }
+
+        if "thumbnail" in loc:
+            new_snip["file"] = loc["thumbnail"]
+
+        snip = log.post_request(**new_snip)
+        locationStorage[loc] = snip
+
+    return locationStorage
+
+
+def _update_proposals(log, locationStorage, proposalsStorage):
+    for proposal in proposalsStorage:
+        ownerGroup = proposal["ownerGroup"]
+
+        loc = proposal["location"]
+        loc = locationStorage[loc]
+
+        new_snip = {
+            "ownerGroup": ownerGroup,
+            "accessGroups": [loc["ownerGroup"]],
+            "isPrivate": False,
+            "name": proposal["title"],
+            "location": loc["id"],
+            "description": proposal["abstract"],
+            "snippetType": "logbook"
+        }
+
+        if "file" in loc:
+            new_snip["thumbnail"] = loc["file"]
+        if not new_snip["name"]:
+            new_snip["name"] = ownerGroup
+        if not new_snip["description"]:
+            new_snip["description"] = "No proposal found."
+
+        snips = log.get_snippets(snippetType="logbook", ownerGroup=ownerGroup)
+
+        if snips:
+            print(f"Logbook exists already for ownerGroup {ownerGroup}")
+            continue
+
+        print(f"Adding new logbook for ownerGroup {ownerGroup}")
+        snip = log.post_snippet(**new_snip)
+        print(snip)
+
+
+
+
+
+if __name__ == "__main__":
+    url = "https://dacat.psi.ch/api/v3/"
+    cat = SciCat(url)
+    props = cat.proposals
+
+    url = "https://lnode2.psi.ch/api/v1"
+    log = SciLog(url)
+    loc_id = prepare_location_snippet(log)
+
+    update_locations_and_proposals(log, loc_id, props)
+
+
+