base information for docker

ersilia/hub/content/card.py

@@ -27,6 +27,9 @@
  SourceCodeBaseInformationError,
  LicenseBaseInformationError,
  GithubBaseInformationError,
+ DockerhubBaseInformationError,
+ DockerArchitectureInformationError,
+ S3BaseInformationError,
  BothIdentifiersBaseInformationError,
 )
 from ...utils.identifiers.model import ModelIdentifier
@@ -61,6 +64,9 @@ def __init__(self, config_json):
  self._source_code = None
  self._license = None
  self._contributor = None
+ self._dockerhub = None
+ self._docker_architecture = None
+ self._s3 = None
 
  def _is_valid_url(self, url_string: str) -> bool:
  result = validators.url(url_string)
@@ -292,6 +298,39 @@ def github(self):
  self._github = "https://github.com/ersilia-os/{0}".format(model_id)
  return self._github
 
+ @property
+ def dockerhub(self):
+ return self._dockerhub
+
+ @dockerhub.setter
+ def dockerhub(self, new_dockerhub_url):
+ if not new_dockerhub_url.startswith("https://hub.docker.com/r/ersiliaos/"):
+ raise DockerhubBaseInformationError
+ self._dockerhub = new_dockerhub_url
+
+ @property
+ def docker_architecture(self):
+ return self._docker_architecture
+
+ @docker_architecture.setter
+ def docker_architecture(self, new_docker_architecture):
+ for d in new_docker_architecture:
+ if d not in self._read_default_fields("Docker Architecture"):
+ raise DockerArchitectureInformationError
+ self._docker_architecture = new_docker_architecture
+
+ @property
+ def s3(self):
+ return self._s3
+
+ @s3.setter
+ def s3(self, new_s3_url):
+ if not new_s3_url.startswith(
+ "https://ersilia-models-zipped.s3.eu-central-1.amazonaws.com/"
+ ):
+ raise S3BaseInformationError
+ self._s3 = new_s3_url
+
  @property
  def both_identifiers(self):
  model_id = self.identifier
@@ -321,6 +360,9 @@ def as_dict(self):
  "Source Code": self.source_code,
  "License": self.license,
  "Contributor": self.contributor,
+ "DockerHub": self.dockerhub,
+ "Docker Architecture": self.docker_architecture,
+ "S3": self.s3,
  }
  data = dict((k, v) for k, v in data.items() if v is not None)
  return data
@@ -345,6 +387,12 @@ def from_dict(self, data):
  self.license = data["License"]
  if "Contributor" in data:
  self.contributor = data["Contributor"]
+ if "DockerHub" in data:
+ self.dockerhub = data["DockerHub"]
+ if "Docker Architecture" in data:
+ self.docker_architecture = data["Docker Architecture"]
+ if "S3" in data:
+ self.s3 = data["S3"]
 
 
 class RepoMetadataFile(ErsiliaBase):
@@ -489,6 +537,15 @@ def write_information(self, data: BaseInformation, readme_path=None):
  text += "* Ersilia contributor: [{0}](https://github.com/{0})\n\n".format(
  d["Contributor"]
  )
+ text += "## Ersilia model URLs\n"
+ text += "* [GitHub]({0})\n".format(data.github)
+ if d["S3"] in d:
+ text += "* [AWS S3]({0})\n".format(d["S3"])
+ if d["DockerHub"] in d:
+ text += "* [DockerHub]({0}) ({1})\n".format(
+ d["DockerHub"], ", ".join(d["Docker Architecture"])
+ )
+ text += "\n"
  text += "## Citation\n\n"
  text += "If you use this model, please cite the [original authors]({0}) of the model and the [Ersilia Model Hub](https://github.com/ersilia-os/ersilia/blob/master/CITATION.cff).\n\n".format(
  d["Publication"]

ersilia/hub/content/metadata/docker_architecture.txt

@@ -0,0 +1,2 @@
+AMD64
+ARM64

ersilia/hub/fetch/fetch.py

@@ -134,6 +134,17 @@ def copy_metadata(self, model_id):
  tag=DOCKERHUB_LATEST_TAG,
  )
 
+ def copy_status(self, model_id):
+ fr_file = "/root/eos/dest/{0}/{1}".format(model_id, STATUS_FILE)
+ to_file = "{0}/dest/{1}/{2}".format(EOS, model_id, STATUS_FILE)
+ self.simple_docker.cp_from_image(
+ img_path=fr_file,
+ local_path=to_file,
+ org=DOCKERHUB_ORG,
+ img=model_id,
+ tag=DOCKERHUB_LATEST_TAG,
+ )
+
  def fetch(self, model_id):
  mp = ModelPuller(model_id=model_id, config_json=self.config_json)
  mp.pull()
@@ -142,6 +153,7 @@ def fetch(self, model_id):
  self.write_apis(model_id)
  self.copy_information(model_id)
  self.copy_metadata(model_id)
+ self.copy_status(model_id)
 
 
 class ModelFetcher(ErsiliaBase):

ersilia/serve/services.py

@@ -577,5 +577,4 @@ def close(self):
  self.logger.debug(
  "Stopping and removing container {0}".format(self.container_id)
  )
- self.container.stop()
- self.container.remove()
+ self._stop_all_containers_of_image()

ersilia/utils/exceptions_utils/card_exceptions.py

@@ -156,6 +156,29 @@ def __init__(self):
  super().__init__(self.message, self.hints)
 
 
+class DockerhubBaseInformationError(ErsiliaError):
+ def __init__(self):
+ self.message = "Wrong Ersilia DockerHub URL"
+ self.hints = "The model does not seem to be publicly available in Ersilia's DockerHub organization profile (ersiliaos). Make sure that a model identifier has been set."
+ super().__init__(self.message, self.hints)
+
+
+class DockerArchitectureInformationError(ErsiliaError):
+ def __init__(self):
+ self.message = "Wrong Docker architecture"
+ self.hints = "Listed Docker architectures are: {}. If you are considering a Docker architecture that is not in this list, please open a PR on the 'docker_architecture.txt' file in the Ersilia repository".format(
+ ", ".join(_read_default_fields("Docker Architecture"))
+ )
+ super().__init__(self.message, self.hints)
+
+
+class S3BaseInformationError(ErsiliaError):
+ def __init__(self):
+ self.message = "Wrong Ersilia AWS S3 URL"
+ self.hints = "The model does not seem to be publicly available in Ersilia's AWS S3 bucket for zipped models. Make sure that a model identifier has been set."
+ super().__init__(self.message, self.hints)
+
+
 class BothIdentifiersBaseInformationError(ErsiliaError):
  def __init__(self):
  self.message = "Both identifiers field error"

notebooks/test-colab-notebook-python-api.ipynb

@@ -184,7 +184,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 1,
+ "execution_count": 4,
  "metadata": {},
  "outputs": [],
  "source": [
@@ -203,7 +203,7 @@
  },
  {
  "cell_type": "code",
- "execution_count": 3,
+ "execution_count": 5,
  "metadata": {},
  "outputs": [],
  "source": [
@@ -218,7 +218,7 @@
  "]\n",
  "\n",
  "em.serve()\n",
- "data = em.predict(smiles, output=\"pandas\")"
+ "data = em.run(smiles, output=\"pandas\")"
  ]
  },
  {
@@ -260,7 +260,7 @@
  "name": "python",
  "nbconvert_exporter": "python",
  "pygments_lexer": "ipython3",
- "version": "3.7.11"
+ "version": "3.10.11"
  },
  "vscode": {
  "interpreter": {