Clean Up branch for PR (after rebasing after lint + release PRs were accepted)

Author: HugoOnghai

.github/workflows/release.yml

@@ -66,11 +66,7 @@ jobs:
         uses: ad-m/github-push-action@master
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
-<<<<<<< HEAD
           branch: master
 
       - name: Build and Deploy!
         run: uvx mkdocs gh-deploy
-=======
-# integrate mkdocs at some point
->>>>>>> a9fa948 (Cleaning up new-core PR, restore workflows and legacy stuff)

legacy/mpcite/models.py

@@ -1,65 +1,101 @@
-from pydantic import BaseModel, Field, ConfigDict
+from pydantic import BaseModel, Field
 from typing import List, Dict, Optional
-import datetime
+from datetime import datetime
 from enum import Enum
 import bibtexparser
-from elinkapi import Elink, Record
-from elinkapi.record import RecordResponse, AccessLimitation, JournalType
-from elinkapi.geolocation import Geolocation
-from elinkapi.identifier import Identifier
-from elinkapi.related_identifier import RelatedIdentifier
-from elinkapi.person import Person
-from elinkapi.organization import Organization
-
-class TestClass(RecordResponse):
-    ...
-    # stuff
+
+
+class ConnectionModel(BaseModel):
+    endpoint: str = Field(..., title="URL Endpoint of the connection")
+    username: str = Field(..., title="User Name")
+    password: str = Field(..., title="Password")
+
+
+class RoboCrysModel(BaseModel):
+    material_id: str
+    last_updated: datetime
+    description: Optional[str] = None
+    error: Optional[str] = None
+
+    @classmethod
+    def get_default_description(cls):
+        return (
+            "Computed materials data using density "
+            "functional theory calculations. These calculations determine "
+            "the electronic structure of bulk materials by solving "
+            "approximations to the Schrodinger equation. For more "
+            "information, see https://materialsproject.org/docs/calculations"
+        )
+
+
+class MaterialModel(BaseModel):
+    last_updated: datetime = Field(
+        None, title="timestamp for the most recent calculation"
+    )
+    updated_at: datetime = Field(None, title="alternative to last_updated")
+    created_at: datetime = Field(
+        None,
+        description="creation time for this material defined by when the first structure "
+        "optimization calculation was run",
+    )
+    task_id: str = Field(
+        "", title="task id for this material. Also called the material id"
+    )
+    # pretty_formula: str = Field(..., title="clean representation of the formula")
+    pretty_formula: str = Field(..., title="clean representation of the formula")
+    chemsys: str
+
 
 class ELinkGetResponseModel(BaseModel):
-    osti_id: Optional[int] = Field(...)
+    osti_id: Optional[str] = Field(...)
     dataset_type: str = Field(default="SM")
     title: str = Field(...)
-    persons: List[Person]
+    creators: str = Field(default="Kristin Persson")  # replace with authors
     contributors: List[Dict[str, str]] = Field(
         default=[{"first_name": "Materials", "last_name": "Project"}],
         description="List of Dict of first name, last name mapping",
     )  # no contributor
-    publication_date: datetime.date
+    product_nos: str = Field(..., title="MP id")
+    accession_num: str = Field(..., title="MP id")
+    contract_nos: str = Field("AC02-05CH11231; EDCBEE")
+    originating_research_org: str = Field(
+        default="Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)"
+    )
+    publication_date: str = Field(...)
+    language: str = Field(default="English")
+    country: str = Field(default="US")
+    sponsor_org: str = Field(
+        default="USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)"
+    )
     site_url: str = Field(...)
+    contact_name: str = Field(default="Kristin Persson")
+    contact_org: str = Field(default="LBNL")
+    contact_email: str = Field(default="feedback@materialsproject.org")
+    contact_phone: str = Field(default="+1(510)486-7218")
+    related_resource: str = Field("https://materialsproject.org/citing")
+    contributor_organizations: str = Field(default="MIT; UC Berkeley; Duke; U Louvain")
+    subject_categories_code: str = Field(default="36 MATERIALS SCIENCE")
+    keywords: str = Field(...)
+    description: str = Field(default="")
     doi: dict = Field(
         {}, title="DOI info", description="Mainly used during GET request"
     )
-    mp_id: str | None = None
-    keywords: List[str] = None
 
     @classmethod
-    def from_elinkapi_record(cls, R):
-        gotResponse = ELinkGetResponseModel(
-            osti_id = R.osti_id,
-            title = R.title,
-            persons = R.persons,
-            # assume default contributors for now, creators vs contributors?
-            publication_date = R.publication_date,
-            site_url = R.site_url,
-            doi = {"doi": R.doi},
-            mp_id = next((id.value for id in R.identifiers if id.type == 'RN'), None),
-            keywords = R.keywords
-        )
-
-        return gotResponse
-
-    def get_title(self):
-        formula = self.keywords[1]
+    def get_title(cls, material: MaterialModel):
+        formula = material.pretty_formula
         return "Materials Data on %s by Materials Project" % formula
 
-    def get_site_url(self):
-        return "https://materialsproject.org/materials/%s" % self.mp_id
+    @classmethod
+    def get_site_url(cls, mp_id):
+        return "https://materialsproject.org/materials/%s" % mp_id
 
-    def get_keywords(self):
-        # keywords = "; ".join(
-        #     ["crystal structure", material.pretty_formula, material.chemsys]
-        # )
-        return self.keywords
+    @classmethod
+    def get_keywords(cls, material):
+        keywords = "; ".join(
+            ["crystal structure", material.pretty_formula, material.chemsys]
+        )
+        return keywords
 
     @classmethod
     def get_default_description(cls):
@@ -77,11 +113,11 @@ def custom_to_dict(cls, elink_record) -> dict:
             return elink_record.dict(exclude={"osti_id", "doi"})
         else:
             return elink_record.dict(exclude={"doi"})
-        
+
 
 class ElinkResponseStatusEnum(Enum):
-        SUCCESS = "SUCCESS"
-        FAILED = "FAILURE"
+    SUCCESS = "SUCCESS"
+    FAILED = "FAILURE"
 
 
 class ELinkPostResponseModel(BaseModel):
@@ -106,4 +142,178 @@ def generate_doi_record(self):
         )
         doi_collection_record.set_status(status=self.doi["@status"])
         doi_collection_record.last_validated_on = datetime.now()
-        return doi_collection_record
+        return doi_collection_record
+
+
+class DOIRecordStatusEnum(str, Enum):
+    COMPLETED = "COMPLETED"
+    PENDING = "PENDING"
+    FAILURE = "FAILURE"
+    INIT = "INIT"
+
+
+class DOIRecordModel(BaseModel):
+    material_id: str = Field(...)
+    doi: str = Field(default="")
+    bibtex: Optional[str] = None
+    status: DOIRecordStatusEnum
+    valid: bool = Field(False)
+    last_updated: datetime = Field(
+        default=datetime.now(),
+        title="DOI last updated time.",
+        description="Last updated is defined as either a Bibtex or status change.",
+    )
+    created_at: datetime = Field(
+        default=datetime.now(),
+        title="DOI Created At",
+        description="creation time for this DOI record",
+    )
+    last_validated_on: datetime = Field(
+        default=datetime.now(),
+        title="Date Last Validated",
+        description="Date that this data is last validated, " "not necessarily updated",
+    )
+    elsevier_updated_on: datetime = Field(
+        default=datetime.now(),
+        title="Date Elsevier is updated",
+        description="If None, means never uploaded to elsevier",
+    )
+    error: Optional[str] = Field(
+        default=None, description="None if no error, else error message"
+    )
+
+    class Config:
+        use_enum_values = True
+
+    def set_status(self, status):
+        self.status = status
+
+    def get_osti_id(self):
+        if self.doi is None or self.doi == "":
+            return ""
+        else:
+            return self.doi.split("/")[-1]
+
+    def get_bibtex_abstract(self):
+        try:
+            if self.bibtex is None:
+                return ""
+            bib_db: bibtexparser.bibdatabase.BibDatabase = bibtexparser.loads(
+                self.bibtex
+            )
+            if bib_db.entries:
+                return bib_db.entries[0]["abstractnote"]
+        except Exception as e:
+            print(e)
+            return ""
+
+
+class OSTIDOIRecordModel(DOIRecordModel):
+    material_id: str = Field(...)
+    doi: str = Field(default="")
+    bibtex: Optional[str] = None
+    valid: bool = Field(False)
+    last_updated: datetime = Field(
+        default=datetime.now(),
+        title="DOI last updated time.",
+        description="Last updated is defined as either a Bibtex or status change.",
+    )
+
+
+class ElsevierPOSTContainerModel(BaseModel):
+    identifier: str = Field(default="", title="mp_id")
+    source: str = "MATERIALS_PROJECT"
+    date: str = datetime.now().date().isoformat().__str__()
+    title: str
+    description: str = ""
+    doi: str
+    authors: List[str] = ["Kristin Persson"]
+    url: str
+    type: str = "dataset"
+    dateAvailable: str = datetime.now().date().isoformat().__str__()
+    dateCreated: str = datetime.now().date().isoformat().__str__()
+    version: str = "1.0.0"
+    funding: str = "USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)"
+    language: str = "en"
+    method: str = "Materials Project"
+    accessRights: str = "Public"
+    contact: str = "Kristin Persson <kapersson@lbl.gov>"
+    dataStandard: str = "https://materialsproject.org/citing"
+    howToCite: str = "https://materialsproject.org/citing"
+    subjectAreas: List[str] = ["36 MATERIALS SCIENCE"]
+    keywords: List[str]
+    institutions: List[str] = ["Lawrence Berkeley National Laboratory"]
+    institutionIds: List[str] = ["AC02-05CH11231; EDCBEE"]
+    spatialCoverage: List[str] = []
+    temporalCoverage: List[str] = []
+    references: List[str] = ["https://materialsproject.org/citing"]
+    relatedResources: List[str] = ["https://materialsproject.org/citing"]
+    location: str = "1 Cyclotron Rd, Berkeley, CA 94720"
+    childContainerIds: List[str] = []
+
+    @classmethod
+    def get_url(cls, mp_id):
+        return "https://materialsproject.org/materials/%s" % mp_id
+
+    @classmethod
+    def get_keywords(cls, material: MaterialModel):
+        return ["crystal structure", material.pretty_formula, material.chemsys]
+
+    @classmethod
+    def get_default_description(cls):
+        return (
+            "Computed materials data using density "
+            "functional theory calculations. These calculations determine "
+            "the electronic structure of bulk materials by solving "
+            "approximations to the Schrodinger equation. For more "
+            "information, see https://materialsproject.org/docs/calculations"
+        )
+
+    @classmethod
+    def get_date_created(cls, material: MaterialModel) -> str:
+        return material.created_at.date().__str__()
+
+    @classmethod
+    def get_date_available(cls, material: MaterialModel) -> str:
+        return material.created_at.date().__str__()
+
+    @classmethod
+    def get_title(cls, material: MaterialModel) -> str:
+        return material.pretty_formula
+
+    @classmethod
+    def from_material_model(cls, material: MaterialModel, doi: str, description: str):
+        model = ElsevierPOSTContainerModel(
+            identifier=material.task_id,
+            title=material.pretty_formula,
+            doi=doi,
+            url="https://materialsproject.org/materials/%s" % material.task_id,
+            keywords=["crystal structure", material.pretty_formula, material.chemsys],
+            date=datetime.now().date().__str__(),
+            dateCreated=material.created_at.date().__str__(),
+            dateAvailable=ElsevierPOSTContainerModel.get_date_available(material),
+            description=description,
+        )
+        return model
+
+
+class ExplorerGetJSONResponseModel(BaseModel):
+    osti_id: str
+    title: str
+    report_number: str
+    doi: str
+    product_type: str
+    language: str
+    country_publication: str
+    description: str
+    site_ownership_code: str
+    publication_date: str
+    entry_date: str
+    contributing_organizations: str
+    authors: List[str]
+    subjects: List[str]
+    contributing_org: str
+    doe_contract_number: str
+    sponsor_orgs: List[str]
+    research_orgs: List[str]
+    links: List[Dict[str, str]]