pub-analyzer 0.2.0__py3-none-any.whl → 0.3.0__py3-none-any.whl

pub_analyzer/models/institution.py

@@ -77,6 +77,12 @@ class InstitutionRole(BaseModel):
     works_count: int
 
 
+class International(BaseModel):
+    """The institution's display name in different languages."""
+
+    display_name: dict[str, str]
+
+
 class Institution(BaseModel):
     """Universities and other organizations to which authors claim affiliations."""
 
@@ -87,11 +93,15 @@ class Institution(BaseModel):
     country_code: str
     type: InstitutionType
     homepage_url: HttpUrl | None = None
+    image_url: HttpUrl | None = None
+
+    display_name_acronyms: list[str]
+    international: International
 
     works_count: int
     cited_by_count: int
-    counts_by_year: list[InstitutionYearCount]
     summary_stats: InstitutionSummaryStats
+    counts_by_year: list[InstitutionYearCount]
 
     geo: InstitutionGeo
     roles: list[InstitutionRole]

pub_analyzer/models/report.py

@@ -6,7 +6,7 @@ from pydantic import BaseModel
 
 from .author import Author
 from .institution import Institution
-from .source import DehydratedSource
+from .source import Source
 from .work import OpenAccessStatus, Work
 
 
@@ -24,7 +24,7 @@ class CitationReport(BaseModel):
     citation_type: CitationType
 
 
-class CitationResume(BaseModel):
+class CitationSummary(BaseModel):
     """Summary of citation information in all works."""
 
     type_a_count: int = 0
@@ -38,7 +38,7 @@ class CitationResume(BaseModel):
             self.type_b_count += 1
 
 
-class OpenAccessResume(BaseModel):
+class OpenAccessSummary(BaseModel):
     """Open Access Type counter."""
 
     gold: int = 0
@@ -75,13 +75,13 @@ class WorkReport(BaseModel):
     work: Work
     cited_by: list[CitationReport]
 
-    citation_resume: CitationResume
+    citation_summary: CitationSummary
 
 
-class SourcesResume(BaseModel):
+class SourcesSummary(BaseModel):
     """Sources model with stats."""
 
-    sources: list[DehydratedSource]
+    sources: list[Source]
 
 
 class AuthorReport(BaseModel):
@@ -90,10 +90,10 @@ class AuthorReport(BaseModel):
     author: Author
     works: list[WorkReport]
 
-    citation_resume: CitationResume
-    open_access_resume: OpenAccessResume
-    works_type_resume: list[WorkTypeCounter]
-    sources_resume: SourcesResume
+    citation_summary: CitationSummary
+    open_access_summary: OpenAccessSummary
+    works_type_summary: list[WorkTypeCounter]
+    sources_summary: SourcesSummary
 
 
 class InstitutionReport(BaseModel):
@@ -102,7 +102,7 @@ class InstitutionReport(BaseModel):
     institution: Institution
     works: list[WorkReport]
 
-    citation_resume: CitationResume
-    open_access_resume: OpenAccessResume
-    works_type_resume: list[WorkTypeCounter]
-    sources_resume: SourcesResume
+    citation_summary: CitationSummary
+    open_access_summary: OpenAccessSummary
+    works_type_summary: list[WorkTypeCounter]
+    sources_summary: SourcesSummary

pub_analyzer/models/source.py

@@ -1,21 +1,77 @@
 """Sources models from OpenAlex API Schema definition."""
 
-from pydantic import BaseModel, HttpUrl
+from pydantic import BaseModel, Field, HttpUrl
+
+
+class SourceSummaryStats(BaseModel):
+    """Citation metrics for this Source."""
+
+    two_yr_mean_citedness: float = Field(..., alias="2yr_mean_citedness")
+    """The 2-year mean citedness for this source. Also known as impact factor."""
+    h_index: int
+    """The h-index for this source."""
+    i10_index: int
+    """The i-10 index for this source."""
+
+
+class SourceYearCount(BaseModel):
+    """Summary of published papers and number of citations in a year."""
+
+    year: int
+    """Year."""
+    works_count: int
+    """The number of Works this source hosts in this year."""
+    cited_by_count: int
+    """The total number of Works that cite a Work hosted in this source in this year."""
 
 
 class DehydratedSource(BaseModel):
     """Stripped-down Source Model."""
 
     id: HttpUrl
+    """The OpenAlex ID for this source."""
     display_name: str
+    """The name of the source."""
 
     issn_l: str | None = None
+    """The ISSN-L identifying this source. The ISSN-L designating a single canonical ISSN
+       for all media versions of the title. It's usually the same as the print ISSN.
+    """
     issn: list[str] | None = None
+    """The ISSNs used by this source. An ISSN identifies all continuing resources, irrespective
+       of their medium (print or electronic). [More info](https://www.issn.org/){target=_blank}.
+    """
 
-    is_oa: bool | None = False
-    is_in_doaj: bool | None = False
+    is_oa: bool
+    """Whether this is currently fully-open-access source."""
+    is_in_doaj: bool
+    """Whether this is a journal listed in the [Directory of Open Access Journals](https://doaj.org){target=_blank} (DOAJ)."""
 
     host_organization: HttpUrl | None = None
+    """The host organization for this source as an OpenAlex ID. This will be an
+       [Institution.id][pub_analyzer.models.institution.Institution.id] if the source is a repository,
+       and a Publisher.id if the source is a journal, conference, or eBook platform
+    """
     host_organization_name: str | None = None
+    """The display_name from the host_organization."""
 
     type: str
+    """The type of source, which will be one of: `journal`, `repository`, `conference`,
+       `ebook platform`, or `book series`.
+    """
+
+
+class Source(DehydratedSource):
+    """Where works are hosted."""
+
+    homepage_url: HttpUrl | None = None
+    """The homepage for this source's website."""
+
+    is_in_doaj: bool
+    """Whether this is a journal listed in the Directory of Open Access Journals (DOAJ)."""
+
+    summary_stats: SourceSummaryStats
+    """Citation metrics for this source."""
+
+    counts_by_year: list[SourceYearCount]
+    """works_count and cited_by_count for each of the last ten years, binned by year."""

pub_analyzer/models/topic.py

@@ -0,0 +1,59 @@
+"""Topics models from OpenAlex API Schema definition."""
+
+from pydantic import BaseModel, HttpUrl
+
+
+class TopicIDs(BaseModel):
+    """External identifiers for a Topic."""
+
+    openalex: HttpUrl
+    """The OpenAlex ID for this Topic."""
+    wikipedia: HttpUrl | None = None
+    """This topic's Wikipedia page URL."""
+
+
+class TopicLevel(BaseModel):
+    """Topic level information."""
+
+    id: HttpUrl
+    """ID for the topic level. For more info, consult the
+       [OpenAlex topic mapping table](https://docs.google.com/spreadsheets/d/1v-MAq64x4YjhO7RWcB-yrKV5D_2vOOsxl4u6GBKEXY8/){target=_blank}.
+    """
+    display_name: str
+    """The English-language label of the level."""
+
+
+class DehydratedTopic(BaseModel):
+    """Stripped-down Topic Model."""
+
+    id: HttpUrl
+    """The OpenAlex ID for this Topic."""
+    display_name: str
+    """The English-language label of the topic."""
+    score: float
+    """The strength of the connection between the work and this topic (higher is stronger)."""
+
+    domain: TopicLevel
+    """The highest level in the Topics structure."""
+    field: TopicLevel
+    """The second-highest level in the Topics structure."""
+    subfield: TopicLevel
+    """The third-highest level in the Topics structure."""
+
+
+class Topic(DehydratedTopic):
+    """Labels which can be used to describe what a paper is about."""
+
+    ids: TopicIDs
+    """All the external identifiers for a Topic."""
+    description: str
+    """A description of this topic, generated by AI."""
+    keywords: list[str]
+    """Keywords consisting of one or several words each, meant to represent
+       the content of the papers in the topic.
+    """
+
+    works_count: int
+    """The number of works tagged with this topic."""
+    cited_by_count: int
+    """The number of citations to works that have been tagged with this topic."""

pub_analyzer/models/work.py

@@ -6,7 +6,9 @@ from typing import Any
 from pydantic import BaseModel, HttpUrl, field_validator
 
 from .author import DehydratedAuthor
+from .concept import DehydratedConcept
 from .source import DehydratedSource
+from .topic import DehydratedTopic
 
 
 class WorkIDs(BaseModel):
@@ -72,6 +74,22 @@ class ArticleProcessingCharge(BaseModel):
     value_usd: int | None
 
 
+class Grant(BaseModel):
+    """Grant Model Object from OpenAlex API definition."""
+
+    funder: HttpUrl
+    funder_display_name: str
+    award_id: str | None = None
+
+
+class Keyword(BaseModel):
+    """Keyword extracted from the work's title and confidence score."""
+
+    id: HttpUrl
+    display_name: str
+    score: float
+
+
 class Work(BaseModel):
     """Work Model Object from OpenAlex API definition."""
 
@@ -97,6 +115,11 @@ class Work(BaseModel):
        To use a verified number that respects the applied filters use [WorkReport][pub_analyzer.models.report.WorkReport].
     """
 
+    grants: list[Grant]
+    keywords: list[Keyword]
+    concepts: list[DehydratedConcept]
+    topics: list[DehydratedTopic]
+
     referenced_works: list[HttpUrl]
     cited_by_api_url: HttpUrl
 

pub_analyzer/widgets/author/cards.py

@@ -54,11 +54,12 @@ class LastInstitutionCard(Card):
         """Compose card."""
         yield Label("[italic]Last Institution:[/italic]", classes="card-title")
 
-        if self.author.last_known_institution:
-            ror = self.author.last_known_institution.ror
-            institution_name = self.author.last_known_institution.display_name
+        if self.author.last_known_institutions:
+            last_known_institution = self.author.last_known_institutions[0]
+            ror = last_known_institution.ror
+            institution_name = last_known_institution.display_name
 
             with Vertical(classes="card-container"):
                 yield Label(f"""[bold]Name:[/bold] [@click=app.open_link('{quote(str(ror))}')]{institution_name}[/]""")
-                yield Label(f"[bold]Country:[/bold] {self.author.last_known_institution.country_code}")
-                yield Label(f"[bold]Type:[/bold] {self.author.last_known_institution.type.value}")
+                yield Label(f"[bold]Country:[/bold] {last_known_institution.country_code}")
+                yield Label(f"[bold]Type:[/bold] {last_known_institution.type.value}")

pub_analyzer/widgets/author/core.py

@@ -5,20 +5,21 @@ from typing import Any
 import httpx
 from textual import on
 from textual.app import ComposeResult
-from textual.containers import Container, Horizontal, Vertical, VerticalScroll
+from textual.containers import Container, Horizontal, Vertical
 from textual.widgets import Button, Collapsible, Label, Static
 
 from pub_analyzer.internal.identifier import get_author_id
 from pub_analyzer.models.author import Author, AuthorResult
 from pub_analyzer.widgets.common.filters import DateRangeFilter, Filter
+from pub_analyzer.widgets.common.summary import SummaryWidget
 from pub_analyzer.widgets.report.core import CreateAuthorReportWidget
 
 from .cards import CitationMetricsCard, IdentifiersCard, LastInstitutionCard
 from .tables import AuthorWorksByYearTable
 
 
-class _AuthorResumeWidget(Static):
-    """Author info resume."""
+class _AuthorSummaryWidget(Static):
+    """Author info summary."""
 
     def __init__(self, author: Author) -> None:
         self.author = author
@@ -62,12 +63,12 @@ class _AuthorResumeWidget(Static):
                 yield DateRangeFilter(checkbox_label="Cited date range:", id="cited-date-range-filter")
 
             # Button
-            with Vertical(classes="block-container button-container"):
+            with Vertical(classes="button-container"):
                 yield Button("Make Report", variant="primary", id="make-report-button")
 
 
-class AuthorResumeWidget(VerticalScroll):
-    """Author info resume container."""
+class AuthorSummaryWidget(SummaryWidget):
+    """Author info summary container."""
 
     def __init__(self, author_result: AuthorResult) -> None:
         self.author_result = author_result
@@ -91,17 +92,17 @@ class AuthorResumeWidget(VerticalScroll):
     async def load_data(self) -> None:
         """Query OpenAlex API and composing the widget."""
         await self._get_info()
-        await self.mount(_AuthorResumeWidget(author=self.author))
+        await self.mount(_AuthorSummaryWidget(author=self.author))
 
         self.loading = False
 
     @on(Filter.Changed)
     def filter_change(self) -> None:
         """Handle filter changes."""
-        filters = [filter for filter in self.query("_AuthorResumeWidget Filter").results(Filter) if not filter.filter_disabled]
+        filters = [filter for filter in self.query("_AuthorSummaryWidget Filter").results(Filter) if not filter.filter_disabled]
         all_filters_valid = all(filter.validation_state for filter in filters)
 
-        self.query_one("_AuthorResumeWidget #make-report-button", Button).disabled = not all_filters_valid
+        self.query_one("_AuthorSummaryWidget #make-report-button", Button).disabled = not all_filters_valid
 
     @on(Button.Pressed, "#make-report-button")
     async def make_report(self) -> None:
@@ -118,4 +119,4 @@ class AuthorResumeWidget(VerticalScroll):
 
         report_widget = CreateAuthorReportWidget(author=self.author, **filters)
         await self.app.query_one("MainContent").mount(report_widget)
-        await self.app.query_one("AuthorResumeWidget").remove()
+        await self.app.query_one("AuthorSummaryWidget").remove()

pub_analyzer/widgets/common/summary.py

@@ -0,0 +1,7 @@
+"""Common Summary format Widget."""
+
+from textual.containers import VerticalScroll
+
+
+class SummaryWidget(VerticalScroll):
+    """Common format summary container."""

pub_analyzer/widgets/institution/core.py

@@ -5,20 +5,21 @@ from typing import Any
 import httpx
 from textual import on
 from textual.app import ComposeResult
-from textual.containers import Container, Horizontal, Vertical, VerticalScroll
+from textual.containers import Container, Horizontal, Vertical
 from textual.widgets import Button, Collapsible, Label, Static
 
 from pub_analyzer.internal.identifier import get_institution_id
 from pub_analyzer.models.institution import Institution, InstitutionResult
 from pub_analyzer.widgets.common.filters import DateRangeFilter, Filter
+from pub_analyzer.widgets.common.summary import SummaryWidget
 from pub_analyzer.widgets.report.core import CreateInstitutionReportWidget
 
 from .cards import CitationMetricsCard, IdentifiersCard, RolesCard
 from .tables import InstitutionWorksByYearTable
 
 
-class _InstitutionResumeWidget(Static):
-    """Institution info resume."""
+class _InstitutionSummaryWidget(Static):
+    """Institution info summary."""
 
     def __init__(self, institution: Institution) -> None:
         self.institution = institution
@@ -66,8 +67,8 @@ class _InstitutionResumeWidget(Static):
                 yield Button("Make Report", variant="primary", id="make-report-button")
 
 
-class InstitutionResumeWidget(VerticalScroll):
-    """Institution info resume container."""
+class InstitutionSummaryWidget(SummaryWidget):
+    """Institution info summary container."""
 
     def __init__(self, institution_result: InstitutionResult) -> None:
         self.institution_result = institution_result
@@ -91,17 +92,17 @@ class InstitutionResumeWidget(VerticalScroll):
     async def load_data(self) -> None:
         """Query OpenAlex API and composing the widget."""
         await self._get_info()
-        await self.mount(_InstitutionResumeWidget(institution=self.institution))
+        await self.mount(_InstitutionSummaryWidget(institution=self.institution))
 
         self.loading = False
 
     @on(Filter.Changed)
     def filter_change(self) -> None:
         """Handle filter changes."""
-        filters = [filter for filter in self.query("_InstitutionResumeWidget Filter").results(Filter) if not filter.filter_disabled]
+        filters = [filter for filter in self.query("_InstitutionSummaryWidget Filter").results(Filter) if not filter.filter_disabled]
         all_filters_valid = all(filter.validation_state for filter in filters)
 
-        self.query_one("_InstitutionResumeWidget #make-report-button", Button).disabled = not all_filters_valid
+        self.query_one("_InstitutionSummaryWidget #make-report-button", Button).disabled = not all_filters_valid
 
     @on(Button.Pressed, "#make-report-button")
     async def make_report(self) -> None:
@@ -118,4 +119,4 @@ class InstitutionResumeWidget(VerticalScroll):
 
         report_widget = CreateInstitutionReportWidget(institution=self.institution, **filters)
         await self.app.query_one("MainContent").mount(report_widget)
-        await self.app.query_one("InstitutionResumeWidget").remove()
+        await self.app.query_one("InstitutionSummaryWidget").remove()

pub_analyzer/widgets/report/cards.py

@@ -11,9 +11,8 @@ from pub_analyzer.models.report import AuthorReport, InstitutionReport, WorkRepo
 from pub_analyzer.models.work import Work
 from pub_analyzer.widgets.common import Card
 
-# Works pane cards.
-
 
+# Works pane cards.
 class ReportCitationMetricsCard(Card):
     """Citation metrics for this report."""
 
@@ -26,8 +25,8 @@ class ReportCitationMetricsCard(Card):
         yield Label("[italic]Citation metrics:[/italic]", classes="card-title")
 
         with Vertical(classes="card-container"):
-            type_a_count = self.report.citation_resume.type_a_count
-            type_b_count = self.report.citation_resume.type_b_count
+            type_a_count = self.report.citation_summary.type_a_count
+            type_b_count = self.report.citation_summary.type_b_count
             cited_by_count = type_a_count + type_b_count
 
             yield Label(f"[bold]Count:[/bold] {cited_by_count}")
@@ -35,8 +34,8 @@ class ReportCitationMetricsCard(Card):
             yield Label(f"[bold]Type B:[/bold] {type_b_count}")
 
 
-class WorksTypeResumeCard(Card):
-    """Works Type Counters Resume Card."""
+class WorksTypeSummaryCard(Card):
+    """Works Type Counters Summary Card."""
 
     def __init__(self, report: AuthorReport | InstitutionReport) -> None:
         self.report = report
@@ -47,11 +46,11 @@ class WorksTypeResumeCard(Card):
         yield Label("[italic]Work Type[/italic]", classes="card-title")
 
         with VerticalScroll(classes="card-container"):
-            for work_type_counter in self.report.works_type_resume:
+            for work_type_counter in self.report.works_type_summary:
                 yield Label(f"[bold]{work_type_counter.type_name}:[/bold] {work_type_counter.count}")
 
 
-class OpenAccessResumeCard(Card):
+class OpenAccessSummaryCard(Card):
     """Open Access counts for this report."""
 
     def __init__(self, report: AuthorReport | InstitutionReport) -> None:
@@ -63,7 +62,7 @@ class OpenAccessResumeCard(Card):
         yield Label("[italic]Open Access[/italic]", classes="card-title")
 
         with VerticalScroll(classes="card-container"):
-            for status, count in self.report.open_access_resume.model_dump().items():
+            for status, count in self.report.open_access_summary.model_dump().items():
                 yield Label(f"[bold]{status}:[/bold] {count}")
 
 
@@ -120,8 +119,8 @@ class CitationMetricsCard(Card):
 
     def compose(self) -> ComposeResult:
         """Compose card."""
-        type_a_count = self.work_report.citation_resume.type_a_count
-        type_b_count = self.work_report.citation_resume.type_b_count
+        type_a_count = self.work_report.citation_summary.type_a_count
+        type_b_count = self.work_report.citation_summary.type_b_count
         cited_by_count = type_a_count + type_b_count
 
         yield Label("[italic]Citation[/italic]", classes="card-title")

pub_analyzer/widgets/report/concept.py

@@ -0,0 +1,47 @@
+"""Concepts Widgets."""
+
+from urllib.parse import quote
+
+from rich.table import Table
+from rich.text import Text
+from textual.app import ComposeResult
+from textual.widgets import Static
+
+from pub_analyzer.models.concept import DehydratedConcept
+
+
+class ConceptsTable(Static):
+    """All Concepts from a work in a table."""
+
+    DEFAULT_CSS = """
+    ConceptsTable .concepts-table {
+        height: auto;
+        padding: 1 2 0 2;
+    }
+    """
+
+    def __init__(self, concepts_list: list[DehydratedConcept]) -> None:
+        self.concepts_list = concepts_list
+        super().__init__()
+
+    def compose(self) -> ComposeResult:
+        """Compose Table."""
+        concepts_table = Table(title="Concepts", expand=True, show_lines=True)
+
+        # Define Columns
+        concepts_table.add_column("", justify="center", vertical="middle")
+        concepts_table.add_column("Name", ratio=5)
+        concepts_table.add_column("Score", ratio=1)
+        concepts_table.add_column("Level", ratio=1)
+
+        for idx, concept in enumerate(self.concepts_list):
+            name = f"""[@click=app.open_link('{quote(str(concept.wikidata))}')][u]{concept.display_name}[/u][/]"""
+
+            concepts_table.add_row(
+                str(idx),
+                Text.from_markup(name, overflow="ellipsis"),
+                Text.from_markup(f"{concept.score:.2f}"),
+                Text.from_markup(f"{concept.level:.1f}"),
+            )
+
+        yield Static(concepts_table, classes="concepts-table")

pub_analyzer/widgets/report/core.py

@@ -3,12 +3,15 @@
 import datetime
 import pathlib
 from enum import Enum
+from typing import ClassVar
 
 import httpx
 from pydantic import TypeAdapter, ValidationError
 from textual import on
 from textual.app import ComposeResult
+from textual.binding import Binding, BindingType
 from textual.containers import Container, Horizontal
+from textual.reactive import reactive
 from textual.widget import Widget
 from textual.widgets import Button, LoadingIndicator, Static, TabbedContent, TabPane
 
@@ -28,6 +31,17 @@ from .work import WorkReportPane
 class ReportWidget(Static):
     """Base report widget."""
 
+    BINDINGS: ClassVar[list[BindingType]] = [
+        Binding(key="ctrl+y", action="toggle_works", description="Toggle empty works"),
+    ]
+
+    show_empty_works: reactive[bool] = reactive(True)
+
+    async def action_toggle_works(self) -> None:
+        """Toggle show empty works attribute."""
+        self.show_empty_works = not self.show_empty_works
+        await self.query_one(WorkReportPane).toggle_empty_works()
+
 
 class AuthorReportWidget(ReportWidget):
     """Author report generator view."""

pub_analyzer/widgets/report/grants.py

@@ -0,0 +1,46 @@
+"""Grants Widgets."""
+
+from urllib.parse import quote
+
+from rich.table import Table
+from rich.text import Text
+from textual.app import ComposeResult
+from textual.widgets import Static
+
+from pub_analyzer.models.work import Grant
+
+
+class GrantsTable(Static):
+    """All Grants from a work in a table."""
+
+    DEFAULT_CSS = """
+    GrantsTable .grants-table {
+        height: auto;
+        padding: 1 2 0 2;
+    }
+    """
+
+    def __init__(self, grants_list: list[Grant]) -> None:
+        self.grants_list = grants_list
+        super().__init__()
+
+    def compose(self) -> ComposeResult:
+        """Compose Table."""
+        grants_table = Table(title="Grants", expand=True, show_lines=True)
+
+        # Define Columns
+        grants_table.add_column("", justify="center", vertical="middle")
+        grants_table.add_column("Name", ratio=3)
+        grants_table.add_column("Award ID", ratio=2)
+
+        for idx, grant in enumerate(self.grants_list):
+            name = f"""[@click=app.open_link('{quote(str(grant.funder))}')][u]{grant.funder_display_name}[/u][/]"""
+            award_id = grant.award_id or "-"
+
+            grants_table.add_row(
+                str(idx),
+                Text.from_markup(name, overflow="ellipsis"),
+                Text.from_markup(award_id),
+            )
+
+        yield Static(grants_table, classes="grants-table")