pub-analyzer 0.1.0__tar.gz → 0.1.2__tar.gz

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pub-analyzer
-Version: 0.1.0
+Version: 0.1.2
 Summary: A text user interface, written in python, which automates the generation of scientific production reports using OpenAlex
 Home-page: https://github.com/alejandrgaspar/pub-analyzer
 License: MIT
@@ -24,7 +24,7 @@ Classifier: Typing :: Typed
 Requires-Dist: httpx (==0.24.1)
 Requires-Dist: jinja2 (==3.1.2)
 Requires-Dist: pydantic (==2.3.0)
-Requires-Dist: textual (==0.34.0)
+Requires-Dist: textual (==0.35.1)
 Requires-Dist: typst (==0.7.0)
 Project-URL: Documentation, https://pub-analyzer.com/
 Project-URL: Repository, https://github.com/alejandrgaspar/pub-analyzer

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/css/report.tcss

@@ -71,6 +71,10 @@ LoadReportWidget .button-container {
 }
 
 /* Export Report Pane */
+ExportReportPane #export-form {
+    height: auto;
+}
+
 ExportReportPane .export-form-input-container {
     height: auto;
     margin-bottom: 2;
@@ -107,6 +111,12 @@ WorkModal #dialog .cards-container {
     grid-gutter: 1 2;
 }
 
+WorkModal #dialog .abstract {
+    height: auto;
+    width: 100%;
+    padding: 1 2;
+}
+
 WorkModal #dialog #tables-container {
     margin: 1 0;
 }

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/internal/report.py

@@ -61,6 +61,24 @@ def _get_citation_type(original_work_authors: list[str], cited_work_authors: lis
 
     return CitationType.TypeA if not original_set.intersection(cited_set) else CitationType.TypeB
 
+
+def _add_work_abstract(work: dict[str, Any]) -> dict[str, Any]:
+    """Get work abtract from abstract_inverted_index and insert new key `abstract`.
+
+    Args:
+        work: Raw work.
+
+    Returns:
+        Work with new key `abstract`.
+    """
+    abstract_inverted_index = work.get("abstract_inverted_index")
+    if abstract_inverted_index:
+        work["abstract"] = " ".join(abstract_inverted_index)
+    else:
+        work["abstract"] = None
+    return work
+
+
 def _get_valid_works(works: list[dict[str, Any]]) -> list[dict[str, Any]]:
     """Skip works that do not contain enough data.
 
@@ -75,7 +93,8 @@ def _get_valid_works(works: list[dict[str, Any]]) -> list[dict[str, Any]]:
         In response, we have chosen to exclude such works at this stage, thus avoiding
         the need to handle exceptions within the Model validators.
     """
-    return [work for work in works if work['title'] is not None]
+    return [_add_work_abstract(work) for work in works if work['title'] is not None]
+
 
 async def _get_works(client: httpx.AsyncClient, url: str) -> list[Work]:
     """Get all works given a URL.
@@ -88,12 +107,18 @@ async def _get_works(client: httpx.AsyncClient, url: str) -> list[Work]:
 
     Returns:
         List of Works Models.
+
+    Raises:
+        httpx.HTTPStatusError: One response from OpenAlex API had an error HTTP status of 4xx or 5xx.
     """
-    response = (await client.get(url=url)).json()
-    meta_info = response["meta"]
+    response = await client.get(url=url)
+    response.raise_for_status()
+
+    json_response = response.json()
+    meta_info = json_response["meta"]
     page_count = math.ceil(meta_info["count"] / meta_info["per_page"])
 
-    works_data = list(_get_valid_works(response["results"]),)
+    works_data = list(_get_valid_works(json_response["results"]),)
 
     for page_number in range(1, page_count):
         page_result = (await client.get(url + f"&page={page_number + 1}")).json()
@@ -112,6 +137,9 @@ async def make_author_report(author: Author, from_date: datetime.date | None = N
 
     Returns:
         Author's scientific production report Model.
+
+    Raises:
+        httpx.HTTPStatusError: One response from OpenAlex API had an error HTTP status of 4xx or 5xx.
     """
     author_id = identifier.get_author_id(author)
 
@@ -188,6 +216,9 @@ async def make_institution_report(
 
     Returns:
         Institution's scientific production report Model.
+
+    Raises:
+        httpx.HTTPStatusError: One response from OpenAlex API had an error HTTP status of 4xx or 5xx.
     """
     institution_id = identifier.get_institution_id(institution)
 

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/internal/templates/author/report.typ

@@ -17,6 +17,7 @@
 
 // Text config
 #set text(size: 10pt)
+#set par(justify: true)
 
 // Override reference
 #show ref: it => {

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/internal/templates/author/works.typ

@@ -1,5 +1,6 @@
 // Works
 = Works.
+
 #linebreak()
 
 #grid(

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/internal/templates/author/works_extended.typ

@@ -6,8 +6,16 @@
 {% endif %}
 
 === #text()[#"{{ work.work.title.replace('"', '\\"') }}"] <work_{{ loop.index }}>
+
+#linebreak()
+
+{% if work.work.abstract %}
+#text()[#"{{ work.work.abstract.replace('"', '\\"') }}"]
+
 #linebreak()
 
+{% endif %}
+
 // Cards
 #grid(
   columns: (1fr, 1fr, 1fr),
@@ -16,7 +24,7 @@
     #align(center)[_Authorships_]
     #parbreak()
     {% for authorship in work.work.authorships[:10] %}
-    - *{{ authorship.author_position }}:* #text({% if authorship.author.display_name == report.author.display_name %}rgb("909d63"){% endif %})[{{ authorship.author.display_name }}]
+    - *{{ authorship.author_position }}:* #underline([#link("{{ authorship.author.orcid or authorship.author.id }}")[#text({% if authorship.author.display_name == report.author.display_name %}rgb("909d63"){% endif %})[{{ authorship.author.display_name }}]]])
     {% endfor %}
     {% if work.work.authorships|length > 10 %}
     - *...*

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/models/work.py

@@ -79,6 +79,7 @@ class Work(BaseModel):
     ids: WorkIDs
 
     title: str
+    abstract: str | None = None
     publication_year: int
     publication_date: str
     language: str | None = None
@@ -92,6 +93,9 @@ class Work(BaseModel):
     authorships: list[Authorship]
 
     cited_by_count: int
+    """This number comes from the OpenAlex API, represents ALL citations to this work, and may not always be correct.
+       To use a verified number that respects the applied filters use [WorkReport][pub_analyzer.models.report.WorkReport].
+    """
 
     referenced_works: list[HttpUrl]
     cited_by_api_url: HttpUrl

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/widgets/author/core.py

@@ -67,10 +67,10 @@ class AuthorResumeWidget(Static):
         from_input = self.query_one("#from-date", DateInput)
         to_input = self.query_one("#to-date", DateInput)
 
-        if checkbox.value and from_input.value and to_input.value:
+        if checkbox.value and (from_input.value or to_input.value):
             date_format = "%Y-%m-%d"
-            from_date = datetime.datetime.strptime(from_input.value, date_format)
-            to_date = datetime.datetime.strptime(to_input.value, date_format)
+            from_date = datetime.datetime.strptime(from_input.value, date_format) if from_input.value else None
+            to_date = datetime.datetime.strptime(to_input.value, date_format) if to_input.value else None
 
             report_widget = CreateAuthorReportWidget(author=self.author, from_date=from_date, to_date=to_date)
         else:

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/widgets/report/cards.py

@@ -117,8 +117,12 @@ 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
+        cited_by_count = type_a_count + type_b_count
+
         yield Label('[italic]Citation[/italic]', classes='card-title')
 
-        yield Label(f'[bold]Count:[/bold] {self.work_report.work.cited_by_count}')
-        yield Label(f'[bold]Type A:[/bold] {self.work_report.citation_resume.type_a_count}')
-        yield Label(f'[bold]Type B:[/bold] {self.work_report.citation_resume.type_b_count}')
+        yield Label(f'[bold]Count:[/bold] {cited_by_count}')
+        yield Label(f'[bold]Type A:[/bold] {type_a_count}')
+        yield Label(f'[bold]Type B:[/bold] {type_b_count}')

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/widgets/report/core.py

@@ -4,6 +4,7 @@ import datetime
 import pathlib
 from enum import Enum
 
+import httpx
 from pydantic import TypeAdapter, ValidationError
 from textual import on
 from textual.app import ComposeResult
@@ -89,7 +90,19 @@ class CreateReportWidget(Static):
 
     async def mount_report(self) -> None:
         """Mount report."""
-        report_widget = await self.make_report()
+        try:
+            report_widget = await self.make_report()
+        except httpx.HTTPStatusError as exc:
+            self.query_one(LoadingIndicator).display = False
+            status_error = f"HTTP Exception for url: {exc.request.url}. Status code: {exc.response.status_code}"
+            self.app.notify(
+                    title="Error making report!",
+                    message=f"The report could not be generated due to a problem with the OpenAlex API. {status_error}",
+                    severity="error",
+                    timeout=20.0
+                )
+            return None
+
         container = self.query_one(Container)
         await container.mount(report_widget)
 
@@ -198,9 +211,10 @@ class LoadReportWidget(Static):
         match event.value:
             case self.EntityType.AUTHOR:
                 self.entity_handler = self.EntityType.AUTHOR
-
             case self.EntityType.INSTITUTION:
                 self.entity_handler = self.EntityType.INSTITUTION
+            case _:
+                raise NotImplementedError
 
     def compose(self) -> ComposeResult:
         """Compose load report widget."""

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/widgets/report/export.py

@@ -4,7 +4,7 @@ import pathlib
 from datetime import datetime
 from enum import Enum
 
-from textual import on
+from textual import on, work
 from textual.app import ComposeResult
 from textual.containers import Horizontal, Vertical, VerticalScroll
 from textual.widgets import Button, Label
@@ -46,9 +46,10 @@ class ExportReportPane(VerticalScroll):
         match event.value:
             case self.ExportFileType.JSON:
                 file_name_input.value = f"{self.suggest_prefix}-{datetime.now().strftime('%m-%d-%Y')}.json"
-
             case self.ExportFileType.PDF:
                 file_name_input.value = f"{self.suggest_prefix}-{datetime.now().strftime('%m-%d-%Y')}.pdf"
+            case _:
+                file_name_input.value = f"{self.suggest_prefix}-{datetime.now().strftime('%m-%d-%Y')}"
 
     @on(FileSystemSelector.FileSelected)
     def enable_button(self, event: FileSystemSelector.FileSelected) -> None:
@@ -58,31 +59,36 @@ class ExportReportPane(VerticalScroll):
         else:
             self.query_one(Button).disabled = True
 
+    @work(exclusive=True, thread=True)
+    async def _export_report(self, file_type: ExportFileType, file_path: pathlib.Path) -> None:
+        """Export report."""
+        match file_type:
+            case self.ExportFileType.JSON:
+                with open(file_path, mode="w", encoding="utf-8") as file:
+                    file.write(self.report.model_dump_json(indent=2, by_alias=True))
+            case self.ExportFileType.PDF:
+                report_bytes = await render_report(report=self.report, file_path=file_path)
+                with open(file_path, mode="wb") as file:
+                    file.write(report_bytes)
+
+        self.app.call_from_thread(
+            self.app.notify,
+            title="Report exported successfully!",
+            message=f"The report was exported correctly. You can go see it at [i]{file_path}[/]",
+            timeout=20.0
+        )
+
     @on(Button.Pressed, "#export-report-button")
     async def export_report(self) -> None:
-        """Export Report."""
+        """Handle export report button."""
         export_path = self.query_one(FileSystemSelector).path_selected
         file_name = self.query_one(Input).value
         file_type = self.query_one(self.ExportTypeSelector).value
 
-        if export_path and file_name:
+        if export_path and file_name and file_type:
             file_path = export_path.joinpath(file_name)
-
-            match file_type:
-                case self.ExportFileType.JSON:
-                    with open(file_path, mode="w", encoding="utf-8") as file:
-                        file.write(self.report.model_dump_json(indent=2, by_alias=True))
-                case self.ExportFileType.PDF:
-                    report_bytes = await render_report(report=self.report, file_path=file_path)
-                    with open(file_path, mode="wb") as file:
-                        file.write(report_bytes)
-
+            self._export_report(file_type=file_type, file_path=file_path)
             self.query_one(Button).disabled = True
-            self.app.notify(
-                title="Report exported successfully!",
-                message=f"The report was exported correctly. You can go see it at [i]{file_path}[/]",
-                timeout=20.0
-            )
 
     def compose(self) -> ComposeResult:
         """Compose content pane."""

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/widgets/report/work.py

@@ -107,7 +107,6 @@ class WorkModal(Modal[None]):
                 # Citation Metrics
                 yield CitationMetricsCard(work_report=self.work_report)
 
-
             with TabbedContent(id="tables-container"):
                 # Citations Table
                 with TabPane("Cited By Works"):
@@ -121,6 +120,10 @@ class WorkModal(Modal[None]):
                         yield LocationsTable(self.work_report.work.locations)
                     else:
                         yield Label("No sources found.")
+                # Abtract if exists
+                if self.work_report.work.abstract:
+                    with TabPane("Abstract"):
+                        yield Label(self.work_report.work.abstract, classes="abstract")
 
 
 class WorksTable(Static):
@@ -154,11 +157,14 @@ class WorksTable(Static):
 
     def compose(self) -> ComposeResult:
         """Generate Table."""
-        first_pub_year = self.report.works[0].work.publication_year
-        last_pub_year = self.report.works[-1].work.publication_year
-
-        work_table = Table(title=f"Works from {first_pub_year} to {last_pub_year}", expand=True, show_lines=True)
-
+        if self.report.works:
+            first_pub_year = self.report.works[0].work.publication_year
+            last_pub_year = self.report.works[-1].work.publication_year
+            title = f"Works from {first_pub_year} to {last_pub_year}"
+        else:
+            title = "Works"
+
+        work_table = Table(title=title, expand=True, show_lines=True)
         work_table.add_column('', justify='center', vertical='middle')
         work_table.add_column('Title', ratio=3)
         work_table.add_column('Type', ratio=2)
@@ -205,4 +211,5 @@ class WorkReportPane(VerticalScroll):
             yield WorksTypeResumeCard(report=self.report)
             yield OpenAccessResumeCard(report=self.report)
 
-        yield WorksTable(report=self.report)
+        if self.report.works:
+            yield WorksTable(report=self.report)

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pub_analyzer/widgets/search/core.py

@@ -86,9 +86,11 @@ class FinderWidget(Static):
             case self.OpenAlexEndPoint.AUTHOR:
                 self.url = self.OpenAlexEndPoint.AUTHOR
                 search_bar.placeholder = "Search author"
-
             case self.OpenAlexEndPoint.INSTITUTION:
                 self.url = self.OpenAlexEndPoint.INSTITUTION
                 search_bar.placeholder = "Search institution"
+            case _:
+                self.url = self.OpenAlexEndPoint.AUTHOR
+                search_bar.placeholder = "Search author"
 
         search_bar.value = ""

{pub_analyzer-0.1.0 → pub_analyzer-0.1.2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "pub-analyzer"
-version = "0.1.0"
+version = "0.1.2"
 description = "A text user interface, written in python, which automates the generation of scientific production reports using OpenAlex"
 
 authors = ["Alejandro Gaspar <alejandro@gaspar.land>"]
@@ -39,7 +39,7 @@ pub-analyzer = "pub_analyzer.main:run"
 [tool.poetry.dependencies]
 python = "^3.10"
 
-textual = "0.34.0"
+textual = "0.35.1"
 httpx = "0.24.1"
 pydantic = "2.3.0"
 
@@ -49,28 +49,28 @@ jinja2 = "3.1.2"
 [tool.poetry.group.dev.dependencies]
 textual-dev = "1.1.0"
 
-pre-commit = "3.3.3"
+pre-commit = "3.4.0"
 mypy = "1.5.1"
-ruff = "0.0.286"
+ruff = "0.0.287"
 
-pytest = "7.4.0"
-pytest-asyncio = "0.21.0"
+pytest = "7.4.1"
+pytest-asyncio = "0.21.1"
 respx = "0.20.2"
 vcrpy = "5.1.0"
 pytest-recording = "0.13.0"
 
 [tool.poetry.group.docs.dependencies]
 mkdocs = "1.5.2"
-mkdocs-material = "9.2.3"
+mkdocs-material = "9.2.8"
 
-mkdocstrings = {extras = ["python"], version = "0.22.0"}
-mkdocstrings-python = "1.5.2"
+mkdocstrings = {extras = ["python"], version = "0.23.0"}
+mkdocstrings-python = "1.6.1"
 
 [tool.mypy]
 strict = true
 
 [tool.ruff]
-required-version = "0.0.286"
+required-version = "0.0.287"
 target-version = "py310"
 
 line-length = 140