Jinze-Lee/codex-skills-workbench

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def attempt_download(url: str, timeout: int) -> dict:     request = urllib.request.Request(

request = urllib.request.Request(

},     )     with urllib.request.urlopen(request, timeout=timeout, context=ssl.create_default_context()) as response:

)     with urllib.request.urlopen(request, timeout=timeout, context=ssl.create_default_context()) as response:         payload = response.read()

with urllib.request.urlopen(request, timeout=timeout, context=ssl.create_default_context()) as response:

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[Credential-related source omitted]

[Credential-related source omitted]

NCBI_BASE = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"

EUROPEPMC_SEARCH_URL = "https://www.ebi.ac.uk/europepmc/webservices/rest/search"

EUROPEPMC_FULLTEXT_XML = "https://www.ebi.ac.uk/europepmc/webservices/rest/{pmcid}/fullTextXML"

CROSSREF_URL = "https://api.crossref.org/works"

OPENALEX_URL = "https://api.openalex.org/works"

def normalize_doi(value: Any) -> str:     text = normalize_text(value)     text = text.replace("https://doi.org/", "").replace("http://doi.org/", "")

text = normalize_text(value)     text = text.replace("https://doi.org/", "").replace("http://doi.org/", "")     text = text.replace("doi:", "").strip().rstrip(".")

text = text.replace("https://doi.org/", "").replace("http://doi.org/", "")

for attempt in range(1, retries + 1):         try:             request = urllib.request.Request(url, headers=request_headers)

try:             request = urllib.request.Request(url, headers=request_headers)             with urllib.request.urlopen(request, timeout=REQUEST_TIMEOUT, context=ssl.create_default_context()) as response:

request = urllib.request.Request(url, headers=request_headers)

with urllib.request.urlopen(request, timeout=REQUEST_TIMEOUT, context=ssl.create_default_context()) as response:

for attempt in range(1, retries + 1):         try:             request = urllib.request.Request(url, headers=request_headers)

try:             request = urllib.request.Request(url, headers=request_headers)             with urllib.request.urlopen(request, timeout=REQUEST_TIMEOUT, context=ssl.create_default_context()) as response:

request = urllib.request.Request(url, headers=request_headers)

with urllib.request.urlopen(request, timeout=REQUEST_TIMEOUT, context=ssl.create_default_context()) as response:

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pdf_url = ""     if clean_text(result.get("hasPDF")).upper() == "Y" and pmcid:         pdf_url = f"https://europepmc.org/articles/{pmcid}?pdf=render"

if clean_text(result.get("hasPDF")).upper() == "Y" and pmcid:         pdf_url = f"https://europepmc.org/articles/{pmcid}?pdf=render"     fulltext_url = ""

pdf_url = f"https://europepmc.org/articles/{pmcid}?pdf=render"

fulltext_url = ""     if pmcid:         fulltext_url = f"https://www.ebi.ac.uk/europepmc/webservices/rest/{pmcid}/fullTextXML"

if pmcid:         fulltext_url = f"https://www.ebi.ac.uk/europepmc/webservices/rest/{pmcid}/fullTextXML"     elif fulltext_urls:

fulltext_url = f"https://www.ebi.ac.uk/europepmc/webservices/rest/{pmcid}/fullTextXML"

"fulltext_url": fulltext_url,         "pdf_url": pdf_url,         "landing_page_url": f"https://europepmc.org/article/MED/{normalize_pmid(result.get('pmid'))}" if normalize_pmid(result.get("pmid")) else clean_text(fulltext_url),

"pdf_url": pdf_url,         "landing_page_url": f"https://europepmc.org/article/MED/{normalize_pmid(result.get('pmid'))}" if normalize_pmid(result.get("pmid")) else clean_text(fulltext_url),         "license": clean_text(result.get("license

"landing_page_url": f"https://europepmc.org/article/MED/{normalize_pmid(result.get('pmid'))}" if normalize_pmid(result.get("pmid")) else clean_text(fulltext_url),

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"publication_type": "; ".join(publication_types),                 "open_access_flag": bool(pmcid),                 "fulltext_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",

"open_access_flag": bool(pmcid),                 "fulltext_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",                 "pdf_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/pdf/" if pmcid else "",

"fulltext_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",

"pdf_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/pdf/" if pmcid else "",

"landing_page_url": f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/" if pmid else "",

url                         for url in [                             f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",

for url in [                             f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",                             f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/pdf/" if pmcid else "",

f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",

f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/pdf/" if pmcid else "",

"publication_type": "",                 "open_access_flag": bool(pmcid),                 "fulltext_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",

"open_access_flag": bool(pmcid),                 "fulltext_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",                 "pdf_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/pdf/" if pmcid else "",

"fulltext_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",

"pdf_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/pdf/" if pmcid else "",

"landing_page_url": f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",

url                         for url in [                             f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",

for url in [                             f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",                             f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/pdf/" if pmcid else "",

f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/" if pmcid else "",

f"https://pmc.ncbi.nlm.nih.gov/articles/{pmcid}/pdf/" if pmcid else "",

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def normalize_doi(value: Any) -> str:     text = clean_text(value).lower()     text = text.replace("https://doi.org/", "").replace("http://doi.org/", "")

text = clean_text(value).lower()     text = text.replace("https://doi.org/", "").replace("http://doi.org/", "")     text = text.replace("doi:", "").strip().rstrip(".")

text = text.replace("https://doi.org/", "").replace("http://doi.org/", "")

def request_url(url: str, timeout: int) -> dict[str, Any]:     request = urllib.request.Request(

request = urllib.request.Request(

},     )     with urllib.request.urlopen(request, timeout=timeout, context=ssl.create_default_context()) as response:

)     with urllib.request.urlopen(request, timeout=timeout, context=ssl.create_default_context()) as response:         return {

with urllib.request.urlopen(request, timeout=timeout, context=ssl.create_default_context()) as response:

doi = normalize_doi(row.get("doi"))     if doi:         urls.append(f"https://doi.org/{doi}")

if doi:         urls.append(f"https://doi.org/{doi}")     unique: list[str] = []

urls.append(f"https://doi.org/{doi}")

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doi = utils.normalize_doi(row.get("doi"))     if doi:         urls.append(f"https://doi.org/{doi}")

if doi:         urls.append(f"https://doi.org/{doi}")     unique: list[str] = []

urls.append(f"https://doi.org/{doi}")

[Credential-related source omitted]

## 模板来源  - 内置模板是 `examples/Template.docx`，格式为 Word `.docx`。模板修改自 https://seuthesis-word.github.io/ ，目前在图表目录和封面上尚未完全完成，请勿直接使用模板带封面的 Word，修改后的模板文件已存放在 `examples/` 中，可以在完成后再额外添加封面等摘要之前的内容。

- 内置模板是 `examples/Template.docx`，格式为 Word `.docx`。模板修改自 https://seuthesis-word.github.io/ ，目前在图表目录和封面上尚未完全完成，请勿直接使用模板带封面的 Word，修改后的模板文件已存放在 `examples/` 中，可以在完成后再额外添加封面等摘要之前的内容。

{   "$schema": "https://json-schema.org/draft/2020-12/schema",

"$schema": "https://json-schema.org/draft/2020-12/schema",

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W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"

R_NS = "http://schemas.openxmlformats.org/officeDocument/2006/relationships"

REL_NS = "http://schemas.openxmlformats.org/package/2006/relationships"

WP_NS = "http://schemas.openxmlformats.org/drawingml/2006/wordprocessingDrawing"

A_NS = "http://schemas.openxmlformats.org/drawingml/2006/main"

PIC_NS = "http://schemas.openxmlformats.org/drawingml/2006/picture"

CT_NS = "http://schemas.openxmlformats.org/package/2006/content-types"

<wp:cNvGraphicFramePr><a:graphicFrameLocks noChangeAspect="1"/></wp:cNvGraphicFramePr>         <a:graphic>           <a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/picture">

<a:graphic>           <a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/picture">             <pic:pic>

<a:graphicData uri="http://schemas.openxmlformats.org/drawingml/2006/picture">

rel = etree.SubElement(rels_root, qn(REL_NS, "Relationship"))         rel.set("Id", rid)         rel.set("Type", "http://schemas.openxmlformats.org/officeDocument/2006/relationships/image")

rel.set("Id", rid)         rel.set("Type", "http://schemas.openxmlformats.org/officeDocument/2006/relationships/image")         rel.set("Target", f"media/{target_name}")

rel.set("Type", "http://schemas.openxmlformats.org/officeDocument/2006/relationships/image")

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PKG_NS = "http://schemas.microsoft.com/office/2006/xmlPackage"

CT_NS = "http://schemas.openxmlformats.org/package/2006/content-types"

def sniff_xml_kind(xml_path: str | Path) -> str:     head = Path(xml_path).read_text(encoding="utf-8", errors="ignore")[:4000]     if "<pkg:package" in head and "http://schemas.microsoft.com/office/2006/xmlPackage" in head:

head = Path(xml_path).read_text(encoding="utf-8", errors="ignore")[:4000]     if "<pkg:package" in head and "http://schemas.microsoft.com/office/2006/xmlPackage" in head:         return "flat_opc"

if "<pkg:package" in head and "http://schemas.microsoft.com/office/2006/xmlPackage" in head:

return "flat_opc"     if "<w:wordDocument" in head and "http://schemas.microsoft.com/office/word/2003/wordml" in head:         return "word_2003_xml"

if "<w:wordDocument" in head and "http://schemas.microsoft.com/office/word/2003/wordml" in head:

payload = base64.b64decode("".join(node.itertext()))

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if pages:             details += f", {pages}"         doi_str = f" https://doi.org/{doi}" if doi else (f" {url}" if url else "")

details += f", {pages}"         doi_str = f" https://doi.org/{doi}" if doi else (f" {url}" if url else "")         return f"{authors_join(authors)} ({year}). {title}. {journal}{details}.{doi_str}"

doi_str = f" https://doi.org/{doi}" if doi else (f" {url}" if url else "")

def fetch_crossref(title: str) -> dict[str, Any] | None:     query = urlencode({"query.bibliographic": title, "rows": 1, "mailto": "thesis-skill@example.com"})     req = Request(f"https://api.crossref.org/works?{query}", headers={"User-Agen

query = urlencode({"query.bibliographic": title, "rows": 1, "mailto": "thesis-skill@example.com"})     req = Request(f"https://api.crossref.org/works?{query}", headers={"User-Agent": "master-thesis-studio/1.0"})     with urlopen(req, timeou

req = Request(f"https://api.crossref.org/works?{query}", headers={"User-Agent": "master-thesis-studio/1.0"})     with urlopen(req, timeout=60) as res:         data = json.loads(res.read().decode("utf-8"))

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R_NS = "http://schemas.openxmlformats.org/officeDocument/2006/relationships"

REL_NS = "http://schemas.openxmlformats.org/package/2006/relationships"

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PKG_NS = "http://schemas.microsoft.com/office/2006/xmlPackage"

W_NS = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"

R_NS = "http://schemas.openxmlformats.org/officeDocument/2006/relationships"

M_NS = "http://schemas.openxmlformats.org/officeDocument/2006/math"

RELS_NS = "http://schemas.openxmlformats.org/package/2006/relationships"

run.append(r_pr_copy)     t = etree.SubElement(run, qn(W_NS, "t"))     t.set("{http://www.w3.org/XML/1998/namespace}space", "preserve")

t = etree.SubElement(run, qn(W_NS, "t"))     t.set("{http://www.w3.org/XML/1998/namespace}space", "preserve")     t.text = text

t.set("{http://www.w3.org/XML/1998/namespace}space", "preserve")

run.append(r_pr_copy)         node = etree.SubElement(run, qn(W_NS, "instrText"))         node.set("{http://www.w3.org/XML/1998/namespace}space", "preserve")

node = etree.SubElement(run, qn(W_NS, "instrText"))         node.set("{http://www.w3.org/XML/1998/namespace}space", "preserve")         node.text = instr

node.set("{http://www.w3.org/XML/1998/namespace}space", "preserve")