From d443d2768b41117290d6b63e47cf62143e5de459 Mon Sep 17 00:00:00 2001 From: wang177777 <132152013+wang177777@users.noreply.github.com> Date: Fri, 24 Jul 2026 16:05:46 +0800 Subject: [PATCH 1/4] Trigger diagnostic JAMA harvest run --- jama_trigger_pr.txt | 2 ++ 1 file changed, 2 insertions(+) create mode 100644 jama_trigger_pr.txt diff --git a/jama_trigger_pr.txt b/jama_trigger_pr.txt new file mode 100644 index 0000000..1028d97 --- /dev/null +++ b/jama_trigger_pr.txt @@ -0,0 +1,2 @@ +triggered_at_utc=2026-07-24T08:20:00Z +attempt=3 From faa04004a05663f9f47238d3231ae30ca61da6d9 Mon Sep 17 00:00:00 2001 From: wang177777 <132152013+wang177777@users.noreply.github.com> Date: Fri, 24 Jul 2026 16:07:50 +0800 Subject: [PATCH 2/4] Fix Crossref request parameters for harvest --- .github/workflows/jama_network_open_harvest.yml | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.github/workflows/jama_network_open_harvest.yml b/.github/workflows/jama_network_open_harvest.yml index 91bfbbb..0489f89 100644 --- a/.github/workflows/jama_network_open_harvest.yml +++ b/.github/workflows/jama_network_open_harvest.yml @@ -35,6 +35,12 @@ jobs: - name: Install dependencies run: python -m pip install --disable-pip-version-check requests beautifulsoup4 lxml + - name: Patch Crossref query compatibility + shell: bash + run: | + sed -i '/"cursor-max": rows,/d' scripts/fetch_jama_network_open.py + sed -i 's/,type:journal-article//' scripts/fetch_jama_network_open.py + - name: Harvest and reconcile records id: harvest shell: bash From 8defa00fe2745e28a8be2fb0c0aed7383f4cfe5b Mon Sep 17 00:00:00 2001 From: wang177777 <132152013+wang177777@users.noreply.github.com> Date: Fri, 24 Jul 2026 16:09:29 +0800 Subject: [PATCH 3/4] Reduce retries for blocked publisher pages --- .github/workflows/jama_network_open_harvest.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.github/workflows/jama_network_open_harvest.yml b/.github/workflows/jama_network_open_harvest.yml index 0489f89..2112323 100644 --- a/.github/workflows/jama_network_open_harvest.yml +++ b/.github/workflows/jama_network_open_harvest.yml @@ -35,11 +35,13 @@ jobs: - name: Install dependencies run: python -m pip install --disable-pip-version-check requests beautifulsoup4 lxml - - name: Patch Crossref query compatibility + - name: Patch source compatibility and retry policy shell: bash run: | sed -i '/"cursor-max": rows,/d' scripts/fetch_jama_network_open.py sed -i 's/,type:journal-article//' scripts/fetch_jama_network_open.py + sed -i 's/for attempt in range(6):/for attempt in range(2):/' scripts/fetch_jama_network_open.py + sed -i 's/if attempt == 5:/if attempt == 1:/' scripts/fetch_jama_network_open.py - name: Harvest and reconcile records id: harvest From f5d0f64c5c96cb24a674a3ac559b151cac579cef Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Fri, 24 Jul 2026 08:10:03 +0000 Subject: [PATCH 4/4] Update JAMA Network Open harvest summary --- jama_output/latest_run.json | 58 +++++++++++++++++++++++++++++++++++++ jama_output/preview_25.csv | 26 +++++++++++++++++ jama_output/summary.json | 51 ++++++++++++++++++++++++++++++++ 3 files changed, 135 insertions(+) create mode 100644 jama_output/latest_run.json create mode 100644 jama_output/preview_25.csv create mode 100644 jama_output/summary.json diff --git a/jama_output/latest_run.json b/jama_output/latest_run.json new file mode 100644 index 0000000..e5c3da2 --- /dev/null +++ b/jama_output/latest_run.json @@ -0,0 +1,58 @@ +{ + "run_id": 30077936420, + "run_attempt": 1, + "commit_sha": "8defa00fe2745e28a8be2fb0c0aed7383f4cfe5b", + "artifact_name": "jama-network-open-six-month-literature", + "harvest_exit_code": "0", + "summary": { + "counts": { + "crossref_records": 1331, + "europe_pmc_records": 1272, + "jama_issue_records": 0, + "merged_full_index": 1331, + "nonresearch_or_pending": 322, + "research_missing_doi": 0, + "research_missing_exact_day": 0, + "research_missing_idea": 13, + "research_records": 1009 + }, + "date_window": { + "end": "2026-07-24", + "inclusive": true, + "start": "2026-01-24" + }, + "generated_at_utc": "2026-07-24T08:10:01Z", + "research_design_counts": { + "Meta分析": 2, + "临床试验": 28, + "二次分析": 3, + "交叉试验": 2, + "决策分析模型": 4, + "卫生经济学评价": 12, + "定性研究": 34, + "整群随机临床试验": 5, + "整群随机试验": 2, + "未自动识别": 100, + "横断面研究": 183, + "混合方法研究": 4, + "病例对照研究": 29, + "系统综述": 22, + "网状Meta分析": 4, + "诊断研究": 9, + "调查研究": 27, + "质量改进研究": 15, + "遗传关联研究": 1, + "重复横断面研究": 8, + "队列研究": 386, + "随机临床试验": 122, + "随机试验": 1, + "预后研究": 5, + "验证研究": 1 + }, + "scope_note": "Full index retains research and nonresearch publication records. Research table includes records with a verifiable study design/abstract and excludes commentaries, editorials, corrections, retractions, masthead material, and similar nonresearch content.", + "source_coverage_counts": { + "Crossref": 60, + "Crossref; Europe PMC": 1271 + } + } +} \ No newline at end of file diff --git a/jama_output/preview_25.csv b/jama_output/preview_25.csv new file mode 100644 index 0000000..4338d0b --- /dev/null +++ b/jama_output/preview_25.csv @@ -0,0 +1,26 @@ +publication_date,study_design_zh,title,research_idea_en,doi,article_url +2026-01-26,横断面研究,Consumer Food Purchases After Glucagon-Like Peptide-1 Receptor Agonist Initiation,This cross-sectional study examines whether initiating glucagon-like peptide-1 receptor agonists (GLP-1RAs) for treatment is associated with changes in the nutritional quality and processing level of supermarket purchases.,10.1001/jamanetworkopen.2025.55449,https://doi.org/10.1001/jamanetworkopen.2025.55449 +2026-01-26,队列研究,"Cumulative Lifespan Stress, Inflammation, and Racial Disparities in Mortality Between Black and White Adults",Objective: To evaluate whether greater cumulative lifespan stress Design/data: This longitudinal cohort study (St Louis Personality and Aging Network) recruited,10.1001/jamanetworkopen.2025.54701,https://doi.org/10.1001/jamanetworkopen.2025.54701 +2026-01-26,队列研究,Deep Learning Prediction of Childhood Myopia Progression Using Fundus Image and Refraction Data,"Objective: To develop and validate a quantitative method, based on a deep learning method and using only fundus images and baseline refraction data, to predict both myopia progression trajectory and high myopia risk in schoolchildren Design/data: This longitudinal school-based cohort study (Anyang Childhood Eye Study) was conducted from February 2012 to May 2018, with annual follow-up examinations from February 2013 to May 2018.",10.1001/jamanetworkopen.2025.53543,https://doi.org/10.1001/jamanetworkopen.2025.53543 +2026-01-26,横断面研究,"Medical Expenditures by Body Mass Index Among Privately Insured US Adults Aged 18 to 64 Years, 2022",This cross-sectional study estimates body mass index–associated medical expenditures among privately insured US adults in 2022.,10.1001/jamanetworkopen.2025.55436,https://doi.org/10.1001/jamanetworkopen.2025.55436 +2026-01-26,临床试验,Mobile Telemedicine for Treating Chronic Hepatitis C Among Rural People Who Inject Drugs,"Objective: To test whether a mobile telemedicine-based HCV treatment Design/data: This open-label, randomized, parallel-group clinical trial compared mobile telemedicine care (MTC) for HCV treatment with enhanced usual care (EUC), both integrated with van-based syringe services, from April 21, 2022, to September 13, 2024",10.1001/jamanetworkopen.2025.55125,https://doi.org/10.1001/jamanetworkopen.2025.55125 +2026-01-26,横断面研究,Pediatric Asthma in a Universally Insured Military Population,"Objective: To investigate racial and ethnic differences in asthma diagnoses, potentially avoidable hospitalizations (PAHs) or emergency department (ED) visits, specialist visits, and asthma-related prescriptions among Military Health System (MHS) pediatric beneficiaries Design/data: This cross-sectional study investigated the prevalence of pediatric asthma among MHS beneficiaries enrolled in TRICARE Prime during fiscal year (FY) 2023.",10.1001/jamanetworkopen.2025.56740,https://doi.org/10.1001/jamanetworkopen.2025.56740 +2026-01-26,横断面研究,Trends in Urgent Care Utilization Among Medicare Beneficiaries From 2012 to 2019,"Objective: To examine UC utilization among older adults and assess whether utilization rates varied by beneficiary sociodemographic and community characteristics Design/data: This cross-sectional study used data from a 20% national sample of fee-for-service Medicare beneficiaries aged 65 years or older using UC centers from January 1, 2012, to December 31, 2019.",10.1001/jamanetworkopen.2025.55345,https://doi.org/10.1001/jamanetworkopen.2025.55345 +2026-01-26,队列研究,"Umbilical Cord Blood pH Level, Apgar Score, and Attention-Deficit/Hyperactivity Disorder","Objective: To identify full-term and near-term newborns exposed to hypoxia by combining the Apgar score and the umbilical cord blood pH level and to investigate their association with ADHD Design/data: This cohort study, with follow-up from birth until December 31, 2022, identified all singleton newborns with a gestational age of 35 weeks or more, without major malformations, born between January 1, 2004, and December 31, 2018, using a Danish nationwide registry.",10.1001/jamanetworkopen.2025.54672,https://doi.org/10.1001/jamanetworkopen.2025.54672 +2026-01-27,随机临床试验,Acupuncture for Migraine Without Aura and Connection-Based Efficacy Prediction,"Objective: To evaluate the clinical efficacy of real acupuncture and sham acupuncture in MWOA, and to identify acupuncture-response brain connectivity patterns using CPM analysis of baseline functional magnetic resonance imaging (fMRI) data Design/data: This single-blinded randomized clinical trial was conducted from June 2021 to June 2023 at Beijing Hospital of Traditional Chinese Medicine in China.",10.1001/jamanetworkopen.2025.55454,https://doi.org/10.1001/jamanetworkopen.2025.55454 +2026-01-27,调查研究,Career Plans Among Graduating US Emergency Medicine Residents,"Objective: To examine the career plans, anticipated career durations, and key factors associated with the career decisions of graduating US EM residents Design/data: This cross-sectional survey study, which sampled graduating residents from all Accreditation Council for Graduate Medical Education–accredited categorical EM programs, was conducted after the 2023 American Board of Emergency Medicine In-Training Examination.",10.1001/jamanetworkopen.2025.55376,https://doi.org/10.1001/jamanetworkopen.2025.55376 +2026-01-27,卫生经济学评价,Cost-Effectiveness of Acceptable-Quality Deceased Donor Kidneys for Transplant in Older Candidates,Objective: To assess the cost-effectiveness of increasing the kidney transplantation rate among older patients with end-stage kidney disease by using acceptable-quality deceased donor kidneys Design/data: This economic evaluation with cost-effectiveness analysis uses a microsimulation model of the kidney transplantation process for a synthetic cohort of adult candidates aged 65 years or older on the transplant waiting list between 2010 and 2019 over their remaining lifetimes.,10.1001/jamanetworkopen.2025.55428,https://doi.org/10.1001/jamanetworkopen.2025.55428 +2026-01-27,队列研究,"Financial Assistance Policy, Hospital Charity Care, and Medical Debt in Collections","Objective: To estimate the association of Oregon’s FAP with medical debt in collections and hospitals’ charity care (ie, free or discounted care for patients qualified for FAPs) and bad debt (ie, total amount of uncollectible patient accounts) expenditures Design/data: This cohort study examined county- and hospital-level difference-in-differences and event study models covering the period from 2015 to 2022.",10.1001/jamanetworkopen.2025.55698,https://doi.org/10.1001/jamanetworkopen.2025.55698 +2026-01-27,队列研究,Follow-Up Assessment of Adherence to Methodological Standards in National Inpatient Sample Research,This cohort study assesses changes in adherence to National Inpatient Sample (NIS) methodological standards among research studies since the original publication of the checklist of best practices.,10.1001/jamanetworkopen.2025.55753,https://doi.org/10.1001/jamanetworkopen.2025.55753 +2026-01-27,队列研究,Geriatric Syndromes and Mortality Among Hospitalized Older Adults,"Objective: To measure the prevalence of geriatric syndromes upon hospital admission and examine the independent association between the number of geriatric syndromes and 90-day mortality Design/data: This cohort study used data from the Creating a Hospital Assessment Network in Geriatrics (CHANGE) study, a multicenter, prospective cohort of 43 hospitals, including 38 in Brazil, 1 in Angola, 1 in Chile, 2 in Colombia, and 1 in Portugal.",10.1001/jamanetworkopen.2025.55740,https://doi.org/10.1001/jamanetworkopen.2025.55740 +2026-01-27,队列研究,Medicaid Expansion and Overall Mortality Among Women With Breast Cancer,"Objective: To evaluate the association between Medicaid expansion and overall mortality among women with breast cancer and to assess whether survival differs by race and ethnicity, disease stage, income, and treatment modality Design/data: This retrospective, hospital-based cohort study used a National Cancer Database cohort of 1 595 845 women aged 40 to 64 years with breast cancer who received a diagnosis from January 1, 2006, to December 31, 2021.",10.1001/jamanetworkopen.2025.54512,https://doi.org/10.1001/jamanetworkopen.2025.54512 +2026-01-27,横断面研究,"Sex Differences in Alzheimer Disease Imaging Biomarkers in a Diverse, Community-Based Cohort","Objective: To examine sex differences in neuroimaging biomarkers of AD-related pathologies in a racially and ethnically diverse cohort Design/data: Data for this cross-sectional study were collected from a community-based sample of adults without cognitive impairment aged 60 to 69 years in New York City from March 1, 2016, to September 31, 2022, and analyzed in March 2025",10.1001/jamanetworkopen.2025.54524,https://doi.org/10.1001/jamanetworkopen.2025.54524 +2026-01-28,队列研究,Blood Lead Concentrations and Depressive and Anxiety Symptoms in Childhood,"Objective: To examine associations between low-level, serial blood lead concentrations in children and symptoms of depression and anxiety and to investigate for periods of susceptibility Design/data: This cohort study used data from a prospective population of 218 caregiver-child dyads (218 children and 218 parents in the Health",10.1001/jamanetworkopen.2025.56019,https://doi.org/10.1001/jamanetworkopen.2025.56019 +2026-01-28,队列研究,Characteristics and Outcomes of Adults Hospitalized With Childhood-Onset Complex Chronic Conditions,"Objective: To identify and characterize young adults with 4Cs in hospitals and compare their outcomes with other hospitalized young adults Design/data: This retrospective cohort study included young adults aged 18 to 39 years who were discharged from 29 hospitals in Ontario, Canada, from January 1 to December 31, 2018.",10.1001/jamanetworkopen.2025.53610,https://doi.org/10.1001/jamanetworkopen.2025.53610 +2026-01-28,临床试验,Deep-Learning Serial CT Prediction of Survival in Immunotherapy-Treated Non–Small Cell Lung Cancer,Objective: To develop and validate a fully automated deep-learning imaging-based biomarker using pretherapy and 12-week follow-up computed tomography (CT) scans Design/data: This prognostic study used retrospectively collected HER data from routine clinical practice (RCP) and clinical trial data from 2013 to 2023.,10.1001/jamanetworkopen.2025.55759,https://doi.org/10.1001/jamanetworkopen.2025.55759 +2026-01-28,队列研究,For-Profit Program for All Inclusive Care for the Elderly Plans and Patient Characteristics,This cohort study describes characteristics and health care use patterns of Medicare enrollees in Program for All Inclusive Care for the Elderly (PACE) plans by ownership type.,10.1001/jamanetworkopen.2025.56296,https://doi.org/10.1001/jamanetworkopen.2025.56296 +2026-01-28,队列研究,Glucagon-Like Peptide-1 Receptor Agonists and Prior Major Adverse Limb Events in Patients With Diabetes,"Objective: To evaluate whether glucagon-like peptide-1 receptor agonists (GLP-1 RAs) are associated with reduced risk of MALEs and major adverse cardiovascular events (MACE) compared with dipeptidyl peptidase-4 (DPP-4) inhibitors in patients with diabetes and prior MALEs Design/data: This retrospective, nationwide cohort study used data from the Taiwan National Health Insurance Research Database from October 2012 to December 2023.",10.1001/jamanetworkopen.2025.55952,https://doi.org/10.1001/jamanetworkopen.2025.55952 +2026-01-28,队列研究,Health Care–Associated Infections Among Neonates During the COVID-19 Pandemic,Objective: To compare rates of viral and bacterial or fungal HAIs in infants admitted to the NICU before and during the pandemic Design/data: This cohort study was conducted at 12 level 3 or level 4 NICUs in the US and Canada,10.1001/jamanetworkopen.2025.55623,https://doi.org/10.1001/jamanetworkopen.2025.55623 +2026-01-28,决策分析模型,"Health, Costs, and Injection-Related Infections at a Hypothetical Overdose Prevention Center","Objective: To estimate the 10-year impact of a hypothetical OPC in Denver, Colorado, on injection-related infections, hospitalizations, mortality, and associated costs from a payer perspective Design/data: This decision analytical modeling study used a calibrated and validated Monte Carlo microsimulation model of the natural history of injection drug use.",10.1001/jamanetworkopen.2025.55965,https://doi.org/10.1001/jamanetworkopen.2025.55965 +2026-01-28,队列研究,Life-Course Psychosocial Stress and Risk of Dementia and Stroke in Middle-Aged and Older Adults,"Objective: To investigate the associations of ACEs and AAEs with dementia and stroke incidence, and to examine whether depression mediates these associations Design/data: This population-based cohort study utilized data from the China Health and Retirement Longitudinal Study (June 2015 to December 2020)",10.1001/jamanetworkopen.2025.56012,https://doi.org/10.1001/jamanetworkopen.2025.56012 +2026-01-28,队列研究,Platelet Transfusion Practices and Outcomes in Neonates and Children,"Objective: To describe the epidemiology of platelet transfusions and associations of blood donor and platelet characteristics with posttransfusion platelet increments, transfusion burden, and clinical outcomes in neonates and children Design/data: This cohort study included patients younger than 18 years of age (with birth weights higher than 2500 g) between April 1, 2019, and June 30, 2023, from the Recipient Epidemiology and Donor Evaluation Study-IV-Pediatric Vein-to-Vein multicenter, retrospective, donor-component-recipient−linked database.",10.1001/jamanetworkopen.2025.54531,https://doi.org/10.1001/jamanetworkopen.2025.54531 diff --git a/jama_output/summary.json b/jama_output/summary.json new file mode 100644 index 0000000..47c92d9 --- /dev/null +++ b/jama_output/summary.json @@ -0,0 +1,51 @@ +{ + "counts": { + "crossref_records": 1331, + "europe_pmc_records": 1272, + "jama_issue_records": 0, + "merged_full_index": 1331, + "nonresearch_or_pending": 322, + "research_missing_doi": 0, + "research_missing_exact_day": 0, + "research_missing_idea": 13, + "research_records": 1009 + }, + "date_window": { + "end": "2026-07-24", + "inclusive": true, + "start": "2026-01-24" + }, + "generated_at_utc": "2026-07-24T08:10:01Z", + "research_design_counts": { + "Meta分析": 2, + "临床试验": 28, + "二次分析": 3, + "交叉试验": 2, + "决策分析模型": 4, + "卫生经济学评价": 12, + "定性研究": 34, + "整群随机临床试验": 5, + "整群随机试验": 2, + "未自动识别": 100, + "横断面研究": 183, + "混合方法研究": 4, + "病例对照研究": 29, + "系统综述": 22, + "网状Meta分析": 4, + "诊断研究": 9, + "调查研究": 27, + "质量改进研究": 15, + "遗传关联研究": 1, + "重复横断面研究": 8, + "队列研究": 386, + "随机临床试验": 122, + "随机试验": 1, + "预后研究": 5, + "验证研究": 1 + }, + "scope_note": "Full index retains research and nonresearch publication records. Research table includes records with a verifiable study design/abstract and excludes commentaries, editorials, corrections, retractions, masthead material, and similar nonresearch content.", + "source_coverage_counts": { + "Crossref": 60, + "Crossref; Europe PMC": 1271 + } +} \ No newline at end of file