update pub images

rnabioco · Jul 16, 2024 · 6745a85 · 6745a85
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diff --git a/atlases/2024-lucas-38194268/index.qmd b/atlases/2024-lucas-38194268/index.qmd
@@ -1,6 +1,7 @@
 ---
 title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
 
+image: /images/2024-lucas-38194268.jpg
 subtitle: '[<i class="bi bi-compass"></i> Atlas](https://morrison-lnsc-browser.s3.amazonaws.com/index.html){.link-box-large}'
 date: 'January 09, 2024'
 categories: [Project-1, Project-2, Core-C, Core-D, 2024]
@@ -11,6 +12,9 @@ about:
   - text: Pubmed
     icon: file-earmark
     href: https://pubmed.ncbi.nlm.nih.gov/38194268/
+  - text: PDF
+    icon: filetype-pdf
+    href: /docs/2024-lucas-38194268.pdf
   - text: GitHub
     icon: github
     href: https://github.com/rnabioco/morrison-lnsc

diff --git a/docs/2024-lucas-38194268.pdf b/docs/2024-lucas-38194268.pdf
diff --git a/funs.R b/funs.R
@@ -211,10 +211,34 @@
   if (is.null(pub_info$image) && !is.null(pdf)) {
     img <- here(img_dir, str_c(pub_info$key, ".jpg"))
 
+    n_pgs <- 5
+
+    # Identify pages with figures based on text search
+    pdf_txt <- pdf_text(pdf)
+
+    pgs <- pdf_txt %>%
+      str_count("Figure [0-9]+\\.")
+
+    if (!any(pgs > 0 & pgs < 3)) pgs <- str_count(pdf_txt, "FIGURE [0-9]+")
+    if (!any(pgs > 0 & pgs < 3)) pgs <- str_count(pdf_txt, "Figure [0-9]+")
+    if (!any(pgs > 0 & pgs < 3)) pgs <- str_count(pdf_txt, "Fig. [0-9]+")
+    if (!any(pgs > 0 & pgs < 3)) pgs <- rep(1, n_pgs)
+
+    pgs <- set_names(pgs, seq_along(pgs))[-1]
+    pgs <- names(pgs[pgs > 0 & pgs < 3])
+
+    n_figs  <- length(pgs)
+    pgs     <- pgs[1:(min(n_pgs - 1, n_figs))]
+    pgs     <- as.numeric(c(1, pgs))
+    txt_pgs <- 1:n_pgs
+    txt_pgs <- txt_pgs[!txt_pgs %in% pgs]
+    pgs     <- c(pgs, txt_pgs)[1:n_pgs]
+
+    # Read pdf and save image
     gc()  # kept getting dynamic elf header error, this fixed it
 
     pdf %>%
-      image_read_pdf(pages = 1:5) %>%
+      image_read_pdf(pages = pgs) %>%
       image_append() %>%
       image_write(path = img, format = "jpg")
 

diff --git a/images/2014-tamburini-24905362.jpg b/images/2014-tamburini-24905362.jpg
diff --git a/images/2018-lucas-30045970.jpg b/images/2018-lucas-30045970.jpg
diff --git a/images/2018-mccarthy-29997290.jpg b/images/2018-mccarthy-29997290.jpg
diff --git a/images/2019-tamburini-31156626.jpg b/images/2019-tamburini-31156626.jpg
diff --git a/images/2020-lucas-33053342.jpg b/images/2020-lucas-33053342.jpg
diff --git a/images/2021-carpentier-34618370.jpg b/images/2021-carpentier-34618370.jpg
diff --git a/images/2021-walsh-33843587.jpg b/images/2021-walsh-33843587.jpg
diff --git a/images/2022-doan-35505125.jpg b/images/2022-doan-35505125.jpg
diff --git a/images/2023-tamburini-37841845.jpg b/images/2023-tamburini-37841845.jpg
diff --git a/images/2024-lucas-38194268.jpg b/images/2024-lucas-38194268.jpg
diff --git a/pre-build.R b/pre-build.R
@@ -9,6 +9,7 @@ library(here)
 library(cli)
 library(jsonlite)
 library(rvest)
+library(pdftools)
 library(magick)
 source(here("funs.R"))
 

diff --git a/pubs.yml b/pubs.yml
@@ -190,6 +190,8 @@
     by infection. Consistent with this idea, we find that antigen acquisition by LECs,
     a key function of LN LECs during infection and immunization, was reduced during
     pathogenic CHIKV infection.
+  pdf: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11143926/pdf/jciinsight-9-176537.pdf
+  image: /images/2024-lucas-38194268.jpg
 - pubmed: https://pubmed.ncbi.nlm.nih.gov/29997290/
   project:
   - project-1
@@ -269,6 +271,8 @@
   - project-2
   - core-c
   - core-d
+  links:
+    geo: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129933
   key: 2019-tamburini-31156626
   title: Chronic Liver Disease in Humans Causes Expansion and Differentiation of Liver
     Lymphatic Endothelial Cells

diff --git a/pubs/2019-tamburini-31156626/index.qmd b/pubs/2019-tamburini-31156626/index.qmd
@@ -15,6 +15,8 @@ about:
   - text: PDF
     icon: filetype-pdf
     href: /docs/2019-tamburini-31156626.pdf
+  - text: NCBI GEO
+    href: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129933
 ---
 
 [Beth Tamburini](https://orcid.org/0000-0003-1991-231X), Jeffrey Finlon, Austin Gillen, Michael Kriss, Kent Riemondy, Rui Fu, Ronald Schuyler, [Jay Hesselberth](https://scholar.google.com/citations?user=EnOmNEYAAAAJ), Hugo Rosen, Matthew Burchill

diff --git a/pubs/2024-lucas-38194268/index.qmd b/pubs/2024-lucas-38194268/index.qmd
@@ -1,6 +1,7 @@
 ---
 title: Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO
 
+image: /images/2024-lucas-38194268.jpg
 subtitle: 'PMID 38194268'
 date: 'January 09, 2024'
 categories: [Project-1, Project-2, Core-C, Core-D, 2024]
@@ -11,6 +12,9 @@ about:
   - text: Pubmed
     icon: file-earmark
     href: https://pubmed.ncbi.nlm.nih.gov/38194268/
+  - text: PDF
+    icon: filetype-pdf
+    href: /docs/2024-lucas-38194268.pdf
   - text: GitHub
     icon: github
     href: https://github.com/rnabioco/morrison-lnsc

diff --git a/renv.lock b/renv.lock
@@ -956,6 +956,17 @@
       ],
       "Hash": "2a0dc8c6adfb6f032e4d4af82d258ab5"
     },
+    "pdftools": {
+      "Package": "pdftools",
+      "Version": "3.4.0",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "Rcpp",
+        "qpdf"
+      ],
+      "Hash": "9f04cfdc668ad1149d865a2996ac2045"
+    },
     "pillar": {
       "Package": "pillar",
       "Version": "1.9.0",
@@ -1046,6 +1057,18 @@
       ],
       "Hash": "1cba04a4e9414bdefc9dcaa99649a8dc"
     },
+    "qpdf": {
+      "Package": "qpdf",
+      "Version": "1.3.2",
+      "Source": "Repository",
+      "Repository": "RSPM",
+      "Requirements": [
+        "Rcpp",
+        "askpass",
+        "curl"
+      ],
+      "Hash": "e233fd211c74cb9297f4ab898ea2c18a"
+    },
     "ragg": {
       "Package": "ragg",
       "Version": "1.2.7",