From cb11cff20149c2a6b6bff48126b733b499475c46 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Tue, 7 Jan 2025 14:28:40 -0800
Subject: [PATCH 1/6] Add request and renewal dates to the output

---
 parse_dars.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/parse_dars.py b/parse_dars.py
index ae10a9a..e76bac9 100644
--- a/parse_dars.py
+++ b/parse_dars.py
@@ -7,6 +7,7 @@
 
 
 def parse_phs_blocks(blocks):
+    #import ipdb; ipdb.set_trace()
     phs = blocks[0]
     request_date_idx = [i for i, item in enumerate(blocks) if re.search("Request Date", item)]
     dar_list = []
@@ -23,6 +24,10 @@ def parse_phs_blocks(blocks):
             this_dar["DAR"] = m.string.split(" : ")[1]
         else:
             this_dar["DAR"] = None
+        # Get the request and renewal dates.
+        date_blocks = blocks[idx].replace(":\n", ": ").split("\n")
+        tmp = {k: v for k, v in (xx.split(' : ') for xx in date_blocks)}
+        this_dar.update(tmp)
         # Now find the consent group.
         j = idx
         try:
@@ -88,7 +93,9 @@ def parse_phs_blocks(blocks):
     # Convert to pandas data frame and write to tsv.
     df = pd.DataFrame(dars)
     df = df.rename(columns={
-        "Abbreviation": "consent_group"
+        "Abbreviation": "consent_group",
+        "Request Date": "request_date",
+        "Last Renewal Date": "last_renewal_date",
     })
 
     # Replace newlines in study with spaces.

From c2e140452872fda25a62696f66805afe0f591720 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Tue, 7 Jan 2025 14:31:46 -0800
Subject: [PATCH 2/6] Add dates to Rmd report

---
 dar_report.Rmd | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/dar_report.Rmd b/dar_report.Rmd
index 0962751..da3264f 100644
--- a/dar_report.Rmd
+++ b/dar_report.Rmd
@@ -46,3 +46,19 @@ tmp <- dars %>%
 nrow(tmp)
 tmp %>% kable()
 ```
+
+# Dates
+
+## Request date
+
+```{r}
+ggplot(dars, aes(request_date)) +
+    geom_histogram()
+```
+
+## Renewal date
+
+```{r}
+ggplot(dars, aes(last_renewal_date)) +
+    geom_histogram()
+```

From 9b4be2b6251d3b96cfb09fd9b410b702f07e20e2 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Tue, 7 Jan 2025 14:32:16 -0800
Subject: [PATCH 3/6] Ignore html files in gitignore

---
 .gitignore | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.gitignore b/.gitignore
index 107e896..fda01b2 100644
--- a/.gitignore
+++ b/.gitignore
@@ -161,4 +161,5 @@ cython_debug/
 
 ###########
 # Custom additions
-dars.tsv
\ No newline at end of file
+dars.tsv
+*.html

From ceba1da46207dece1843f944590020e42bfbd5a3 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Tue, 7 Jan 2025 14:39:02 -0800
Subject: [PATCH 4/6] Update README with --no-cache

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index c28e7e1..d4881c5 100644
--- a/README.md
+++ b/README.md
@@ -46,6 +46,6 @@ python parse_dars.py <path_to_application_pdf> <path_to_output_tsv>
 ## Updating the docker images
 
 ```
-docker build -t uwgac/parse-dbgap-application:<tag> .
+docker build --no-cache -t uwgac/parse-dbgap-application:<tag> .
 docker push uwgac/parse-dbgap-application:<tag>
 ```

From b3d79cb14eb479debaed6d966ec52e03fc213f48 Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Tue, 7 Jan 2025 14:39:12 -0800
Subject: [PATCH 5/6] Update WDL to use v0.2 of docker image

---
 parse_dbgap_application.wdl | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/parse_dbgap_application.wdl b/parse_dbgap_application.wdl
index 2f84277..758176d 100644
--- a/parse_dbgap_application.wdl
+++ b/parse_dbgap_application.wdl
@@ -37,7 +37,7 @@ task extract_dars {
     }
 
     runtime {
-        docker: "uwgac/parse-dbgap-application:0.1"
+        docker: "uwgac/parse-dbgap-application:0.2"
     }
 }
 
@@ -54,6 +54,6 @@ task render_report {
         File dar_report = "dar_report.html"
     }
     runtime {
-        docker: "uwgac/parse-dbgap-application:0.1"
+        docker: "uwgac/parse-dbgap-application:0.2"
     }
 }

From f1b1f6e418ba7b3daa021df473cbb2fa7c499dbf Mon Sep 17 00:00:00 2001
From: Adrienne Stilp <amstilp@uw.edu>
Date: Wed, 8 Jan 2025 14:14:58 -0800
Subject: [PATCH 6/6] Handle dates correctly for new DARs

---
 parse_dars.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parse_dars.py b/parse_dars.py
index e76bac9..2dc2bc3 100644
--- a/parse_dars.py
+++ b/parse_dars.py
@@ -26,7 +26,7 @@ def parse_phs_blocks(blocks):
             this_dar["DAR"] = None
         # Get the request and renewal dates.
         date_blocks = blocks[idx].replace(":\n", ": ").split("\n")
-        tmp = {k: v for k, v in (xx.split(' : ') for xx in date_blocks)}
+        tmp = {k.strip(): v.strip() for k, v in (xx.split(":") for xx in date_blocks)}
         this_dar.update(tmp)
         # Now find the consent group.
         j = idx