From a36d4918d84520f18da3e6c488f9d5bfe5361947 Mon Sep 17 00:00:00 2001
From: TanyaStere42 <tstere@wildme.org>
Date: Fri, 8 Nov 2024 14:06:06 -0800
Subject: [PATCH] ia pathways docs

---
 docs/_static/custom.css   |  8 +++++--
 docs/contribute/ia-dev.md | 47 +++++++++++++++++++++++++++++++++++++++
 docs/contribute/index.md  |  1 +
 docs/index.md             |  5 +++++
 4 files changed, 59 insertions(+), 2 deletions(-)
 create mode 100644 docs/contribute/ia-dev.md

diff --git a/docs/_static/custom.css b/docs/_static/custom.css
index 90b41cb..9be3446 100644
--- a/docs/_static/custom.css
+++ b/docs/_static/custom.css
@@ -11,11 +11,13 @@ html[data-theme='light'] {
 }
 
 html[data-theme='dark'] a {
-    color:#0267FD;
+    color:#007599;
+    text-decoration: none;
 }
 
 html[data-theme='dark'] a:hover {
     color:#007599;
+    text-decoration: underline;
 }
 
 html [data-theme='dark'] .search-button-field {
@@ -23,9 +25,11 @@ html [data-theme='dark'] .search-button-field {
 }
 
 html[data-theme='light'] a {
-    color:#0267FD;
+    color:#007599;
+    text-decoration: none;
 }
 
 html[data-theme='light'] a:hover {
     color:#007599;
+    text-decoration: underline;
 }
\ No newline at end of file
diff --git a/docs/contribute/ia-dev.md b/docs/contribute/ia-dev.md
new file mode 100644
index 0000000..95c7a8f
--- /dev/null
+++ b/docs/contribute/ia-dev.md
@@ -0,0 +1,47 @@
+# Image Analysis Development
+
+## Code Pathways to IA
+
+### Single Encounter Submission
+1. User starts on submit.jsp
+2. `EncounterForm`
+  - `IA.intakeMediaAssets(myShepherd, enc.getMedia().parentTask);`
+  - `IA. intakeMediaAssetsOneSpecies(myShepherd, assetsBySpecies.get(0), parentTask);`
+  - `intakeMediaAssetsOneSpecies(myShepherd, mas, taxy, parentTask);	`
+  - `intakeMediaAssetsOneSpecies(Shepherd myShepherd, List<MediaAsset> mas,Taxonomy taxy, final Task parentTask, int tweetAssetId)`
+  - `IAGateway.addToDetectionQueue(context,qjob.toString());`
+3. WBIA detection occurs independently
+4. `IBEISIA.processCallback`
+  - `processCallbackDetect(...)`
+  - `IA.intakeAnnotations(myShepherd2, needIdentifying, parentTask, false);`
+  - `IAGateway.addToQueue(context, qjob.toString());`
+5. `IBEISIA.processCallback`
+  - `IBEISIA.processCallbackIdentify`
+6. Results visible from "match results" button on annotation on Encounter page
+
+### Bulk Import
+_Assumes bulk detection on the ImportTask has already occurred._
+
+1. User has completed a bulk import and is looking at it on the related import.jsp page.
+2. `resendBulkImportID.jsp`
+  - `IA.intakeAnnotations(myShepherd, matchMeAnns, subParentTask,false);`
+  - `IAGateway.addToQueue(context, qjob.toString());`
+3. Queue (“IA”) sends to WBIA
+4. `IBEISIA.processCallback` when job returned by WBIA to /ia
+  - `IBEISIA.processCallbackIdentify`
+5. Results visible from “match results” button on annotation on an imported Encounter page or from the import.jsp for the bulk import.
+
+### Manual 'Start Match' from Encounter Page
+_Assumes detection has already run, and annotations already exist._
+
+1. User clicks “start match” or “start another match”  from encounter.jsp
+  - `encounter.jsp.iaMatchFilterGo(...)`
+  - `ia.IBEIS.js.restCall(...)`
+2. `IAGateway.java`
+  - doPost
+  - `if (j.optBoolean("enqueue", false) || j.optBoolean("v2", false)) { `
+  - `addToDetectionQueue(context, j.toString());` or `addToQueue (...)` depending on fastlane status
+3. Queue (“detection”/fastlane) - except for HotSpotter jobs which are sent to “IA” queue sends to WBIA
+4. `IBEISIA.processCallback` when job returned by WBIA to /ia
+  - `IBEISIA.processCallbackIdentify`
+5. Results visible from “match results” button on annotation on Encounter page
diff --git a/docs/contribute/index.md b/docs/contribute/index.md
index 1633546..d6b7eec 100644
--- a/docs/contribute/index.md
+++ b/docs/contribute/index.md
@@ -6,6 +6,7 @@
 dev-setup
 pr-workflow
 code-guide
+ia-dev
 copy-guide
 roadmap
 ```
diff --git a/docs/index.md b/docs/index.md
index a4d3e4f..ec6dfb2 100644
--- a/docs/index.md
+++ b/docs/index.md
@@ -19,4 +19,9 @@ Want to put your talents to use fighting the 6th mass extinction? We're excited
 
 ```{toctree}
 contribute/index
+contribute/dev-setup
+contribute/pr-workflow
+contribute/code-guide
+contribute/copy-guide
+contribute/roadmap
 ```