updated docs and refactoring

spawaskar-cora · Jan 5, 2024 · 686729c · 686729c
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diff --git a/docs/forensics-anthro-guide/anomalies.md b/docs/forensics-anthro-guide/anomalies.md
@@ -2,7 +2,7 @@
 
 In this section we present the anomalies available within CoRA for assignment to individual specimens. Anomalies are organized by Bone
 
-!!! question "How can I add a new anomalies to CoRA?"
+!!! question "How can I add new anomalies to CoRA?"
 
     You can request new anomalies to be added to CoRA if the one you are looking for is not present 
     by creating an issue on our [issue tracker].

diff --git a/docs/forensics-anthro-guide/methods.md b/docs/forensics-anthro-guide/methods.md
@@ -2,7 +2,7 @@
 
 In this section we present an annotated bibliography of analytical methods available in CoRA. This list will be updated as new methods are developed, published and added to the CoRA environment.
 
-!!! question "How can I add a new methods to CoRA?"
+!!! question "How can I add new methods to CoRA?"
 
     You can request new methods to be added to CoRA if the one you are looking for is not present 
     by creating an issue on our [issue tracker].

diff --git a/docs/forensics-anthro-guide/pathologies.md b/docs/forensics-anthro-guide/pathologies.md
@@ -3,7 +3,7 @@
 In this section we present the pathologies available within CoRA for assignment to individual specimens. 
 Pathologies are organized by abnormality category
 
-!!! question "How can I add a new pathologies to CoRA?"
+!!! question "How can I add new pathologies to CoRA?"
 
     You can request new pathologies to be added to CoRA if the one you are looking for is not present 
     by creating an issue on our [issue tracker].

diff --git a/docs/forensics-anthro-guide/taphonomy.md b/docs/forensics-anthro-guide/taphonomy.md
@@ -3,7 +3,7 @@
 In this section we present the taphonomies available within CoRA for assignment to individual specimens. 
 We currently only have Bio Taphonomy within CoRA as it is most relevant to forensic anthropologists.
 
-!!! question "How can I add a new taphonomies to CoRA?"
+!!! question "How can I add new taphonomies to CoRA?"
 
     You can request new taphonomies to be added to CoRA if the one you are looking for is not present 
     by creating an issue on our [issue tracker].

diff --git a/docs/forensics-anthro-guide/traumas.md b/docs/forensics-anthro-guide/traumas.md
@@ -3,7 +3,7 @@
 In this section we present the traumas available within CoRA for assignment to individual specimens. 
 Traumas are organized by timing
 
-!!! question "How can I add a new traumas to CoRA?"
+!!! question "How can I add new traumas to CoRA?"
 
     You can request new traumas to be added to CoRA if the one you are looking for is not present 
     by creating an issue on our [issue tracker].

diff --git a/docs/user-guide/modules/index.md b/docs/user-guide/modules/index.md
@@ -2,8 +2,31 @@
 
 ## Design Methodology
 
-CoRA consists of a core body of code, which is composed of the navigational and authentication components. The rest of the site consists of individual modules, which are then tied into the existing site. 
+CoRA is built on an architectural framework consisting of various components including some core components such as the navigational and authentication components. The rest of the site is logically structured around modules, which are plugged into the framework and they interact with each other.
 
-The current modules which have been delivered are the Skeletal Elements and DNA module. 
+## Modules
+
+CoRA is structured around some core modules such as Specimens, DNA, Isotopes, Dental, Missing Persons and Individuals modules. Each of these modules 
+is described in more detail below.
 
 ![currentModules1](../../assets/screenshots/dashboard/currentModules.png)
+
+### Specimens
+
+
+### DNA
+
+
+### Isotopes
+
+
+### Dental
+
+
+### Missing Persons
+
+
+### Individual
+
+An individual is a collection of specimens that the forensic anthropologist believe should go together and belong to an unknown individual. The selection of specimens that go together is done in blind so as to not introduce any bias towards the segregation process.
+
diff --git a/docs/user-guide/modules/individuals.md b/docs/user-guide/modules/individuals.md
diff --git a/docs/user-guide/modules/individuals/individuals.md b/docs/user-guide/modules/individuals/individuals.md
@@ -0,0 +1,9 @@
+# Individuals
+
+An individual is a collection of specimens that the forensic anthropologist believe should go together and belong to an unknown individual. The selection of specimens that go together is done in blind so as to not introduce any bias towards the segregation process.
+
+!!! warning
+
+    This page is work in progress.
+
+## Create Individuals
diff --git a/docs/user-guide/modules/specimens/specimens.md b/docs/user-guide/modules/specimens/specimens.md
@@ -37,7 +37,7 @@ Provenance2      |String         |32 chars   |Can only contain letters, numbers,
 **Designator**   |Alphanumeric   |32 chars   |Can only contain letters and numbers                                          | Required
 **Bone**         |Id             |id         |valid bones via dropdown                                                      | Required
 **Side**         |String         |8 chars    |valid sides via dropdown (Left, Right, Middle, Unsided)                       | Required
-**Completeness** |String         |8 chars    |valid completeness via dropdown (Complete, Incomplete)                        | Required
+**Completeness** |String         |16 chars   |valid completeness via dropdown (Complete, Incomplete)                        | Required
 
 
 Once these details are filled and the specimen is saved, a new specimen with an appropriate `id` is generated and the user is navigated to the below screen. The screen is in View state and the user can edit it by clicking on the edit icon.
@@ -57,7 +57,7 @@ Provenance2         |String         |32 chars   |Can only contain letters, numbe
 **Designator**      |Alphanumeric   |32 chars   |Can only contain letters and numbers                                          | Required
 **Bone**            |Id             |id         |valid bones via dropdown                                                      | Required
 **Side**            |String         |8 chars    |valid sides via dropdown (Left, Right, Middle, Unsided)                       | Required
-**Completeness**    |String         |8 chars    |valid completeness via dropdown (Complete, Incomplete)                        | Required
+**Completeness**    |String         |16 chars   |valid completeness via dropdown (Complete, Incomplete)                        | Required
 Measured            |Boolean        |           |true/false toggle                                                             | Optional
 DNA Sampled         |Boolean        |           |true/false toggle                                                             | Optional
 Isotope Sampled     |Boolean        |           |true/false toggle                                                             | Optional
@@ -111,7 +111,7 @@ Attributes              |Data Type      |Size           |Validation Rule
 Bone Group              |String         |64 chars       |can only contain letters                                                      | Required
 Bone Group Id           |String         |64 chars       |valid UUID, auto generated                                                    | Required
 **Side**                |String         |8 chars        |valid sides via dropdown (Left, Right, Middle, Unsided)                       | Required
-**Completeness**        |String         |8 chars        |valid completeness via dropdown (Complete, Incomplete)                        | Required
+**Completeness**        |String         |16 chars       |valid completeness via dropdown (Complete, Incomplete)                        | Required
 **Accession**           |String         |32 chars       |can only contain letters, numbers, dash and space and should have min 3 chars | Required
 Provenance1             |String         |32 chars       |can only contain letters, numbers, dash and space                             | Optional
 Provenance2             |String         |32 chars       |can only contain letters, numbers, dash and space                             | Optional

diff --git a/mkdocs.yml b/mkdocs.yml
@@ -251,12 +251,10 @@ nav:
     - Modules:
       - user-guide/modules/index.md
       - Specimens: user-guide/modules/specimens/specimens.md
-      # - Old Specimens: user-guide/specimens.md
       - DNA: user-guide/modules/dnas/dnas.md
-      # - Old DNA: user-guide/dnas.md
       - Dental: user-guide/modules/dental/dental.md
       - Isotopes: user-guide/modules/isotopes/isotopes.md
-      - Individuals: user-guide/modules/individuals.md
+      - Individuals: user-guide/modules/individuals/individuals.md
       - Missing Persons: user-guide/modules/missing-persons/missing-persons.md
     - Search: 
       - user-guide/search/index.md