readme, softwarechecklist, version: 1.0.0-beta

Author: B0SKAMP

README.md

@@ -8,24 +8,29 @@
 ## Java implementation of the FAIR Data Pipeline API
 
 
-Documentation can be found on https://fairdatapipeline.github.io/
+Documentation can be found on https://fairdatapipeline.org/docs/API/Java/
 
+JavaDocs are automatically published on https://fairdatapipeline.org/javaDataPipeline/
 
-The main class for the FAIR Data Pipeline JAVA API is `Coderun`
+To use a release version (latest: 1.0.0-beta) include the following dependency (available from mavenCentral):
 
-Users should initialise this library using a try-with-resources block or ensure that .close() is explicitly closed when the required file handles have been accessed.
+```gradle
+group: 'org.fairdatapipeline',
+name: 'api',
+version: '1.0.0-beta'
+```
 
-## Usage example
+## javaSimpleModel
 
-```
-try (var coderun = new Coderun(configPath, scriptPath)) {
-       ImmutableSamples samples = ImmutableSamples.builder().addSamples(1, 2, 3).rng(rng).build();
-       String dataProduct = "animal/dodo";
-       String component1 = "example-samples-dodo1";
-       Data_product_write dp = coderun.get_dp_for_write(dataProduct, "toml");
-       Object_component_write oc1 = dp.getComponent(component1);
-       oc1.raise_issue("something is terribly wrong with this component", 10);
-       oc1.writeSamples(samples);
-     }
-```
+Please have a look at https://github.com/FAIRDataPipeline/javaSimpleModel
+for a simple example on how to use the javaDataPipeline, including an example of the <a href="https://www.fairdatapipeline.org/docs/interface/config/">user written config.yaml</a>, 
+and how to integrate it with the <a href="https://www.fairdatapipeline.org/docs/interface/fdp/">FAIR CLI</a> command line interface.
+
+## What does it implement?
 
+* It reads the *config.yaml* that is re-written by <a href="https://www.fairdatapipeline.org/docs/interface/fdp/">FAIR CLI</a> (not to be confused with the <a href="https://www.fairdatapipeline.org/docs/interface/config/">user written config.yaml</a>)
+* It registers a model Coderun session in the <a href="https://www.fairdatapipeline.org/docs/data_registry/">FAIR Data Registry</a>, including all the data inputs and/or outputs, from the model, and its code repository, its config.yaml, and its submission (startup) script.
+* It allows the Coderun session to raise Issues with Object_components, codeRepo, config file, and submission script, and these Issues are registered in the Data Registry.
+* It allows reading and writing of Data_products whose Object contains either 1 whole_object unnamed Object_component (for reading and writing 'external' whole-file file formats). 
+* It allows reading and writing of Data_products containing a FAIR Data Pipeline (TOML) Parameter File. 
+* It does not yet support HDF5 files.

api/build.gradle

@@ -7,7 +7,7 @@ plugins {
 }
 
 group 'org.fairdatapipeline'
-version '1.0.0-alpha'
+version '1.0.0-beta'
 
 repositories {
     mavenCentral()

dataregistry/build.gradle

@@ -7,7 +7,7 @@ plugins {
 }
 
 group 'org.fairdatapipeline'
-version '1.0.0-alpha'
+version '1.0.0-beta'
 
 java {
     sourceCompatibility = JavaVersion.VERSION_11
@@ -26,8 +26,9 @@ repositories {
 
 dependencies {
     testImplementation(platform('org.junit:junit-bom:5.8.1'))
-    testImplementation('org.junit.jupiter:junit-jupiter:5.8.1')
+    testImplementation 'org.junit.jupiter:junit-jupiter:5.8.1'
     testImplementation 'org.hamcrest:hamcrest:2.2'
+    testImplementation 'org.mockito:mockito-core:3.12.4'
     implementation 'org.glassfish.jersey.core:jersey-client:3.0.3'
     implementation 'org.glassfish.jersey.inject:jersey-hk2:3.0.3'
     implementation 'org.glassfish.jersey:jersey-bom:3.0.3'
@@ -40,8 +41,7 @@ dependencies {
     implementation 'org.apache.commons:commons-lang3:3.12.0'
     implementation 'jakarta.activation:jakarta.activation-api:2.0.1'
     implementation 'org.slf4j:slf4j-api:1.7.32'
-    implementation('org.slf4j:slf4j-simple:1.7.32')
-    testImplementation 'org.mockito:mockito-core:3.12.4'
+    implementation 'org.slf4j:slf4j-simple:1.7.32'
 }
 
 spotless {

dataregistry/src/main/java/org/fairdatapipeline/dataregistry/oauth2token/OAuth2ClientTokenFilter.java

@@ -6,7 +6,7 @@
 import jakarta.ws.rs.client.ClientRequestFilter;
 import jakarta.ws.rs.core.HttpHeaders;
 
-/** */
+/** OAuth2 filter using 'Token' instead of 'Bearer' in the auth header. */
 @Priority(Priorities.AUTHENTICATION)
 class OAuth2ClientTokenFilter implements ClientRequestFilter {
 

softwarechecklist.md

@@ -15,11 +15,11 @@ In order to use this checklist for the SCRC FAIR data pipeline components, three
 
 ### Date
 
-> 04/10/2021
+> 10/10/2021
 
 ### Version identifier
 
-> 0.0.3
+> 1.0.0-beta
 
 ## This assessment
 
@@ -108,7 +108,7 @@ Additionally, for each question please explain the situation and include any rel
 > - [ ] Some work remaining or caveats
 > - [ ] Needs to be addressed
 > 
-> JAVA compiler warnings have been addressed.
+> JAVA compiler warnings have been addressed. Spotless has been used to keep the code in tidy google java format.
 
 ### Is the code clean, generally understandable and readable and written according to good software engineering principles?
 
@@ -117,10 +117,10 @@ Additionally, for each question please explain the situation and include any rel
 - Avoiding red flags such as very long functions, global variables, copy and pasted code, etc.?
 
 > - [ ] Sufficiently addressed
-> - [ ] Some work remaining or caveats
+> - [x] Some work remaining or caveats
 > - [ ] Needs to be addressed
 > 
-> This should be judged by someone else.
+> There are things that can be improved to make the code more easy to understand for developers or for users. 
 
 ### Is there sufficient documentation?
 
@@ -134,7 +134,8 @@ Additionally, for each question please explain the situation and include any rel
 > - [x] Some work remaining or caveats
 > - [ ] Needs to be addressed
 > 
-> I'm still working on the documentation. There is a readme which I will improve.
+> There is a readme, there are javaDocs, there is user documentation, there is an example 'javaSimpleModel' to show how to use the
+> library. All of this can still be improved, as can the developer documentation.
 
 ### Is there suitable collaboration infrastructure?
 
@@ -165,14 +166,14 @@ Additionally, for each question please explain the situation and include any rel
 > - [ ] Sufficiently addressed
 > - [ ] Some work remaining or caveats
 > - [ ] Needs to be addressed
-> - [ ] N/A
+> - [x] N/A
 > 
 > Response here
 
 
 ## Contributors and licence
 
-Contributors:
+Contributors: [to the software checklist template]
 * Alys Brett
 * James Cook
 * Peter Fox