Add publish endpoint and webapp UI for marking models as published

docs/publications-api.md

@@ -0,0 +1,104 @@
+# Publications and Model Curation
+
+## Overview
+
+Publications in VCell link scientific papers to the computational models (BioModels and MathModels) that were used or described in those papers. The publication system also drives the **curation workflow**, which controls model visibility and permanence.
+
+## Domain Concepts
+
+### Publication
+
+A publication record represents a scientific paper and its metadata:
+
+- **title**, **authors**, **year**, **citation** - bibliographic information
+- **pubmedid**, **doi**, **url** - external identifiers and links
+- **biomodelRefs** - array of BioModel references linked to this publication
+- **mathmodelRefs** - array of MathModel references linked to this publication
+
+Publications are managed by curators (users with the `publicationEditors` special claim).
+
+### Model References (BiomodelRef / MathmodelRef)
+
+Model references are lightweight pointers to BioModels or MathModels that are associated with a publication. Each reference includes:
+
+- **key** (`bmKey` / `mmKey`) - the model's database identifier
+- **name** - model name
+- **ownerName** / **ownerKey** - the model owner
+- **versionFlag** - the model's curation status (see below)
+
+### VersionFlag (Curation Status)
+
+`VersionFlag` represents a model's position in the curation lifecycle. It is **not** access control - that is handled separately by `GroupAccess`.
+
+| State | Int Value | Description |
+|-------|-----------|-------------|
+| **Current** | 0 | Default state. Model is in active development. Can be modified or deleted. |
+| **Archived** | 1 | Model has been archived. Cannot be deleted without admin intervention. |
+| **Published** | 3 | Model has been curated and published. Cannot be deleted without admin intervention. |
+
+**Key constraint**: Archived and Published models cannot be deleted through the normal API. This ensures the permanence of curated scientific models.
+
+### GroupAccess (Access Control)
+
+`GroupAccess` controls who can view a model. It is independent of `VersionFlag`.
+
+| Type | GroupID | Description |
+|------|---------|-------------|
+| **GroupAccessAll** | 0 | Public - visible to everyone |
+| **GroupAccessNone** | 1 | Private - visible only to the owner |
+| **GroupAccessSome** | (hash) | Shared with a specific group of users |
+
+## Curation Workflow
+
+When a curator publishes models linked to a publication, two things happen atomically for each model:
+
+1. **Access is set to public**: `GroupAccess` is changed to `GroupAccessAll` (groupid = 0)
+2. **Status is set to published**: `VersionFlag` is changed to `Published` (value = 3)
+
+This is performed by `PublicationService.publishDirectly()`, which delegates to `DbDriver.publishDirectly()` to update the `vc_biomodel` and `vc_mathmodel` database tables.
+
+### Selective Publishing
+
+Curators can publish all models linked to a publication at once, or selectively choose which models to publish by providing specific model keys in the `PublishModelsRequest`.
+
+## REST API
+
+Base path: `/api/v1/publications`
+
+| Method | Path | Operation | Auth | Description |
+|--------|------|-----------|------|-------------|
+| GET | `/` | getPublications | Public | List all publications |
+| GET | `/{id}` | getPublicationById | Public | Get a single publication |
+| POST | `/` | createPublication | Curator | Create a new publication |
+| PUT | `/` | updatePublication | Curator | Update publication metadata and model links |
+| DELETE | `/{id}` | deletePublication | Curator | Delete a publication |
+| PUT | `/{id}/publish` | publishBioModels | Curator | Publish models linked to a publication |
+
+### Publish Endpoint
+
+`PUT /api/v1/publications/{id}/publish`
+
+Request body (`PublishModelsRequest`, optional):
+```json
+{
+  "biomodelKeys": [12345, 67890],
+  "mathmodelKeys": [11111]
+}
+```
+
+- If the request body is null or keys arrays are empty, **all** models linked to the publication are published.
+- If specific keys are provided, only those models are published.
+
+## Key Source Files
+
+| File | Purpose |
+|------|---------|
+| `handlers/PublicationResource.java` | REST endpoint definitions |
+| `services/PublicationService.java` | Business logic for publication CRUD and publishing |
+| `models/Publication.java` | Publication REST model |
+| `models/BiomodelRef.java` | BioModel reference REST model |
+| `models/MathmodelRef.java` | MathModel reference REST model |
+| `models/PublishModelsRequest.java` | Request body for selective publishing |
+| `vcell-core/.../VersionFlag.java` | Curation status enum |
+| `vcell-core/.../GroupAccess.java` | Access control base class |
+| `vcell-server/.../DbDriver.java` | Database-level publish logic |

docs/publications.md

@@ -0,0 +1,124 @@
+# VCell Publications and Model Curation
+
+## What is a Publication in VCell?
+
+A VCell publication links a scientific paper to the computational models (BioModels and MathModels) that support it. Publications serve two purposes:
+
+1. **Discovery** - Users can browse publications to find curated, peer-reviewed models relevant to their research.
+2. **Curation** - Publications drive the process of reviewing, approving, and permanently preserving models in the VCell database.
+
+## How Users Find Published Models
+
+In the VCell desktop client, the **Database** panel (lower left of any document window) organizes public models into three folders:
+
+- **Published** - Models created by users and linked to a scientific publication. Grouped by publication citation.
+- **Curated** - Models created by the VCell team or collaborators to reproduce results described in a publication.
+- **Uncurated** - Public models that have not been peer-reviewed or linked to a publication.
+
+Published and Curated models represent the highest quality tier - they have been reviewed, are permanently preserved, and are linked to their corresponding papers.
+
+## How to Publish a VCell Model (Author Instructions)
+
+When your paper is accepted and you want to associate your VCell model with the publication, follow these steps:
+
+### 1. Make Your Model Public
+
+Change your model's permissions in the VCell Database:
+- Navigate to **File > Permissions...**
+- Select **Public**
+- Click **OK**
+
+The model will initially appear in the **Uncurated** public models folder. You can also share with specific users by selecting **Grant Access to Specific Users** and adding their VCell usernames.
+
+### 2. Reference VCell in Your Publication
+
+Include your username and model name so readers can find your model:
+
+> "The Virtual Cell Model, *[modelname]* by user *[username]*, can be accessed within the VCell software (available at https://vcell.org)."
+
+### 3. Acknowledge the Funding Source
+
+Include this acknowledgment in your manuscript:
+
+> "The Virtual Cell is supported by NIH Grant R24 GM137787 from the National Institute for General Medical Sciences."
+
+### 4. Cite the Required VCell Papers
+
+All publications using VCell must cite:
+- Schaff, J., C. C. Fink, B. Slepchenko, J. H. Carson, and L. M. Loew. 1997. A general computational framework for modeling cellular structure and function. Biophysical journal 73:1135-1146. PMC1181013 PMID: 9284281 DOI: 10.1016/S0006-3495(97)78146-3
+- Cowan, A. E., Moraru, II, J. C. Schaff, B. M. Slepchenko, and L. M. Loew. 2012. Spatial modeling of cell signaling networks. Methods Cell Biol 110:195-221. PMC3519356 PMID: 22482950 DOI: 10.1016/B978-0-12-388403-9.00008-4
+
+Additional citations for specialized model types:
+- **Rule-Based models**: 
+  - Blinov, M. L., J. C. Schaff, D. Vasilescu, Moraru, II, J. E. Bloom, and L. M. Loew. 2017. Compartmental and Spatial Rule-Based Modeling with Virtual Cell. Biophysical journal 113:1365-1372. PMC5627391 PMID: 28978431 DOI: 10.1016/j.bpj.2017.08.022 
+- **Spatial Hybrid Deterministic-Stochastic models**: 
+  - Schaff, J. C., F. Gao, Y. Li, I. L. Novak, and B. M. Slepchenko. 2016. Numerical Approach to Spatial Deterministic-Stochastic Models Arising in Cell Biology. PLoS Comput Biol 12:e1005236. PMC5154471 PMID: 27959915 DOI: 10.1371/journal.pcbi.1005236
+
+### 5. Submit Your Publication Information
+
+Complete the [VCell Publication Submission Form](https://vcell.org/publish-a-vcell-model) with:
+- Your name, email, and VCell username
+- Article title, authors, and journal citation
+- Publication date
+- Model type (BioModel or MathModel) and model name
+
+Upon approval by the VCell team, your model will be archived, listed on the VCell website, and protected from modification or deletion.
+
+### Archiving Without Publishing (Deprecated)
+
+Previously, authors could archive models independently through the VCell desktop client by right-clicking a model in the Database panel and selecting **Archive**. Archiving protected a model from deletion or alteration but did not link it to a publication. This option was removed because it caused confusion among users about the distinction between archiving and publishing.
+
+## Model Lifecycle
+
+Every model in VCell has a **curation status** (`VersionFlag`) that tracks where it is in the curation lifecycle:
+
+```
+  Current (0)  -->  Archived (1)  -->  Published (3)
+   (default)       (protected)        (protected + public)
+```
+
+| Status | Who can see it | Can it be deleted? | Typical meaning |
+|--------|---------------|-------------------|-----------------|
+| **Current** | Depends on access settings | Yes | Work in progress or uncurated model |
+| **Archived** | Depends on access settings | No (admin only) | Preserved for reference, may or may not be linked to a publication |
+| **Published** | Everyone (public) | No (admin only) | Curated, peer-reviewed, linked to a publication |
+
+Curation status is independent from access control. A model can be publicly visible but still in "Current" status (not yet curated), or it could be archived but only visible to certain users.
+
+## Access Control (GroupAccess)
+
+Access control determines who can view a model. It is a separate concept from curation status.
+
+| Level | Description |
+|-------|-------------|
+| **Private** | Only the model owner can see it (default) |
+| **Shared** | The owner and specific named users can see it |
+| **Public** | Everyone can see it |
+
+When a model is published through the curation workflow, its access is automatically set to Public. However, a model author can independently make their model public at any time without it being "published" in the curation sense.
+
+## Curator Workflow
+
+Curators are VCell team members with the `publicationEditors` role. Curation is performed through the Angular webapp at [vcell.cam.uchc.edu](https://vcell.cam.uchc.edu). Curators are responsible for:
+
+- Creating and editing publication records (title, authors, DOI, PubMed ID, etc.)
+- Linking the correct model versions to each publication
+- Reviewing models for correctness and completeness
+- **Publishing** models - the act that makes them permanently public and protected from deletion
+
+### What Happens When a Curator Publishes Models
+
+When a curator clicks "Publish Selected Models" in the webapp (or calls the publish API), two things happen atomically for each selected model:
+
+1. **Access becomes public** - The model's access control is set to `GroupAccessAll`, making it visible to all VCell users.
+2. **Status becomes Published** - The model's `VersionFlag` is set to `Published`, protecting it from deletion.
+
+This is an intentionally irreversible operation through normal means. Published models are part of the scientific record and should not be casually removed.
+
+### Selective Publishing
+
+Curators can choose to publish all models linked to a publication at once, or selectively publish individual models. This is useful when a publication links to multiple models but only some are ready for curation.
+
+## For Developers
+
+See [publications-api.md](publications-api.md) for the REST API reference, data models, and source file locations.

lib/maven-repo/com/sun/media/jai-codec/1.1.3/jai-codec-1.1.3.jar.md5

@@ -0,0 +1 @@
+1b0f328c9eda0992167ce503b0a5afcc

lib/maven-repo/com/sun/media/jai-codec/1.1.3/jai-codec-1.1.3.jar.sha1

@@ -0,0 +1 @@
+34a67ba62097778e4695c951156bf189c2c8e016

lib/maven-repo/com/sun/media/jai-codec/1.1.3/jai-codec-1.1.3.pom

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd" xmlns="http://maven.apache.org/POM/4.0.0"
+    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
+  <modelVersion>4.0.0</modelVersion>
+  <groupId>com.sun.media</groupId>
+  <artifactId>jai-codec</artifactId>
+  <version>1.1.3</version>
+</project>

lib/maven-repo/com/sun/media/jai-codec/1.1.3/jai-codec-1.1.3.pom.md5

@@ -0,0 +1 @@
+0b104bf9f7e078b213bfb969621875fc

lib/maven-repo/com/sun/media/jai-codec/1.1.3/jai-codec-1.1.3.pom.sha1

@@ -0,0 +1 @@
+ba3dbcbaed61466418f7a3b65d956c63249fc1d7

lib/maven-repo/edu/ucar/netcdf/4.3.22/netcdf-4.3.22.jar.md5

@@ -0,0 +1 @@
+0b57289af4bd2627b6d8c923ba29c114

lib/maven-repo/edu/ucar/netcdf/4.3.22/netcdf-4.3.22.jar.sha1

@@ -0,0 +1 @@
+a9b0be3ddf020c3aebf6498fcfc3ef007805cec0