dhti-cli 0.1.0

package/LICENSE

@@ -0,0 +1,409 @@
+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at https://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.
+
+---------------------
+
+Healthcare Disclaimer
+
+In the United States, or any other jurisdictions where they may apply, the
+following additional disclaimer of warranty and limitation of liability are
+hereby incorporated into the terms and conditions of MPL 2.0:
+
+1.    No warranties of any kind whatsoever are made as to the results that
+      You will obtain from relying upon the covered code (or any information
+      or content obtained by way of the covered code), including but not
+      limited to compliance with privacy laws or regulations or clinical
+      care industry standards and protocols. Use of the covered code is not
+      a substitute for a health care provider’s standard practice or
+      professional judgment. Any decision with regard to the appropriateness
+      of treatment, or the validity or reliability of information or content
+      made available by the covered code, is the sole responsibility of the
+      health care provider. Consequently, it is incumbent upon each health
+      care provider to verify all medical history and treatment plans with
+      each patient.
+
+2.    Under no circumstances and under no legal theory, whether tort
+      (including negligence), contract, or otherwise, shall any Contributor,
+      or anyone who distributes Covered Software as permitted by the
+      license, be liable to You for any indirect, special, incidental,
+      consequential damages of any character including, without limitation,
+      damages for loss of goodwill, work stoppage, computer failure or
+      malfunction, or any and all other damages or losses, of any nature
+      whatsoever (direct or otherwise) on account of or associated with the
+      use or inability to use the covered content (including, without
+      limitation, the use of information or content made available by the
+      covered code, all documentation associated therewith, and the failure
+      of the covered code to comply with privacy laws and regulations or
+      clinical care industry standards and protocols), even if such party
+      shall have been informed of the possibility of such damages.

package/README.md

@@ -0,0 +1,239 @@
+
+<p align="center">
+  <img src="https://github.com/dermatologist/dhti/blob/develop/notes/dhti-logo.jpg" />
+</p>
+
+[![npm version](https://badge.fury.io/js/dhti.svg)](https://www.npmjs.com/package/dhti)
+[![npm](https://img.shields.io/npm/dt/dhti)](https://www.npmjs.com/package/dhti)
+[![Build](https://github.com/dermatologist/dhti/workflows/CI/badge.svg)](https://nuchange.ca)
+[![Known Vulnerabilities](https://snyk.io/test/github/dermatologist/dhti/badge.svg)](https://www.npmjs.com/package/dhti)
+[![Documentation](https://badgen.net/badge/icon/documentation?icon=libraries&label)](https://dermatologist.github.io/dhti/)
+
+## About
+- 🚀 *Dhanvantari rose out of the water with his four hands, holding a pot full of elixirs!*
+
+TL; DR: **dhti-cli is for quick prototyping, developing, sharing and testing of Gen AI applications, models, and UI elements within the context of an electronic health record.**
+[Paper coming soon!](https://nuchange.ca)
+
+Gen AI can transform medicine. But it needs a framework for collaborative research and practice. DHTI is a reference architecture and an implementation for such a framework that integrates an EMR ([OpenMRS](https://openmrs.org/)), :link: Gen AI application server ([LangServe](https://python.langchain.com/v0.2/docs/langserve/)), self-hosted LLMs for privacy ([Ollama](https://ollama.com/)), tools on [MCP server](https://github.com/dermatologist/fhir-mcp-server),  vector store for RAG ([redis](https://redis.io/)), monitoring ([LangFuse](https://langfuse.com/)), 🔥 FHIR repository with [CQL](https://nuchange.ca/2025/06/v-llm-in-the-loop-cql-execution-with-unstructured-data-and-fhir-terminology-support.html) support ([HAPI](https://cloud.alphora.com/sandbox/r4/cqm/)) and graph utilities ([Neo4j](https://neo4j.com/)) in one docker-compose! DHTI is inspired by [Bahmni](https://www.bahmni.org/) and **aims to facilitate GenAI adoption and research in areas with low resources.** The MCP server hosts pluggable, agent-invokable tools (FHIR query, summarization, terminology lookup, custom analytics, etc.) that you can extend without modifying core services.
+
+The essence of DHTI is *modularity* with an emphasis on *configuration!* It is non-opinionated on LLMs, hyperparameters and pretty much everything. DHTI supports installable Gen AI routines through [LangChain templates](https://templates.langchain.com/) (which we call :curry: **elixir**) and installable UI elements through [OpenMRS O3](https://o3-docs.openmrs.org/) React container (which we call :shell: **conch**). 🔥 FHIR is used for backend and [CDS-Hooks](https://cds-hooks.org/) for frontend communication, decoupling conches from OpenMRS, making them potentially usable with any health information system. We have a [fork of the cds-hook sandbox](https://github.com/dermatologist/cds-hooks-sandbox/tree/dhti-1) for testing that uses the [order-select](https://cds-hooks.org/hooks/order-select/) hook, utilizing the contentString from the [FHIR CommunicationRequest](https://build.fhir.org/communicationrequest.html) within the [cds-hook context](https://cds-hooks.org/examples/) for user inputs (recommended).
+
+<p align="center">
+  <img src="https://github.com/dermatologist/dhti/blob/develop/notes/cds-hook-sandbox.jpg" />
+</p>
+
+🚀 dhti-cli is a CLI tool for quick prototyping and testing of elixirs and conches. You can create a new docker-compose with required modules, start/stop services, install Elixirs and conch, create Docker images for them, and more. 🚀 This helps to test new ideas and share them with others quickly. 🚀 Once tested, you can transition them to the production team for deployment. Adoption of standards makes this transition easier!
+
+⭐️ **Pitched at [Falling Walls Lab Illinois](https://falling-walls.com/falling-walls-lab-illinois) and released on 09/12/2025.**
+
+## What problems do DHTI solve?
+
+| Why | How |
+| --- | --- |
+| I know LangChain, but I don’t know how to build a chain/agent based on data in our EHR. | [This template](https://github.com/dermatologist/dhti-elixir-template) adopts FHIR and cds-hooks as standards for data retrieval and display. The [base class](https://github.com/dermatologist/dhti-elixir-base) provides reusable artifacts |
+| I need a simple platform for experimenting. | This repository provides  everything to start experimenting fast. The command-line tools help to virtualize and orchestrate your experiments using [Docker](https://www.docker.com/)|
+| I am a UI designer. I want to design helpful UI for real users. | See [this template](https://github.com/dermatologist/openmrs-esm-dhti-template). It shows how to build interface components (conches) for [OpenMRS](https://openmrs.org/) an open-source EMR used by many. Read more about [OpenMRS UI](https://o3-docs.openmrs.org/) |
+| We use another EMR  |  Your EMR may support CDS-Hook for displaying components. In that case, you can use [cds-hooks-sandbox for testing](https://github.com/dermatologist/cds-hooks-sandbox/tree/dhti-1) |
+| Our IT team is often unable to take my experiments to production. | Use DHTI, follow the recommended patterns, and you will make their lives easier.|
+
+
+## Architecture
+<p align="center">
+  <img src="https://github.com/dermatologist/dhti/blob/develop/notes/arch-1.drawio.svg" />
+</p>
+
+## ✨ Features
+* **Modular**: Supports installable Gen AI routines and UI elements.
+* **Quick prototyping**: CLI helps in quick prototyping and testing of Gen AI routines and UI elements.
+* **Easy to use**: Can be installed in a few minutes.
+* **Developer friendly**: Copy working files to running containers for testing.
+* **Dependency Injection**: Dependency injection for models and hyperparameters for configuring elixirs.
+* **Generate synthetic data**: DHTI supports generating synthetic data for testing.
+* **CQL support**: [CQL for clinical decision support](https://nuchange.ca/2025/06/v-llm-in-the-loop-cql-execution-with-unstructured-data-and-fhir-terminology-support.html).
+* **FHIR**: Data exchange with FHIR schema.
+* **MCP**: Built in MCP server for pluggable tools.
+* **EMR**: Built in EMR, OpenMRS, for patient records.
+* **Vector store**: Redis for vector store.
+* **Monitoring**: LangFuse for monitoring.
+* **Graph utilities**: Neo4j for graph utilities.
+* **LLM**: Ollama for self-hosting LLM models.
+
+## 🔧 For Gen AI Developers
+
+*Developers can build elixirs and conchs for DHTI.*
+
+:curry: Elixirs are [LangChain templates]((https://templates.langchain.com/)) for backend GenAI functionality. By convention, Elixirs are prefixed with *dhti-elixir-* and all elixirs depend on [dhti-elixir-base](https://github.com/dermatologist/dhti-elixir-base) which provides some base classes and defines dependencies. You can use [this template](https://github.com/dermatologist/dhti-elixir-template) to build new elixirs, and license it the way you want (We :heart: open-source!).
+
+:shell: Conches are [OpenMRS O3s](https://o3-docs.openmrs.org/) and follow the standard naming convention *openmrs-esm-*. A separate OpenMRS independant container for conchs is on our roadmap for use outside OpenMRS. You can use [this template](https://github.com/dermatologist/openmrs-esm-dhti-template) to build new conches.
+
+:white_check_mark:
+* **Developer friendly**: Copy working files to running containers for testing.
+* **Dependency Injection**: Dependency injection for models and hyperparameters for configuring elixirs.
+
+## 🧠 For Gen AI Researchers
+
+*DHTI provides a platform to deploy language models and Gen AI applications in the context of an electronic health record.*
+
+DHTI serves as a platform for testing prompts, chains and agents in healthcare applications.  Since the stack uses the :fire: FHIR data model, it is easy to load synthetic data.
+
+Tools to fine-tune language models for the stack are on our roadmap. We encourage all language models built for this platform to be open sourced on [HuggingFace](https://huggingface.co/) with the names starting with *dhti-*.
+
+:white_check_mark:
+* **Generate synthetic data**: DHTI supports generating synthetic data for testing.
+* **CQL support**: [CQL for clinical decision support](https://nuchange.ca/2025/06/v-llm-in-the-loop-cql-execution-with-unstructured-data-and-fhir-terminology-support.html).
+* **FHIR**: Data exchange with FHIR schema.
+* **EMR**: Built in EMR, OpenMRS, for patient records.
+
+ 🌈 *Join us to make the Gen AI equitable and help doctors save lives!*
+
+## :sparkles: Resources
+* [fhiry](https://github.com/dermatologist/fhiry): FHIR to pandas dataframe for data analytics, AI and ML!
+* [pyOMOP](https://github.com/dermatologist/pyomop): For OMOP CDM support
+
+## :sparkles: Resources (in Beta)
+* [dhti-elixir-base](https://github.com/dermatologist/dhti-elixir-base): Base classes for dhti-elixir
+* [dhti-elixir-template](https://github.com/dermatologist/dhti-elixir-template): A template for creating new dhti-elixirs.
+* [fhir-mcp-server](https://github.com/dermatologist/fhir-mcp-server): A MCP server for hosting FHIR-compliant tools.
+
+## :sparkles: Resources (in Alpha)
+* [cookiecutter for scaffolding elixirs](https://github.com/dermatologist/cookiecutter-uv)
+* [cds-hooks-sandbox for testing](https://github.com/dermatologist/cds-hooks-sandbox/tree/dhti-1)
+
+## :sunglasses: Coming soon
+
+* [dhti-elixir-fhire](https://github.com/dermatologist/dhti-elixir-fhire): An elixir for extracting embeddings from FHIR resources for Q&A on patient records.
+* [dhti-elixir-fhirs](https://github.com/dermatologist/dhti-elixir-fhirs): An elixir for text to FHIR search query conversion.
+* [dhti-elixir-upload](https://github.com/dermatologist/dhti-elixir-upload-file): Upload documents to the vector store for clinical knowledgebase and clinical trial matching.
+* [openmrs-esm-qa](https://github.com/dermatologist/openmrs-esm-genai): A sample conch for Q&A on patient records using the dhti-elixir-fhire elixir.
+
+## 🔧 Usage
+
+### List of plugins
+```
+dhti-cli help
+```
+
+### Get help for each plugin
+* As an example, get help for compose:
+
+```
+dhti-cli compose --help
+```
+
+### 🏗️ *Try it out! It takes only a few minutes to setup GenAI backed EMR in your local machine!*
+
+You only need:
+* docker
+* nodejs
+
+## :walking: Step 1
+
+* Git clone this repository: `git clone https://github.com/dermatologist/dhti.git && cd dhti`
+* Install the required packages: `npm install`
+* Build the CLI: `npm run build`
+* Install CLI locally: `npm link`
+* Test the CLI: `dhti-cli help`  *This will show the available commands.*
+* The working directory is `~/dhti` (Customizable)
+
+### 🔧 Create a new docker-compose
+* Create a new docker-compose file: `dhti-cli compose add -m openmrs -m langserve`
+
+* The docker-compose.yml is created with the following modules:
+    - OpenMRS (EMR)
+    - LangServe (API for LLM models)
+
+Other available modules: `ollama, langfuse, cqlFhir, redis, neo4j and mcpFhir` (Documentation in progress)
+
+You can read the newly created docker-compose by: `dhti-cli compose read`
+
+
+### 🚀 Start the services for initial setup
+* Start the services: `dhti-cli docker -u`
+
+It may take a while to download the images and start the services. ([OpenMRS](https://openmrs.org/) may take upto 45 mins the first time to setup the database)
+
+
+### 🚀 Access OpenMRS and login:
+* Go to `http://localhost/openmrs/spa/home`
+* Login with the following credentials:
+    - Username: admin
+    - Password: Admin123
+    - Choose any location and click on 'confirm'.
+
+### 🚀 Access the LangServe API
+* Go to `localhost:8001/docs` (Empty Swagger UI)
+
+## Congratulations! You have successfully setup DHTI! :tada:
+* Shut down the services: `dhti-cli docker -d`
+
+## :running: STEP 2: 🛠️ *Now let us Install an Elixir (Gen AI functionalities are packaged as elixirs)*
+
+* Let's install the elixir here: https://github.com/dermatologist/dhti-elixir-template. This is just a template that uses a Mock LLM to output random text. You can use this template to build your own elixirs! (Cookiecutter to be released soon!) Later you will see how to add real LLM support.
+
+:running:
+
+`dhti-cli elixir install -g https://github.com/dermatologist/dhti-elixir-template.git -n dhti-elixir-template`.
+
+You may also install from PyPi or a wheel file!
+
+### 🔍 Examine bootstrap.py (Optional)
+`cat ~/dhti/elixir/app/bootstrap.py`
+
+This is where you can override defaults in the elixir for *LLM, embedding model, hyperparameters etc that are injected at runtime.* Refer to each elixir for the available options. [You may check out how to inject a real LLM using Google Gemini!](/notes/add-llm.md)
+
+### 🔧 Create docker container
+`dhti-cli docker -n beapen/genai-test:1.0 -t elixir`
+
+(You may replace `beapen/genai-test:1.0` with your own image name)
+
+### 🚀 Congratulations! You installed your first elixir. We will see it in action later!
+
+While developing you can copy the app folder to a running container for testing (provided there are no changes in dependencies). Read more [here](/notes/dev-copy.md).
+
+## STEP 3: :shell: *Now let us Install a Conch (The UI component)*
+
+* Let's install the conch here:https://github.com/dermatologist/openmrs-esm-dhti-template. This uses the elixir template that we installed in STEP 2 as the backend. You can use the template to build your own conchs.
+
+:shell: `dhti-cli conch install -g https://github.com/dermatologist/openmrs-esm-dhti-template.git -n openmrs-esm-dhti-template`
+
+We can also install from a dev folder after cloning the repository. While developing you can copy the dist folder to a running container for testing. Read more [here](/notes/dev-copy.md).
+
+### 🔧 Create new docker container
+`dhti-cli docker -n beapen/conch-test:1.0 -t conch`
+
+## 🚀 It is now time to start DHTI!
+
+`dhti-cli docker -u`
+
+### :clap: Access the Conch in OpenMRS and test the integration
+
+* Go to `http://localhost/openmrs/spa/home`
+* Login with the following credentials:
+    - Username: admin
+    - Password: Admin123
+
+You will see the new conch in the left margin. Click on **Dhti app** to see the UI.
+This is just a template, though. You can build your own conchs!
+
+Add some text to the text area and click on **Submit**.
+You will see the text above the textbox.
+
+### Stop the services
+You can remove the services by: `dhti-cli docker -d`
+
+### The demo uses a template with mock LLM. [Check out how to add real LLM support using Google Gemini.](/notes/add-llm.md)
+
+:hugs: **Thank you for trying out DHTI!**
+
+## 🚀 Advanced
+
+* [Setting up Ollama](/notes/setup-ollama.md)
+* [CLI Options](/notes/cli-options.md)
+
+## Give us a star ⭐️
+If you find this project useful, give us a star. It helps others discover the project.
+
+## Contributors
+
+* [Bell Eapen](https://nuchange.ca) | [![Twitter Follow](https://img.shields.io/twitter/follow/beapen?style=social)](https://twitter.com/beapen)

package/bin/dev.cmd

@@ -0,0 +1,3 @@
+@echo off
+
+node --loader ts-node/esm --no-warnings=ExperimentalWarning "%~dp0\dev" %*

package/bin/dev.js

@@ -0,0 +1,6 @@
+#!/usr/bin/env -S node --loader ts-node/esm --no-warnings=ExperimentalWarning
+
+// eslint-disable-next-line n/shebang
+import {execute} from '@oclif/core'
+
+await execute({development: true, dir: import.meta.url})

package/bin/run.cmd

@@ -0,0 +1,3 @@
+@echo off
+
+node "%~dp0\run" %*

package/bin/run.js

@@ -0,0 +1,5 @@
+#!/usr/bin/env node
+
+import {execute} from '@oclif/core'
+
+await execute({dir: import.meta.url})

package/oclif.manifest.json

@@ -0,0 +1,4 @@
+{
+  "commands": {},
+  "version": "0.1.0"
+}

package/package.json

@@ -0,0 +1,88 @@
+{
+  "name": "dhti-cli",
+  "description": "DHTI CLI",
+  "version": "0.1.0",
+  "author": "Bell Eapen",
+  "bin": {
+    "dhti-cli": "bin/run.js"
+  },
+  "bugs": "https://github.com/dermatologist/dhti/issues",
+  "dependencies": {
+    "@langchain/community": "^0.3.53",
+    "@langchain/ollama": "^0.2.3",
+    "@oclif/core": "^4",
+    "@oclif/plugin-help": "^6",
+    "@oclif/plugin-plugins": "^5",
+    "child_process": "^1.0.2",
+    "js-yaml": "^4.1.0",
+    "medpromptjs": ">=0.4.3",
+    "ora": "^8.0.1",
+    "request": "^2.88.2"
+  },
+  "devDependencies": {
+    "@oclif/prettier-config": "^0.2.1",
+    "@oclif/test": "^4",
+    "@types/chai": "^4",
+    "@types/js-yaml": "^4.0.9",
+    "@types/mocha": "^10",
+    "@types/node": "^18",
+    "@types/request": "^2.48.12",
+    "@types/sinon": "^17.0.4",
+    "chai": "^4",
+    "eslint": "^8",
+    "eslint-config-oclif": "^5",
+    "eslint-config-oclif-typescript": "^3",
+    "eslint-config-prettier": "^9",
+    "mocha": "^10",
+    "oclif": "^4",
+    "shx": "^0.3.3",
+    "sinon": "^21.0.0",
+    "ts-node": "^10",
+    "typescript": "^5"
+  },
+  "engines": {
+    "node": ">=18.0.0"
+  },
+  "files": [
+    "bin",
+    "dist",
+    "oclif.manifest.json"
+  ],
+  "homepage": "https://github.com/dermatologist/dhti",
+  "keywords": [
+    "oclif"
+  ],
+  "license": "Apache-2.0",
+  "main": "dist/index.js",
+  "type": "module",
+  "oclif": {
+    "bin": "dhti-cli",
+    "dirname": "dhti-cli",
+    "commands": "./dist/commands",
+    "plugins": [
+      "@oclif/plugin-help",
+      "@oclif/plugin-plugins"
+    ],
+    "topicSeparator": " ",
+    "topics": {
+      "hello": {
+        "description": "Say hello to the world and others"
+      }
+    }
+  },
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/dermatologist/dhti.git"
+  },
+  "scripts": {
+    "build": "shx rm -rf dist && tsc -b",
+    "lint": "eslint . --ext .ts",
+    "fix": "eslint . --ext .ts --fix",
+    "postpack": "shx rm -f oclif.manifest.json",
+    "posttest": "echo 'npm run lint'",
+    "prepack": "oclif manifest && oclif readme",
+    "test": "mocha --forbid-only \"test/**/*.test.ts\"",
+    "version": "oclif readme && git add README.md"
+  },
+  "types": "dist/index.d.ts"
+}