diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md deleted file mode 100644 index 1af794e..0000000 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ /dev/null @@ -1,30 +0,0 @@ ---- -name: Bug report -about: Create a report to help us improve -title: '' -labels: 'bug' -assignees: '' - ---- - -**Describe the bug** -A clear and concise description of what the bug is. - -**To Reproduce** -Steps to reproduce the behavior: -1. Code with explanation -2. How to run code -3. The error - -**Expected behavior** -A clear and concise description of what you expected to happen. - -**Screenshots** -If applicable, add screenshots to help explain your problem. - -**Environment (please complete the following information):** - - OS: [e.g. Linux] - - Package versions implicated in the error (torch, mdlearn versions, etc) - -**Additional context** -Add any other context about the problem here. diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml deleted file mode 100644 index 3ba13e0..0000000 --- a/.github/ISSUE_TEMPLATE/config.yml +++ /dev/null @@ -1 +0,0 @@ -blank_issues_enabled: false diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md deleted file mode 100644 index 36014cd..0000000 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ /dev/null @@ -1,20 +0,0 @@ ---- -name: Feature request -about: Suggest an idea for this project -title: '' -labels: 'enhancement' -assignees: '' - ---- - -**Is your feature request related to a problem? Please describe.** -A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] - -**Describe the solution you'd like** -A clear and concise description of what you want to happen. - -**Describe alternatives you've considered** -A clear and concise description of any alternative solutions or features you've considered. - -**Additional context** -Add any other context or screenshots about the feature request here. diff --git a/.github/ISSUE_TEMPLATE/other.md b/.github/ISSUE_TEMPLATE/other.md deleted file mode 100644 index 66da7ad..0000000 --- a/.github/ISSUE_TEMPLATE/other.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -name: Other issue template -about: Any issue that does not fit the other templates -title: '' -labels: '' -assignees: '' - ---- - -**Description** diff --git a/.github/ISSUE_TEMPLATE/question-issue-template.md b/.github/ISSUE_TEMPLATE/question-issue-template.md deleted file mode 100644 index a422d18..0000000 --- a/.github/ISSUE_TEMPLATE/question-issue-template.md +++ /dev/null @@ -1,10 +0,0 @@ ---- -name: Question issue template -about: Ask a question about how to use mdlearn -title: '' -labels: question -assignees: '' - ---- - -**Describe the question** diff --git a/.github/workflows/pre-commit.yaml b/.github/workflows/pre-commit.yaml new file mode 100644 index 0000000..f01c862 --- /dev/null +++ b/.github/workflows/pre-commit.yaml @@ -0,0 +1,20 @@ +name: Pre-Commit Checks + +on: + push: # Run for every push + branches: ["*"] + tags: ["*"] + workflow_dispatch: # Run manually + +jobs: + pre-commit: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + name: Checkout code + - uses: actions/setup-python@v4 + name: Setup Python + with: + python-version: 3.9 + - uses: pre-commit/action@v3.0.1 + name: Run Pre-Commit Checks diff --git a/.gitignore b/.gitignore index c3d8e0a..08afec0 100644 --- a/.gitignore +++ b/.gitignore @@ -560,3 +560,5 @@ cython_debug/ # option (not recommended) you can uncomment the following to ignore the entire idea folder. #.idea/ +# MADSci runtime state (logs, ID registry) — per-machine, not shared +.madsci/ diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 8153ae3..3fe2351 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,9 +1,8 @@ repos: - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.6.0 + rev: v6.0.0 hooks: - id: check-yaml - - id: check-json - id: check-toml - id: check-ast - id: check-merge-conflict @@ -12,15 +11,19 @@ repos: - id: end-of-file-fixer - id: trailing-whitespace - repo: https://github.com/kynan/nbstripout - rev: 0.7.1 + rev: 0.8.1 hooks: - id: nbstripout - repo: https://github.com/astral-sh/ruff-pre-commit # Ruff version. - rev: v0.5.7 + rev: v0.14.5 hooks: # Run the linter. - id: ruff args: [--fix] # Run the formatter. - id: ruff-format + - repo: https://gitlab.com/bmares/check-json5 + rev: v1.0.0 + hooks: + - id: check-json5 diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md deleted file mode 100644 index 5f3f6b1..0000000 --- a/CODE_OF_CONDUCT.md +++ /dev/null @@ -1,128 +0,0 @@ -# Contributor Covenant Code of Conduct - -## Our Pledge - -We as members, contributors, and leaders pledge to make participation in our -community a harassment-free experience for everyone, regardless of age, body -size, visible or invisible disability, ethnicity, sex characteristics, gender -identity and expression, level of experience, education, socio-economic status, -nationality, personal appearance, race, religion, or sexual identity -and orientation. - -We pledge to act and interact in ways that contribute to an open, welcoming, -diverse, inclusive, and healthy community. - -## Our Standards - -Examples of behavior that contributes to a positive environment for our -community include: - -* Demonstrating empathy and kindness toward other people -* Being respectful of differing opinions, viewpoints, and experiences -* Giving and gracefully accepting constructive feedback -* Accepting responsibility and apologizing to those affected by our mistakes, - and learning from the experience -* Focusing on what is best not just for us as individuals, but for the - overall community - -Examples of unacceptable behavior include: - -* The use of sexualized language or imagery, and sexual attention or - advances of any kind -* Trolling, insulting or derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or email - address, without their explicit permission -* Other conduct which could reasonably be considered inappropriate in a - professional setting - -## Enforcement Responsibilities - -Community leaders are responsible for clarifying and enforcing our standards of -acceptable behavior and will take appropriate and fair corrective action in -response to any behavior that they deem inappropriate, threatening, offensive, -or harmful. - -Community leaders have the right and responsibility to remove, edit, or reject -comments, commits, code, wiki edits, issues, and other contributions that are -not aligned to this Code of Conduct, and will communicate reasons for moderation -decisions when appropriate. - -## Scope - -This Code of Conduct applies within all community spaces, and also applies when -an individual is officially representing the community in public spaces. -Examples of representing our community include using an official e-mail address, -posting via an official social media account, or acting as an appointed -representative at an online or offline event. - -## Enforcement - -Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported to the community leaders responsible for enforcement at -kyle.hippe@gmail.com. -All complaints will be reviewed and investigated promptly and fairly. - -All community leaders are obligated to respect the privacy and security of the -reporter of any incident. - -## Enforcement Guidelines - -Community leaders will follow these Community Impact Guidelines in determining -the consequences for any action they deem in violation of this Code of Conduct: - -### 1. Correction - -**Community Impact**: Use of inappropriate language or other behavior deemed -unprofessional or unwelcome in the community. - -**Consequence**: A private, written warning from community leaders, providing -clarity around the nature of the violation and an explanation of why the -behavior was inappropriate. A public apology may be requested. - -### 2. Warning - -**Community Impact**: A violation through a single incident or series -of actions. - -**Consequence**: A warning with consequences for continued behavior. No -interaction with the people involved, including unsolicited interaction with -those enforcing the Code of Conduct, for a specified period of time. This -includes avoiding interactions in community spaces as well as external channels -like social media. Violating these terms may lead to a temporary or -permanent ban. - -### 3. Temporary Ban - -**Community Impact**: A serious violation of community standards, including -sustained inappropriate behavior. - -**Consequence**: A temporary ban from any sort of interaction or public -communication with the community for a specified period of time. No public or -private interaction with the people involved, including unsolicited interaction -with those enforcing the Code of Conduct, is allowed during this period. -Violating these terms may lead to a permanent ban. - -### 4. Permanent Ban - -**Community Impact**: Demonstrating a pattern of violation of community -standards, including sustained inappropriate behavior, harassment of an -individual, or aggression toward or disparagement of classes of individuals. - -**Consequence**: A permanent ban from any sort of public interaction within -the community. - -## Attribution - -This Code of Conduct is adapted from the [Contributor Covenant][homepage], -version 2.0, available at -https://www.contributor-covenant.org/version/2/0/code_of_conduct.html. - -Community Impact Guidelines were inspired by [Mozilla's code of conduct -enforcement ladder](https://github.com/mozilla/diversity). - -[homepage]: https://www.contributor-covenant.org - -For answers to common questions about this code of conduct, see the FAQ at -https://www.contributor-covenant.org/faq. Translations are available at -https://www.contributor-covenant.org/translations. \ No newline at end of file diff --git a/LICENSE b/LICENSE index 747a89a..704342c 100644 --- a/LICENSE +++ b/LICENSE @@ -13,8 +13,8 @@ The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHidexServiceNTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHidexServiceLL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE diff --git a/README.md b/README.md index 84816c0..25777d0 100644 --- a/README.md +++ b/README.md @@ -2,14 +2,39 @@ Contains `hidex_node`, providing an interface and adapter that works alongside the Hidex Plate Reader's first party driver to control the instrument. -## Installation Notes +## Building the C# Solution -To make the server accessible, run the following in a terminal as Administrator +To use this interface, you must first open `src/hidex_interface/HidexInterface.sln` and build the solution. -``` -netsh http add urlacl url=http://+:2005/ user= listen=yes delegate=yes -``` +## Python Installation/Usage -Replace `2005` with the port you intend to use, if it differs from the default, and `` with the username that will be running the server (you may need to use the form `DOMAIN/USER`) +This package is Windows-only. -To interface with the module from another device, you'll need to [open up the port](https://www.windowscentral.com/how-open-port-windows-firewall) you intend to run the module's server on (2005 by default). +### Using virtualenv + +1. Open Command Prompt and navigate to the project directory. +2. Create a virtual environment: + ``` + python -m venv venv + ``` +3. Activate the virtual environment: + ``` + venv\Scripts\activate + ``` +4. Install the package and dependencies: + ``` + pip install -r requirements.txt + ``` + +### Using pdm + +1. Install PDM if you don't have it: https://pdm-project.org/latest/#installation +2. Navigate to the project directory. +3. Install dependencies: + ``` + pdm install + ``` +4. To start the node: + ``` + pdm run python src/hidex_rest_node.py + ``` diff --git a/default.node.info.yaml b/default.node.info.yaml new file mode 100644 index 0000000..7917a27 --- /dev/null +++ b/default.node.info.yaml @@ -0,0 +1,210 @@ +node_name: default.node +node_id: 01KA2A8X6YVXP01W9HY8QESN60 +node_description: null +node_type: device +module_name: hidex_node +module_version: 0.0.1 +capabilities: + get_info: true + get_state: true + get_status: true + send_action: true + get_action_status: true + get_action_result: true + get_action_history: true + action_files: true + send_admin_commands: true + set_config: true + get_resources: false + get_log: true + admin_commands: + - cancel + - lock + - reset + - shutdown + - unlock +node_url: null +actions: + open: + name: open + description: Open the plate carrier + args: {} + locations: {} + files: {} + results: {} + blocking: true + asynchronous: true + accepts_var_args: false + accepts_var_kwargs: false + var_args_schema: null + var_kwargs_schema: null + close: + name: close + description: Closes the plate carrier + args: {} + locations: {} + files: {} + results: {} + blocking: true + asynchronous: true + accepts_var_args: false + accepts_var_kwargs: false + var_args_schema: null + var_kwargs_schema: null + run_assay: + name: run_assay + description: Runs the specificed assay on the current sample + args: + assay_name: + name: assay_name + description: Name of the assay to run + argument_type: str + required: true + default: null + wait_for_result: + name: wait_for_result + description: Whether we should wait for the results of the assay before returning + argument_type: bool + required: false + default: true + locations: {} + files: {} + results: + file: + result_label: file + description: null + result_type: file + blocking: true + asynchronous: true + accepts_var_args: false + accepts_var_kwargs: false + var_args_schema: null + var_kwargs_schema: null +config: + node_definition: default.node.yaml + node_info_path: null + update_node_files: true + status_update_interval: 2.0 + state_update_interval: 2.0 + node_url: http://suestorm.cels.anl.gov:3000/ + uvicorn_kwargs: + limit_concurrency: 10 + enable_rate_limiting: true + rate_limit_requests: 100 + rate_limit_window: 60 + rate_limit_short_requests: 50 + rate_limit_short_window: 1 + rate_limit_cleanup_interval: 300 + output_path: C:\Users\RPL\Documents\HidexData +config_schema: + description: Configuration for the Hidex REST node + properties: + node_definition: + anyOf: + - type: string + - format: path + type: string + - type: 'null' + default: default.node.yaml + description: Path to the node definition file to use. If set, the node will + load the definition from this file on startup. Otherwise, a default configuration + will be created. + title: Node Definition File + node_info_path: + anyOf: + - type: string + - format: path + type: string + - type: 'null' + default: null + description: Path to export the generated node info file. If not set, will use + the node name and the node_definition's path. + title: Node Info Path + update_node_files: + default: true + description: Whether to update the node definition and info files on startup. + If set to False, the node will not update the files even if they are out of + date. + title: Update Node Files + type: boolean + status_update_interval: + anyOf: + - type: number + - type: 'null' + default: 2.0 + description: The interval in seconds at which the node should update its status. + title: Status Update Interval + state_update_interval: + anyOf: + - type: number + - type: 'null' + default: 2.0 + description: The interval in seconds at which the node should update its state. + title: State Update Interval + node_url: + default: http://127.0.0.1:2000/ + description: The URL used to communicate with the node. This is the base URL + for the REST API. + format: uri + minLength: 1 + title: Node URL + type: string + uvicorn_kwargs: + additionalProperties: true + description: Configuration for the Uvicorn server that runs the REST API. By + default, sets limit_concurrency=10 to protect against connection exhaustion + attacks. + title: Uvicorn Configuration + type: object + enable_rate_limiting: + default: true + description: Enable rate limiting middleware for the REST API. + title: Enable Rate Limiting + type: boolean + rate_limit_requests: + default: 100 + description: Maximum number of requests allowed per long time window (only used + if enable_rate_limiting is True). + minimum: 1 + title: Rate Limit Requests + type: integer + rate_limit_window: + default: 60 + description: Long time window in seconds for rate limiting (only used if enable_rate_limiting + is True). + minimum: 1 + title: Rate Limit Window + type: integer + rate_limit_short_requests: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + default: 50 + description: Maximum number of requests allowed per short time window for burst + protection (only used if enable_rate_limiting is True). If None, short window + limiting is disabled. + title: Rate Limit Short Requests + rate_limit_short_window: + anyOf: + - minimum: 1 + type: integer + - type: 'null' + default: 1 + description: Short time window for burst protection in seconds (only used if + enable_rate_limiting is True). If None, short window limiting is disabled. + title: Rate Limit Short Window + rate_limit_cleanup_interval: + default: 300 + description: Interval in seconds between cleanup operations to prevent memory + leaks (only used if enable_rate_limiting is True). + minimum: 1 + title: Rate Limit Cleanup Interval + type: integer + output_path: + default: C:\Users\RPL\Desktop\results + format: path + title: Output Path + type: string + title: HidexNodeConfig + type: object diff --git a/default.node.yaml b/default.node.yaml new file mode 100644 index 0000000..37ca73d --- /dev/null +++ b/default.node.yaml @@ -0,0 +1,7 @@ +node_name: default.node +node_id: 01KA2A8X6YVXP01W9HY8QESN60 +node_description: null +node_type: device +module_name: hidex_node +module_version: 0.0.1 +capabilities: null diff --git a/definitions/hidex_howard.info.yaml b/definitions/hidex_howard.info.yaml new file mode 100644 index 0000000..98935d9 --- /dev/null +++ b/definitions/hidex_howard.info.yaml @@ -0,0 +1,157 @@ +node_name: hidex_howard +node_id: 01JWHD6HPNXMCKNHZK53VYVNQH +node_description: A rest node for the Hidex located on the East end of the Baker Enclosure + in ANL's RAPID 350 SDL +node_type: device +module_name: hidex_module +module_version: 1.1.0 +capabilities: + get_info: true + get_state: true + get_status: true + send_action: true + get_action_status: true + get_action_result: true + get_action_history: true + action_files: true + send_admin_commands: true + set_config: true + get_resources: false + get_log: true + admin_commands: + - cancel + - lock + - reset + - shutdown + - unlock +node_url: null +actions: + open: + name: open + description: Open the plate carrier + args: {} + locations: {} + files: {} + results: {} + blocking: false + asynchronous: true + accepts_var_args: false + accepts_var_kwargs: false + var_args_schema: null + var_kwargs_schema: null + close: + name: close + description: Closes the plate carrier + args: {} + locations: {} + files: {} + results: {} + blocking: false + asynchronous: true + accepts_var_args: false + accepts_var_kwargs: false + var_args_schema: null + var_kwargs_schema: null + run_assay: + name: run_assay + description: Runs the specificed assay on the current sample + args: + assay_name: + name: assay_name + description: Name of the assay to run + argument_type: str + required: true + default: null + wait_for_result: + name: wait_for_result + description: Whether we should wait for the results of the assay before returning + argument_type: bool + required: false + default: true + locations: {} + files: {} + results: + file: + result_label: file + description: null + result_type: file + blocking: false + asynchronous: true + accepts_var_args: false + accepts_var_kwargs: false + var_args_schema: null + var_kwargs_schema: null +config: + node_definition: C:\\Users\\RPL\\source\\repos\\hidex_module\\definitions\\hidex_howard.node.yaml + node_info_path: null + update_node_files: true + status_update_interval: 2.0 + state_update_interval: 2.0 + node_url: http://suestorm.cels.anl.gov:3000/ + uvicorn_kwargs: {} + output_path: C:\Users\RPL\Desktop\results +config_schema: + description: Configuration for the Hidex REST node + properties: + node_definition: + anyOf: + - type: string + - format: path + type: string + - type: 'null' + default: default.node.yaml + description: Path to the node definition file to use. If set, the node will + load the definition from this file on startup. Otherwise, a default configuration + will be created. + title: Node Definition File + node_info_path: + anyOf: + - type: string + - format: path + type: string + - type: 'null' + default: null + description: Path to export the generated node info file. If not set, will use + the node name and the node_definition's path. + title: Node Info Path + update_node_files: + default: true + description: Whether to update the node definition and info files on startup. + If set to False, the node will not update the files even if they are out of + date. + title: Update Node Files + type: boolean + status_update_interval: + anyOf: + - type: number + - type: 'null' + default: 2.0 + description: The interval in seconds at which the node should update its status. + title: Status Update Interval + state_update_interval: + anyOf: + - type: number + - type: 'null' + default: 2.0 + description: The interval in seconds at which the node should update its state. + title: State Update Interval + node_url: + default: http://127.0.0.1:2000/ + description: The URL used to communicate with the node. This is the base URL + for the REST API. + format: uri + minLength: 1 + title: Node URL + type: string + uvicorn_kwargs: + additionalProperties: true + description: Configuration for the Uvicorn server that runs the REST API. + title: Uvicorn Configuration + type: object + output_path: + default: C:\Users\RPL\Desktop\results + format: path + title: Output Path + type: string + title: HidexNodeConfig + type: object diff --git a/definitions/hidex_howard.node.yaml b/definitions/hidex_howard.node.yaml new file mode 100644 index 0000000..653cac7 --- /dev/null +++ b/definitions/hidex_howard.node.yaml @@ -0,0 +1,8 @@ +node_name: hidex_howard +node_id: 01JWHD6HPNXMCKNHZK53VYVNQH +node_description: A rest node for the Hidex located on the East end of the Baker Enclosure + in ANL's RAPID 350 SDL +node_type: device +module_name: hidex_module +module_version: 1.1.0 +capabilities: null diff --git a/example.env b/example.env new file mode 100644 index 0000000..d320427 --- /dev/null +++ b/example.env @@ -0,0 +1,90 @@ +# NODE_URL=http://localhost:2000 +NODE_DEFINITION=definitions/hidex.node.yaml + + +### MadsciContext + +# LAB_SERVER_URL=null +# EVENT_SERVER_URL=null +# EXPERIMENT_SERVER_URL=null +# DATA_SERVER_URL=null +# RESOURCE_SERVER_URL=null +# WORKCELL_SERVER_URL=null + +### EventClientConfig + +# EVENT_CLIENT_NAME=null +# EVENT_SERVER_URL=null +# EVENT_CLIENT_LOG_LEVEL=20 +# EVENT_CLIENT_LOG_DIR="~/.madsci/logs" + +### OwnershipInfo + +# EVENT_CLIENT_SOURCE__USER_ID=null +# EVENT_CLIENT_SOURCE__EXPERIMENT_ID=null +# EVENT_CLIENT_SOURCE__CAMPAIGN_ID=null +# EVENT_CLIENT_SOURCE__PROJECT_ID=null +# EVENT_CLIENT_SOURCE__NODE_ID=null +# EVENT_CLIENT_SOURCE__WORKCELL_ID=null +# EVENT_CLIENT_SOURCE__LAB_ID=null +# EVENT_CLIENT_SOURCE__STEP_ID=null +# EVENT_CLIENT_SOURCE__WORKFLOW_ID=null +# EVENT_CLIENT_SOURCE__MANAGER_ID=null + +### ObjectStorageSettings + +# OBJECT_STORAGE_ENDPOINT=null +# OBJECT_STORAGE_ACCESS_KEY="" +# OBJECT_STORAGE_SECRET_KEY="" +# OBJECT_STORAGE_SECURE=false +# OBJECT_STORAGE_DEFAULT_BUCKET="madsci-data" +# OBJECT_STORAGE_REGION=null + +### DataManagerSettings + +# DATA_SERVER_URL="http://localhost:8004/" +# DATA_MANAGER_DEFINITION="data.manager.yaml" +# DATA_DB_URL="mongodb://localhost:27017" +# DATA_FILE_STORAGE_PATH="~/.madsci/datapoints" + +### EventManagerSettings + +# EVENT_SERVER_URL="http://localhost:8001" +# EVENT_MANAGER_DEFINITION="event.manager.yaml" +# EVENTS_DB_URL="mongodb://localhost:27017" +# EVENTS_COLLECTION_NAME="madsci_events" +# EVENTS_ALERT_LEVEL=40 +# EVENTS_EMAIL_ALERTS=null + +### WorkcellManagerSettings + +# WORKCELL_SERVER_URL="http://localhost:8005/" +# WORKCELL_DEFINITION="workcell.manager.yaml" +# WORKCELLS_DIRECTORY="~/.madsci/workcells" +# WORKCELL_REDIS_HOST="localhost" +# WORKCELL_REDIS_PORT=6379 +# WORKCELL_REDIS_PASSWORD=null +# WORKCELL_SCHEDULER_UPDATE_INTERVAL=2.0 +# WORKCELL_NODE_UPDATE_INTERVAL=1.0 +# WORKCELL_COLD_START_DELAY=0 +# WORKCELL_SCHEDULER="madsci.workcell_manager.schedulers.default_scheduler" +# WORKCELL_MONGO_URL=null +# WORKCELL_GET_ACTION_RESULT_RETRIES=3 + +### ExperimentManagerSettings + +# EXPERIMENT_SERVER_URL="http://localhost:8002" +# EXPERIMENT_MANAGER_DEFINITION="experiment.manager.yaml" +# EXPERIMENTS_DB_URL="mongodb://localhost:27017" + +### ResourceManagerSettings + +# RESOURCE_SERVER_URL="http://localhost:8003" +# RESOURCE_MANAGER_DEFINITION="resource.manager.yaml" +# RESOURCES_DB_URL="postgresql://madsci:madsci@localhost:5432/resources" + +### LabManagerSettings + +# LAB_SERVER_URL="http://localhost:8000/" +# LAB_DASHBOARD_FILES_PATH="~/MADSci/src/madsci_squid/ui/dist" +# LAB_DEFINITION="lab.manager.yaml" diff --git a/hidex_node/.gitignore b/hidex_node/.gitignore deleted file mode 100644 index e427405..0000000 --- a/hidex_node/.gitignore +++ /dev/null @@ -1,401 +0,0 @@ -## Ignore Visual Studio temporary files, build results, and -## files generated by popular Visual Studio add-ons. -## -## Get latest from https://github.com/github/gitignore/blob/main/VisualStudio.gitignore - -# User-specific files -*.rsuser -*.suo -*.user -*.userosscache -*.sln.docstates - -# User-specific files (MonoDevelop/Xamarin Studio) -*.userprefs - -# Mono auto generated files -mono_crash.* - -# Build results -[Dd]ebug/ -[Dd]ebugPublic/ -[Rr]elease/ -[Rr]eleases/ -x64/ -x86/ -[Ww][Ii][Nn]32/ -[Aa][Rr][Mm]/ -[Aa][Rr][Mm]64/ -bld/ -[Bb]in/ -[Oo]bj/ -[Ll]og/ -[Ll]ogs/ - -# Visual Studio 2015/2017 cache/options directory -.vs/ -# Uncomment if you have tasks that create the project's static files in wwwroot -#wwwroot/ - -# Visual Studio 2017 auto generated files -Generated\ Files/ - -# MSTest test Results -[Tt]est[Rr]esult*/ -[Bb]uild[Ll]og.* - -# NUnit -*.VisualState.xml -TestResult.xml -nunit-*.xml - -# Build Results of an ATL Project -[Dd]ebugPS/ -[Rr]eleasePS/ -dlldata.c - -# Benchmark Results -BenchmarkDotNet.Artifacts/ - -# .NET Core -project.lock.json -project.fragment.lock.json -artifacts/ - -# ASP.NET Scaffolding -ScaffoldingReadMe.txt - -# StyleCop -StyleCopReport.xml - -# Files built by Visual Studio -*_i.c -*_p.c -*_h.h -*.ilk -*.meta -*.obj -*.iobj -*.pch -*.pdb -*.ipdb -*.pgc -*.pgd -*.rsp -*.sbr -*.tlb -*.tli -*.tlh -*.tmp -*.tmp_proj -*_wpftmp.csproj -*.log -*.tlog -*.vspscc -*.vssscc -.builds -*.pidb -*.svclog -*.scc - -# Chutzpah Test files -_Chutzpah* - -# Visual C++ cache files -ipch/ -*.aps -*.ncb -*.opendb -*.opensdf -*.sdf -*.cachefile -*.VC.db -*.VC.VC.opendb - -# Visual Studio profiler -*.psess -*.vsp -*.vspx -*.sap - -# Visual Studio Trace Files -*.e2e - -# TFS 2012 Local Workspace -$tf/ - -# Guidance Automation Toolkit -*.gpState - -# ReSharper is a .NET coding add-in -_ReSharper*/ -*.[Rr]e[Ss]harper -*.DotSettings.user - -# TeamCity is a build add-in -_TeamCity* - -# DotCover is a Code Coverage Tool -*.dotCover - -# AxoCover is a Code Coverage Tool -.axoCover/* -!.axoCover/settings.json - -# Coverlet is a free, cross platform Code Coverage Tool -coverage*.json -coverage*.xml -coverage*.info - -# Visual Studio code coverage results -*.coverage -*.coveragexml - -# NCrunch -_NCrunch_* -.*crunch*.local.xml -nCrunchTemp_* - -# MightyMoose -*.mm.* -AutoTest.Net/ - -# Web workbench (sass) -.sass-cache/ - -# Installshield output folder -[Ee]xpress/ - -# DocProject is a documentation generator add-in -DocProject/buildhelp/ -DocProject/Help/*.HxT -DocProject/Help/*.HxC -DocProject/Help/*.hhc -DocProject/Help/*.hhk -DocProject/Help/*.hhp -DocProject/Help/Html2 -DocProject/Help/html - 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Backup files are not needed, -# because we have git ;-) -_UpgradeReport_Files/ -Backup*/ -UpgradeLog*.XML -UpgradeLog*.htm -ServiceFabricBackup/ -*.rptproj.bak - -# SQL Server files -*.mdf -*.ldf -*.ndf - -# Business Intelligence projects -*.rdl.data -*.bim.layout -*.bim_*.settings -*.rptproj.rsuser -*- [Bb]ackup.rdl -*- [Bb]ackup ([0-9]).rdl -*- [Bb]ackup ([0-9][0-9]).rdl - -# Microsoft Fakes -FakesAssemblies/ - -# GhostDoc plugin setting file -*.GhostDoc.xml - -# Node.js Tools for Visual Studio -.ntvs_analysis.dat -node_modules/ - -# Visual Studio 6 build log -*.plg - -# Visual Studio 6 workspace options file -*.opt - -# Visual Studio 6 auto-generated workspace file (contains which files were open etc.) -*.vbw - -# Visual Studio 6 auto-generated project file (contains which files were open etc.) -*.vbp - -# Visual Studio 6 workspace and project file (working project files containing files to include in project) -*.dsw -*.dsp - -# Visual Studio 6 technical files -*.ncb -*.aps - -# 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Visual Studio History (VSHistory) files -.vshistory/ - -# BeatPulse healthcheck temp database -healthchecksdb - -# Backup folder for Package Reference Convert tool in Visual Studio 2017 -MigrationBackup/ - -#Connected Services -Connected\ Services/ - -# Ionide (cross platform F# VS Code tools) working folder -.ionide/ - -# Fody - auto-generated XML schema -FodyWeavers.xsd - -# VS Code files for those working on multiple tools -.vscode/* -!.vscode/settings.json -!.vscode/tasks.json -!.vscode/launch.json -!.vscode/extensions.json -*.code-workspace - -# Local History for Visual Studio Code -.history/ - -# Windows Installer files from build outputs -*.cab -*.msi -*.msix -*.msm -*.msp - -# JetBrains Rider -*.sln.iml diff --git a/hidex_node/App.config b/hidex_node/App.config deleted file mode 100644 index 5575884..0000000 --- a/hidex_node/App.config +++ /dev/null @@ -1,32 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/hidex_node/GlobalSuppressions.cs b/hidex_node/GlobalSuppressions.cs deleted file mode 100644 index 0e9a8cd..0000000 --- a/hidex_node/GlobalSuppressions.cs +++ /dev/null @@ -1,8 +0,0 @@ -// This file is used by Code Analysis to maintain SuppressMessage -// attributes that are applied to this project. -// Project-level suppressions either have no target or are given -// a specific target and scoped to a namespace, type, member, etc. - -using System.Diagnostics.CodeAnalysis; - -[assembly: SuppressMessage("CodeQuality", "IDE0051:Remove unused private members", Justification = "", Scope = "member", Target = "~M:HidexNode.Program.OnExecute")] diff --git a/hidex_node/HidexNode.cs b/hidex_node/HidexNode.cs deleted file mode 100644 index af23a49..0000000 --- a/hidex_node/HidexNode.cs +++ /dev/null @@ -1,14 +0,0 @@ -using HidexNode.HidexAutomation; -using System; - -namespace HidexNode -{ - - public class Callback_Wrapper : IHidexSenseAutomationServiceCallback - { - public void OnStateChanged() - { - Console.WriteLine("Initialized!"); - } - } -} \ No newline at end of file diff --git a/hidex_node/HidexNode.csproj b/hidex_node/HidexNode.csproj deleted file mode 100644 index 6754fb8..0000000 --- a/hidex_node/HidexNode.csproj +++ /dev/null @@ -1,269 +0,0 @@ - - - - - Debug - AnyCPU - {3D5637E3-94E5-4641-98FB-0FD8178CE2B5} - Library - HidexNode - HidexNode - v4.7.2 - 512 - true - true - publish\ - true - Disk - false - Foreground - 7 - Days - false - false - true - 0 - 1.0.0.%2a - false - false - true - - - AnyCPU - true - full - false - bin\Debug\ - DEBUG;TRACE - prompt - 4 - - - AnyCPU - pdbonly - true - bin\Release\ - TRACE - prompt - 4 - - - - - - - - - Designer - - - Reference.svcmap - - - Designer - - - - Designer - - - - Designer - - - - - - - - - - - - packages\Grapeseed.5.0.0-rc.10\lib\netstandard2.0\Grapeseed.dll - - - packages\Grapevine.5.0.0-rc.10\lib\netstandard2.0\Grapevine.dll - - - 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{1C565858-F302-471E-B409-F180AA4ABEC6} - 1 - 0 - 0 - tlbimp - False - True - - - {58FBCF7C-E7A9-467C-80B3-FC65E8FCCA08} - 1 - 0 - 0 - tlbimp - False - True - - - - - False - Microsoft .NET Framework 4.7.2 %28x86 and x64%29 - true - - - False - .NET Framework 3.5 SP1 - false - - - - \ No newline at end of file diff --git a/hidex_node/HidexRestServer.cs b/hidex_node/HidexRestServer.cs deleted file mode 100644 index 4101179..0000000 --- a/hidex_node/HidexRestServer.cs +++ /dev/null @@ -1,158 +0,0 @@ -using Grapevine; -using HidexNode.HidexAutomation; -using Newtonsoft.Json; -using System; -using System.Collections.Generic; -using System.IO; -using System.Linq; -using System.Threading; -using System.Threading.Tasks; - -namespace HidexNode -{ - [RestResource] - public class HidexRestServer - { - private readonly IRestServer _server; - - public HidexRestServer(IRestServer server) - { - _server = server; - } - - [RestRoute("Get", "/state")] - public async Task State(IHttpContext context) - { - string state = _server.Locals.GetAs("state"); - Dictionary response = new Dictionary - { - ["State"] = state - }; - Console.WriteLine(state); - await context.Response.SendResponseAsync(JsonConvert.SerializeObject(response)); - } - - [RestRoute("Get", "/about")] - public async Task About(IHttpContext context) - { - // TODO - await context.Response.SendResponseAsync(@" -{ - ""name"":""Hidex"", - ""model"":""Hidex Sense Microplate Reader"", - ""interface"":""wei_rest_node"", - ""version"":""0.2.0"", - ""description"":""Module for automating the hidex platereader."", - ""actions"": [ - {""name"":""open"",""args"":[],""files"":[]}, - {""name"":""close"",""args"":[],""files"":[]}, - {""name"":""run_assay"",""args"":[{""name"":""assay_name"",""type"":""str"",""default"":null,""required"":true,""description"":""Name of the assay to run""}],""files"":[]} - ], - ""resource_pools"":[] -}" - ); - } - - [RestRoute("Get", "/resources")] - public async Task Resources(IHttpContext context) - { - // TODO - await context.Response.SendResponseAsync("resources"); - } - - [RestRoute("Post", "/action")] - public async Task Action(IHttpContext context) - { - string action_handle = context.Request.QueryString["action_handle"]; - string action_vars = context.Request.QueryString["action_vars"]; - Dictionary args = JsonConvert.DeserializeObject>(action_vars); - var result = UtilityFunctions.action_response(); - string state = _server.Locals.GetAs("state"); - HidexSenseAutomationServiceClient client = _server.Locals.GetAs("client"); - - if (state == ModuleStatus.BUSY) - { - result = UtilityFunctions.action_response(StepStatus.FAILED, "", "Module is Busy"); - await context.Response.SendResponseAsync(JsonConvert.SerializeObject(result)); - } - try - { - _server.Locals.TryUpdate("state", ModuleStatus.BUSY, _server.Locals.GetAs("state")); - switch (action_handle) - { - case "open": - Console.WriteLine("Action Started: open"); - client.OpenPlateCarrier(); - while (client.GetState() == InstrumentState.Busy) ; - result = UtilityFunctions.action_response(StepStatus.SUCCEEDED, "Opened Hidex", ""); - Console.WriteLine("Action Finished: open"); - break; - case "run_assay": - Console.WriteLine("Action Started: run_assay"); - string output_path = _server.Locals.GetAs("output_path"); - DirectoryInfo output_dir = new DirectoryInfo(output_path); - string previous_filename = _server.Locals.GetAs("previous_filename"); - client.SetAutoExportPath(output_path); - client.StartAssay(args["assay_name"]); - while (client.GetState() == InstrumentState.Busy) ; - string filename = output_dir.GetFiles().OrderByDescending(f => f.LastWriteTime).First().FullName; - string wait_until_complete_string = "true"; - if (args.TryGetValue("wait_until_complete", out wait_until_complete_string) && wait_until_complete_string.ToLower() != "true") - { - result = UtilityFunctions.action_response(StepStatus.SUCCEEDED, "Ran Assay", ""); - } - else - { - while (filename == previous_filename) - { - filename = output_dir.GetFiles().OrderByDescending(f => f.LastWriteTime).First().FullName; - } - _server.Locals.TryUpdate("previous_filename", filename, previous_filename); - context.Response.Headers.Add("x-wei-action_response", StepStatus.SUCCEEDED); - context.Response.Headers.Add("x-wei-action_log", ""); - context.Response.Headers.Add("x-wei-action_msg", filename); - FileStream fs; - while (true) - { - try - { - fs = File.OpenRead(filename); - BinaryReader binaryReader = new BinaryReader(fs); - var Excelbytes = binaryReader.ReadBytes((int)fs.Length); - _server.Locals.TryUpdate("state", ModuleStatus.IDLE, _server.Locals.GetAs("state")); - Console.WriteLine("Action Finished: run_assay"); - await context.Response.SendResponseAsync(Excelbytes); - return; - } - catch (IOException) - { - Thread.Sleep(1000); - } - } - } - break; - case "close": - Console.WriteLine("Action Started: close"); - client.ClosePlateCarrier(); - while (client.GetState() == InstrumentState.Busy) ; - result = UtilityFunctions.action_response(StepStatus.SUCCEEDED, "Closed Hidex", ""); - Console.WriteLine("Action Finished: close"); - break; - default: - Console.WriteLine("Unknown action: " + action_handle); - result = UtilityFunctions.action_response(StepStatus.FAILED, "", "Unknown action: " + action_handle); - break; - } - _server.Locals.TryUpdate("state", ModuleStatus.IDLE, _server.Locals.GetAs("state")); - } - catch (Exception ex) - { - _server.Locals.TryUpdate("state", ModuleStatus.ERROR, _server.Locals.GetAs("state")); - Console.WriteLine(ex.ToString()); - result = UtilityFunctions.action_response(StepStatus.FAILED, "", "Step failed: " + ex.ToString()); - } - - await context.Response.SendResponseAsync(JsonConvert.SerializeObject(result)); - } - } -} diff --git a/hidex_node/packages.config b/hidex_node/packages.config deleted file mode 100644 index 913d797..0000000 --- a/hidex_node/packages.config +++ /dev/null @@ -1,40 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/hidex_node/utils.cs b/hidex_node/utils.cs deleted file mode 100644 index 09942ab..0000000 --- a/hidex_node/utils.cs +++ /dev/null @@ -1,37 +0,0 @@ -using System.Collections.Generic; - -namespace HidexNode -{ - public static class ModuleStatus - { - public const string - INIT = "INIT", - IDLE = "IDLE", - BUSY = "BUSY", - ERROR = "ERROR", - UNKNOWN = "UNKNOWN"; - } - - public static class StepStatus - { - public const string - IDLE = "idle", - RUNNING = "running", - SUCCEEDED = "succeeded", - FAILED = "failed"; - } - - public static class UtilityFunctions - { - public static Dictionary action_response(string action_response = StepStatus.IDLE, string action_msg = "", string action_log = "") - { - Dictionary response = new Dictionary(); - response["action_response"] = action_response; - response["action_msg"] = action_msg; - response["action_log"] = action_log; - return response; - } - - } - -} diff --git a/pdm.lock b/pdm.lock new 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Lewis", email="ryan.lewis@anl.gov"}, {name="Tobias Ginsburg", email="tginsburg@anl.gov"}] -# TODO: Add additional dependencies here +version = "1.2.0" +description = "MADSci Module for controlling the Hidex Sense Platereader" +authors = [ + {name = "Doga Ozgulbas", email="dozgulbas@anl.gov"}, + {name = "Ryan D. Lewis", email="ryan.lewis@anl.gov"}, + {name = "Tobias Ginsburg", email = "tginsburg@anl.gov"}, +] dependencies = [ - "fastapi>=0.103", - "uvicorn>=0.14.0", - "ad_sdl.wei>=0.6.0", - "pytest", "pythonnet", + "madsci.node_module~=0.8.0", + "madsci.client~=0.8.0", + "madsci.common~=0.8.0", ] -requires-python = ">=3.8.1" +requires-python = ">=3.10,<3.14" readme = "README.md" license = {text = "MIT"} [project.urls] homepage = "https://github.com/AD-SDL/hidex_module" -##################### -# Development Tools # -##################### - -[tool.ruff] -# https://docs.astral.sh/ruff/configuration/ - -# Exclude a variety of commonly ignored directories. -exclude = [ - ".bzr", - ".direnv", - ".eggs", - ".git", - ".git-rewrite", - ".hg", - ".mypy_cache", - ".nox", - ".pants.d", - ".pytype", - ".ruff_cache", - ".svn", - ".tox", - ".venv", - "__pypackages__", - "_build", - "buck-out", - "build", - "dist", - "node_modules", - "venv", - "docs", -] - -# Same as Black. -line-length = 88 -indent-width = 4 - -# Assume Python 3.8 -target-version = "py38" - -[tool.ruff.lint] -# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`) codes by default. -select = [ - # pycodestyle - "E", - # Pyflakes - "F", - # pyupgrade - # "UP", - # flake8-bugbear - "B", - # flake8-simplify - # "SIM", - # isort - "I", - # Warning - "W", - # pydocstyle - "D100", "D101", "D102", "D103", "D104", "D105", "D106", "D107", - # ruff - # "RUF" -] -ignore = [ - "E501" # Line too long -] - -# Allow fix for all enabled rules (when `--fix`) is provided. -fixable = ["ALL"] -unfixable = [] - -# Allow unused variables when underscore-prefixed. -dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$" - -[tool.ruff.format] -# Like Black, use double quotes for strings. -quote-style = "double" - -# Like Black, indent with spaces, rather than tabs. -indent-style = "space" - -# Like Black, respect magic trailing commas. -skip-magic-trailing-comma = false - -# Like Black, automatically detect the appropriate line ending. -line-ending = "auto" - -[tool.pytest.ini_options] -# https://docs.pytest.org/en/stable/customize.html -addopts = "-x" -junit_family="xunit1" -filterwarnings = [ - "ignore::DeprecationWarning", - "ignore::pottery.exceptions.InefficientAccessWarning", +###################### +# Build Info + Tools # +###################### +[build-system] +requires = ["setuptools>=61", "wheel"] +build-backend = "setuptools.build_meta" + +[dependency-groups] +dev = [ + "pre-commit>=4.2.0", + "ruff>=0.11.7", + "pytest", ] - -[tool.mypy] -# https://mypy.readthedocs.io/en/stable/config_file.html#using-a-pyproject-toml -show_error_codes = true -check_untyped_defs = true -follow_imports = "normal" -strict_optional = true -plugins = ["pydantic.mypy"] -strict = true -disallow_untyped_defs = true -implicit_reexport = true diff --git a/ruff.toml b/ruff.toml new file mode 100644 index 0000000..db2463c --- /dev/null +++ b/ruff.toml @@ -0,0 +1,125 @@ +# https://docs.astral.sh/ruff/configuration/ + +# Exclude a variety of commonly ignored directories. +exclude = [ + ".bzr", + ".direnv", + ".eggs", + ".git", + ".git-rewrite", + ".hg", + ".mypy_cache", + ".nox", + ".pants.d", + ".pytype", + ".ruff_cache", + ".svn", + ".tox", + ".venv", + "__pypackages__", + "_build", + "buck-out", + "build", + "dist", + "node_modules", + "venv", + ".venv", + "docs", +] + +# Same as Black. +line-length = 88 +indent-width = 4 + +# Assume Python 3.9 +target-version = "py39" + +[lint] +# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`) codes by default. +select = [ + # pycodestyle + "E", + # Pyflakes + "F", + # pyupgrade + "UP", + # flake8-bugbear + "B", + # flake8-simplify + "SIM", + # isort + "I", + # Warning + "W", + # pydocstyle + "D100", "D101", "D102", "D103", "D104", "D105", "D106", "D107", + # ruff + "RUF", + # McCabe Complexity + "C90", + # pep8-naming (N) + "N", + # flake8-2020 (YTT) + "YTT", + # flake8-annotations (ANN) + "ANN", + # flake8-async + "ASYNC", + # flake8-bandit + "S", + # flake8-commas + "COM", + # flake8-use-pathlib + "PTH", + # FastAPI + "FAST", + # flake8-logging + "LOG", + # flake8-comprehensions + "C4", + # flake8-pie + "PIE", + # flake8-return + "RET", + # Pylint + "PL", + # eradicate + "ERA", + # refurb + "FURB", + # flake-8-unused-arguments + "ARG", + # flake-8-print + "T20", +] +ignore = [ + "E501", # Line too long + "B006", # Do not use mutable data structures for argument defaults + "ANN401", # Don't flag Any types + "COM812", # Don't fight over trailing commas + "PLR0913", # Allow for a reasonable number of arguments + "PLR2004", # Magic value used in comparison +] + +# Allow fix for all enabled rules (when `--fix`) is provided. +fixable = ["ALL"] +unfixable = [] + +# Allow unused variables when underscore-prefixed. +dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$" + +[lint.per-file-ignores] +"**/tests/**/*.py" = ["S101"] + +[format] +# Like Black, use double quotes for strings. +quote-style = "double" + +# Like Black, indent with spaces, rather than tabs. +indent-style = "space" + +# Like Black, respect magic trailing commas. +skip-magic-trailing-comma = false + +# Like Black, automatically detect the appropriate line ending. +line-ending = "auto" diff --git a/run_hidex.bat b/run_hidex.bat new file mode 100644 index 0000000..a3c7afc --- /dev/null +++ b/run_hidex.bat @@ -0,0 +1,4 @@ +cd /d "%~dp0" +call ".venv\Scripts\activate.bat" +python "src\hidex_rest_node.py" --node_url http://suestorm.cels.anl.gov:3000 --node_definition "C:\\Users\\RPL\\source\\repos\\hidex_module\\definitions\\hidex_howard.node.yaml" +pause diff --git a/src/hidex_interface/App.config b/src/hidex_interface/App.config new file mode 100644 index 0000000..8a09df8 --- /dev/null +++ b/src/hidex_interface/App.config @@ -0,0 +1,22 @@ + + + + + + + + + + + + + + + + + + + + diff --git a/hidex_node/Connected Services/HidexAutomation/Arrays.xsd b/src/hidex_interface/Connected Services/HidexService/Arrays.xsd similarity index 97% rename from hidex_node/Connected Services/HidexAutomation/Arrays.xsd rename to src/hidex_interface/Connected Services/HidexService/Arrays.xsd index c7a5d70..b155124 100644 --- a/hidex_node/Connected Services/HidexAutomation/Arrays.xsd +++ b/src/hidex_interface/Connected Services/HidexService/Arrays.xsd @@ -6,4 +6,4 @@ - \ No newline at end of file + diff --git a/hidex_node/Connected Services/HidexAutomation/HidexNode.HidexAutomation.InstrumentState.datasource b/src/hidex_interface/Connected Services/HidexService/HidexInterface.HidexService.InstrumentState.datasource similarity index 64% rename from hidex_node/Connected Services/HidexAutomation/HidexNode.HidexAutomation.InstrumentState.datasource rename to src/hidex_interface/Connected Services/HidexService/HidexInterface.HidexService.InstrumentState.datasource index 97f620f..0ccaaa4 100644 --- a/hidex_node/Connected Services/HidexAutomation/HidexNode.HidexAutomation.InstrumentState.datasource +++ b/src/hidex_interface/Connected Services/HidexService/HidexInterface.HidexService.InstrumentState.datasource @@ -1,10 +1,10 @@  - HidexNode.HidexAutomation.InstrumentState, Connected Services.HidexAutomation.Reference.cs.dll, Version=0.0.0.0, Culture=neutral, PublicKeyToken=null - \ No newline at end of file + HidexInterface.HidexService.InstrumentState, Connected Services.HidexService.Reference.cs.dll, Version=0.0.0.0, Culture=neutral, PublicKeyToken=null + diff --git a/hidex_node/Connected Services/HidexAutomation/HidexSense.Automation.xsd b/src/hidex_interface/Connected Services/HidexService/HidexSense.Automation.xsd similarity index 97% rename from hidex_node/Connected Services/HidexAutomation/HidexSense.Automation.xsd rename to src/hidex_interface/Connected Services/HidexService/HidexSense.Automation.xsd index e54557d..824e6dc 100644 --- a/hidex_node/Connected Services/HidexAutomation/HidexSense.Automation.xsd +++ b/src/hidex_interface/Connected Services/HidexService/HidexSense.Automation.xsd @@ -8,4 +8,4 @@ - \ No newline at end of file + diff --git a/hidex_node/Connected Services/HidexAutomation/HidexSenseAutomation.wsdl b/src/hidex_interface/Connected Services/HidexService/HidexSenseAutomation.wsdl similarity index 94% rename from hidex_node/Connected Services/HidexAutomation/HidexSenseAutomation.wsdl rename to src/hidex_interface/Connected Services/HidexService/HidexSenseAutomation.wsdl index eb615dc..1db6cca 100644 --- a/hidex_node/Connected Services/HidexAutomation/HidexSenseAutomation.wsdl +++ b/src/hidex_interface/Connected Services/HidexService/HidexSenseAutomation.wsdl @@ -1,5 +1,5 @@  - + @@ -166,4 +166,4 @@ - \ No newline at end of file + diff --git a/hidex_node/Connected Services/HidexAutomation/HidexSenseAutomation.xsd b/src/hidex_interface/Connected Services/HidexService/HidexSenseAutomation.xsd similarity index 99% rename from hidex_node/Connected Services/HidexAutomation/HidexSenseAutomation.xsd rename to src/hidex_interface/Connected Services/HidexService/HidexSenseAutomation.xsd index 3823ec2..f72ee47 100644 --- a/hidex_node/Connected Services/HidexAutomation/HidexSenseAutomation.xsd +++ b/src/hidex_interface/Connected Services/HidexService/HidexSenseAutomation.xsd @@ -189,4 +189,4 @@ - \ No newline at end of file + diff --git a/hidex_node/Connected Services/HidexAutomation/Reference.cs b/src/hidex_interface/Connected Services/HidexService/Reference.cs similarity index 92% rename from hidex_node/Connected Services/HidexAutomation/Reference.cs rename to src/hidex_interface/Connected Services/HidexService/Reference.cs index 124825b..b0da3f2 100644 --- a/hidex_node/Connected Services/HidexAutomation/Reference.cs +++ b/src/hidex_interface/Connected Services/HidexService/Reference.cs @@ -8,331 +8,331 @@ // //------------------------------------------------------------------------------ -namespace HidexNode.HidexAutomation { +namespace HidexInterface.HidexService { using System.Runtime.Serialization; - - + + [System.CodeDom.Compiler.GeneratedCodeAttribute("System.Runtime.Serialization", "4.0.0.0")] [System.Runtime.Serialization.DataContractAttribute(Name="InstrumentState", Namespace="http://schemas.datacontract.org/2004/07/HidexSense.Automation")] public enum InstrumentState : int { - + [System.Runtime.Serialization.EnumMemberAttribute()] Unknown = 0, - + [System.Runtime.Serialization.EnumMemberAttribute()] Idle = 1, - + [System.Runtime.Serialization.EnumMemberAttribute()] Busy = 2, } - + [System.CodeDom.Compiler.GeneratedCodeAttribute("System.ServiceModel", "4.0.0.0")] - [System.ServiceModel.ServiceContractAttribute(Namespace="http://AurentiaSolutions/HidexSenseAutomation", ConfigurationName="HidexAutomation.IHidexSenseAutomationService", CallbackContract=typeof(HidexNode.HidexAutomation.IHidexSenseAutomationServiceCallback), SessionMode=System.ServiceModel.SessionMode.Required)] + [System.ServiceModel.ServiceContractAttribute(Namespace="http://AurentiaSolutions/HidexSenseAutomation", ConfigurationName="HidexService.IHidexSenseAutomationService", CallbackContract=typeof(HidexInterface.HidexService.IHidexSenseAutomationServiceCallback), SessionMode=System.ServiceModel.SessionMode.Required)] public interface IHidexSenseAutomationService { - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CanRun" + "Assay", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CanRun" + "AssayResponse")] bool CanRunAssay(string templateName); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CanRun" + "Assay", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CanRun" + "AssayResponse")] System.Threading.Tasks.Task CanRunAssayAsync(string templateName); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CanRun" + "AssayWithSampleData", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CanRun" + "AssayWithSampleDataResponse")] bool CanRunAssayWithSampleData(string templateName, string sampleDataCsvContent); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CanRun" + "AssayWithSampleData", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CanRun" + "AssayWithSampleDataResponse")] System.Threading.Tasks.Task CanRunAssayWithSampleDataAsync(string templateName, string sampleDataCsvContent); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CloseP" + "lateCarrier", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CloseP" + "lateCarrierResponse")] void ClosePlateCarrier(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CloseP" + "lateCarrier", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/CloseP" + "lateCarrierResponse")] System.Threading.Tasks.Task ClosePlateCarrierAsync(); - + [System.ServiceModel.OperationContractAttribute(Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/Connec" + "t", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/Connec" + "tResponse")] void Connect(bool allowSimulation); - + [System.ServiceModel.OperationContractAttribute(Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/Connec" + "t", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/Connec" + "tResponse")] System.Threading.Tasks.Task ConnectAsync(bool allowSimulation); - + [System.ServiceModel.OperationContractAttribute(IsTerminating=true, IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/Discon" + "nect", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/Discon" + "nectResponse")] void Disconnect(); - + [System.ServiceModel.OperationContractAttribute(IsTerminating=true, IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/Discon" + "nect", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/Discon" + "nectResponse")] System.Threading.Tasks.Task DisconnectAsync(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetAss" + "ays", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetAss" + "aysResponse")] string[] GetAssays(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetAss" + "ays", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetAss" + "aysResponse")] System.Threading.Tasks.Task GetAssaysAsync(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetAut" + "oExportPath", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetAut" + "oExportPathResponse")] string GetAutoExportPath(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetAut" + "oExportPath", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetAut" + "oExportPathResponse")] System.Threading.Tasks.Task GetAutoExportPathAsync(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetInt" + "erfaceVersion", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetInt" + "erfaceVersionResponse")] string GetInterfaceVersion(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetInt" + "erfaceVersion", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetInt" + "erfaceVersionResponse")] System.Threading.Tasks.Task GetInterfaceVersionAsync(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetSta" + "te", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetSta" + "teResponse")] - HidexNode.HidexAutomation.InstrumentState GetState(); - + HidexInterface.HidexService.InstrumentState GetState(); + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetSta" + "te", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/GetSta" + "teResponse")] - System.Threading.Tasks.Task GetStateAsync(); - + System.Threading.Tasks.Task GetStateAsync(); + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/OpenPl" + "ateCarrier", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/OpenPl" + "ateCarrierResponse")] void OpenPlateCarrier(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/OpenPl" + "ateCarrier", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/OpenPl" + "ateCarrierResponse")] System.Threading.Tasks.Task OpenPlateCarrierAsync(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/SetAut" + "oExportPath", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/SetAut" + "oExportPathResponse")] void SetAutoExportPath(string exportPath); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/SetAut" + "oExportPath", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/SetAut" + "oExportPathResponse")] System.Threading.Tasks.Task SetAutoExportPathAsync(string exportPath); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssay", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayResponse")] void StartAssay(string templateName); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssay", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayResponse")] System.Threading.Tasks.Task StartAssayAsync(string templateName); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayWithMetadata", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayWithMetadataResponse")] void StartAssayWithMetadata(string templateName, string resultTitle, string resultComment); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayWithMetadata", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayWithMetadataResponse")] System.Threading.Tasks.Task StartAssayWithMetadataAsync(string templateName, string resultTitle, string resultComment); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayWithSampleData", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayWithSampleDataResponse")] void StartAssayWithSampleData(string templateName, string resultTitle, string resultComment, string sampleDataCsvContent); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayWithSampleData", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StartA" + "ssayWithSampleDataResponse")] System.Threading.Tasks.Task StartAssayWithSampleDataAsync(string templateName, string resultTitle, string resultComment, string sampleDataCsvContent); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StopAs" + "say", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StopAs" + "sayResponse")] void StopAssay(); - + [System.ServiceModel.OperationContractAttribute(IsInitiating=false, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StopAs" + "say", ReplyAction="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/StopAs" + "sayResponse")] System.Threading.Tasks.Task StopAssayAsync(); } - + [System.CodeDom.Compiler.GeneratedCodeAttribute("System.ServiceModel", "4.0.0.0")] public interface IHidexSenseAutomationServiceCallback { - + [System.ServiceModel.OperationContractAttribute(IsOneWay=true, Action="http://AurentiaSolutions/HidexSenseAutomation/IHidexSenseAutomationService/OnStat" + "eChanged")] void OnStateChanged(); } - + [System.CodeDom.Compiler.GeneratedCodeAttribute("System.ServiceModel", "4.0.0.0")] - public interface IHidexSenseAutomationServiceChannel : HidexNode.HidexAutomation.IHidexSenseAutomationService, System.ServiceModel.IClientChannel { + public interface IHidexSenseAutomationServiceChannel : HidexInterface.HidexService.IHidexSenseAutomationService, System.ServiceModel.IClientChannel { } - + [System.Diagnostics.DebuggerStepThroughAttribute()] [System.CodeDom.Compiler.GeneratedCodeAttribute("System.ServiceModel", "4.0.0.0")] - public partial class HidexSenseAutomationServiceClient : System.ServiceModel.DuplexClientBase, HidexNode.HidexAutomation.IHidexSenseAutomationService { - - public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance) : + public partial class HidexSenseAutomationServiceClient : System.ServiceModel.DuplexClientBase, HidexInterface.HidexService.IHidexSenseAutomationService { + + public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance) : base(callbackInstance) { } - - public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance, string endpointConfigurationName) : + + public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance, string endpointConfigurationName) : base(callbackInstance, endpointConfigurationName) { } - - public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance, string endpointConfigurationName, string remoteAddress) : + + public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance, string endpointConfigurationName, string remoteAddress) : base(callbackInstance, endpointConfigurationName, remoteAddress) { } - - public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance, string endpointConfigurationName, System.ServiceModel.EndpointAddress remoteAddress) : + + public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance, string endpointConfigurationName, System.ServiceModel.EndpointAddress remoteAddress) : base(callbackInstance, endpointConfigurationName, remoteAddress) { } - - public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance, System.ServiceModel.Channels.Binding binding, System.ServiceModel.EndpointAddress remoteAddress) : + + public HidexSenseAutomationServiceClient(System.ServiceModel.InstanceContext callbackInstance, System.ServiceModel.Channels.Binding binding, System.ServiceModel.EndpointAddress remoteAddress) : base(callbackInstance, binding, remoteAddress) { } - + public bool CanRunAssay(string templateName) { return base.Channel.CanRunAssay(templateName); } - + public System.Threading.Tasks.Task CanRunAssayAsync(string templateName) { return base.Channel.CanRunAssayAsync(templateName); } - + public bool CanRunAssayWithSampleData(string templateName, string sampleDataCsvContent) { return base.Channel.CanRunAssayWithSampleData(templateName, sampleDataCsvContent); } - + public System.Threading.Tasks.Task CanRunAssayWithSampleDataAsync(string templateName, string sampleDataCsvContent) { return base.Channel.CanRunAssayWithSampleDataAsync(templateName, sampleDataCsvContent); } - + public void ClosePlateCarrier() { base.Channel.ClosePlateCarrier(); } - + public System.Threading.Tasks.Task ClosePlateCarrierAsync() { return base.Channel.ClosePlateCarrierAsync(); } - + public void Connect(bool allowSimulation) { base.Channel.Connect(allowSimulation); } - + public System.Threading.Tasks.Task ConnectAsync(bool allowSimulation) { return base.Channel.ConnectAsync(allowSimulation); } - + public void Disconnect() { base.Channel.Disconnect(); } - + public System.Threading.Tasks.Task DisconnectAsync() { return base.Channel.DisconnectAsync(); } - + public string[] GetAssays() { return base.Channel.GetAssays(); } - + public System.Threading.Tasks.Task GetAssaysAsync() { return base.Channel.GetAssaysAsync(); } - + public string GetAutoExportPath() { return base.Channel.GetAutoExportPath(); } - + public System.Threading.Tasks.Task GetAutoExportPathAsync() { return base.Channel.GetAutoExportPathAsync(); } - + public string GetInterfaceVersion() { return base.Channel.GetInterfaceVersion(); } - + public System.Threading.Tasks.Task GetInterfaceVersionAsync() { return base.Channel.GetInterfaceVersionAsync(); } - - public HidexNode.HidexAutomation.InstrumentState GetState() { + + public HidexInterface.HidexService.InstrumentState GetState() { return base.Channel.GetState(); } - - public System.Threading.Tasks.Task GetStateAsync() { + + public System.Threading.Tasks.Task GetStateAsync() { return base.Channel.GetStateAsync(); } - + public void OpenPlateCarrier() { base.Channel.OpenPlateCarrier(); } - + public System.Threading.Tasks.Task OpenPlateCarrierAsync() { return base.Channel.OpenPlateCarrierAsync(); } - + public void SetAutoExportPath(string exportPath) { base.Channel.SetAutoExportPath(exportPath); } - + public System.Threading.Tasks.Task SetAutoExportPathAsync(string exportPath) { return base.Channel.SetAutoExportPathAsync(exportPath); } - + public void StartAssay(string templateName) { base.Channel.StartAssay(templateName); } - + public System.Threading.Tasks.Task StartAssayAsync(string templateName) { return base.Channel.StartAssayAsync(templateName); } - + public void StartAssayWithMetadata(string templateName, string resultTitle, string resultComment) { base.Channel.StartAssayWithMetadata(templateName, resultTitle, resultComment); } - + public System.Threading.Tasks.Task StartAssayWithMetadataAsync(string templateName, string resultTitle, string resultComment) { return base.Channel.StartAssayWithMetadataAsync(templateName, resultTitle, resultComment); } - + public void StartAssayWithSampleData(string templateName, string resultTitle, string resultComment, string sampleDataCsvContent) { base.Channel.StartAssayWithSampleData(templateName, resultTitle, resultComment, sampleDataCsvContent); } - + public System.Threading.Tasks.Task StartAssayWithSampleDataAsync(string templateName, string resultTitle, string resultComment, string sampleDataCsvContent) { return base.Channel.StartAssayWithSampleDataAsync(templateName, resultTitle, resultComment, sampleDataCsvContent); } - + public void StopAssay() { base.Channel.StopAssay(); } - + public System.Threading.Tasks.Task StopAssayAsync() { return base.Channel.StopAssayAsync(); } diff --git a/hidex_node/Connected Services/HidexAutomation/Reference.svcmap b/src/hidex_interface/Connected Services/HidexService/Reference.svcmap similarity index 76% rename from hidex_node/Connected Services/HidexAutomation/Reference.svcmap rename to src/hidex_interface/Connected Services/HidexService/Reference.svcmap index 9758726..124ef09 100644 --- a/hidex_node/Connected Services/HidexAutomation/Reference.svcmap +++ b/src/hidex_interface/Connected Services/HidexService/Reference.svcmap @@ -1,5 +1,5 @@ - + false true @@ -22,15 +22,15 @@ - - - - - - + + + + + + - \ No newline at end of file + diff --git a/hidex_node/Connected Services/HidexAutomation/configuration.svcinfo b/src/hidex_interface/Connected Services/HidexService/configuration.svcinfo similarity index 53% rename from hidex_node/Connected Services/HidexAutomation/configuration.svcinfo rename to src/hidex_interface/Connected Services/HidexService/configuration.svcinfo index 96344f7..defeb52 100644 --- a/hidex_node/Connected Services/HidexAutomation/configuration.svcinfo +++ b/src/hidex_interface/Connected Services/HidexService/configuration.svcinfo @@ -1,10 +1,10 @@  - + - + - \ No newline at end of file + diff --git a/hidex_node/Connected Services/HidexAutomation/configuration91.svcinfo b/src/hidex_interface/Connected Services/HidexService/configuration91.svcinfo similarity index 97% rename from hidex_node/Connected Services/HidexAutomation/configuration91.svcinfo rename to src/hidex_interface/Connected Services/HidexService/configuration91.svcinfo index 0966156..de62b4f 100644 --- a/hidex_node/Connected Services/HidexAutomation/configuration91.svcinfo +++ b/src/hidex_interface/Connected Services/HidexService/configuration91.svcinfo @@ -1,5 +1,5 @@ - + @@ -142,7 +142,7 @@ - + net.pipe://localhost/HidexSenseAutomation/ @@ -157,7 +157,7 @@ CustomBinding_IHidexSenseAutomationService - HidexAutomation.IHidexSenseAutomationService + HidexService.IHidexSenseAutomationService System.ServiceModel.Configuration.AddressHeaderCollectionElement @@ -228,4 +228,4 @@ - \ No newline at end of file + diff --git a/hidex_node/Connected Services/HidexAutomation/service.wsdl b/src/hidex_interface/Connected Services/HidexService/service.wsdl similarity index 89% rename from hidex_node/Connected Services/HidexAutomation/service.wsdl rename to src/hidex_interface/Connected Services/HidexService/service.wsdl index aed2591..2a7af7a 100644 --- a/hidex_node/Connected Services/HidexAutomation/service.wsdl +++ b/src/hidex_interface/Connected Services/HidexService/service.wsdl @@ -1,5 +1,5 @@  - + @@ -167,4 +167,4 @@ - \ No newline at end of file + diff --git a/hidex_node/Connected Services/HidexAutomation/service.xsd b/src/hidex_interface/Connected Services/HidexService/service.xsd similarity index 99% rename from hidex_node/Connected Services/HidexAutomation/service.xsd rename to src/hidex_interface/Connected Services/HidexService/service.xsd index b4d5ff0..72a2247 100644 --- a/hidex_node/Connected Services/HidexAutomation/service.xsd +++ b/src/hidex_interface/Connected Services/HidexService/service.xsd @@ -39,4 +39,4 @@ - \ No newline at end of file + diff --git a/src/hidex_interface/HidexInterface.cs b/src/hidex_interface/HidexInterface.cs new file mode 100644 index 0000000..923d8fc --- /dev/null +++ b/src/hidex_interface/HidexInterface.cs @@ -0,0 +1,13 @@ +using System; +using HidexInterface.HidexService; + +namespace HidexInterface +{ + public class Callback_Wrapper : IHidexSenseAutomationServiceCallback + { + public void OnStateChanged() + { + Console.WriteLine("State changed in HidexSenseAutomationService."); + } + } +} diff --git a/src/hidex_interface/HidexInterface.csproj b/src/hidex_interface/HidexInterface.csproj new file mode 100644 index 0000000..764c070 --- /dev/null +++ b/src/hidex_interface/HidexInterface.csproj @@ -0,0 +1,92 @@ + + + + + Debug + AnyCPU + {BA8378C6-DDAD-473E-B4C2-27551A1996AA} + Library + HidexInterface + HidexInterface + v4.7.2 + 512 + true + true + + + AnyCPU + true + full + false + bin\Debug\ + DEBUG;TRACE + prompt + 4 + false + + + AnyCPU + pdbonly + true + bin\Release\ + TRACE + prompt + 4 + + + + + + + + Designer + + + Reference.svcmap + + + Designer + + + + Designer + + + + Designer + + + + + + + + + + + + + + + + + + + + + + + WCF Proxy Generator + Reference.cs + + + + + True + True + Reference.svcmap + + + + + diff --git a/hidex_node/HidexNode.sln b/src/hidex_interface/HidexInterface.sln similarity index 56% rename from hidex_node/HidexNode.sln rename to src/hidex_interface/HidexInterface.sln index 7990b18..f52917e 100644 --- a/hidex_node/HidexNode.sln +++ b/src/hidex_interface/HidexInterface.sln @@ -1,9 +1,9 @@  Microsoft Visual Studio Solution File, Format Version 12.00 # Visual Studio Version 17 -VisualStudioVersion = 17.6.33829.357 +VisualStudioVersion = 17.6.33717.318 MinimumVisualStudioVersion = 10.0.40219.1 -Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "HidexNode", "HidexNode.csproj", "{3D5637E3-94E5-4641-98FB-0FD8178CE2B5}" +Project("{FAE04EC0-301F-11D3-BF4B-00C04F79EFBC}") = "HidexInterface", "HidexInterface.csproj", "{BA8378C6-DDAD-473E-B4C2-27551A1996AA}" EndProject Global GlobalSection(SolutionConfigurationPlatforms) = preSolution @@ -11,15 +11,15 @@ Global Release|Any CPU = Release|Any CPU EndGlobalSection GlobalSection(ProjectConfigurationPlatforms) = postSolution - {3D5637E3-94E5-4641-98FB-0FD8178CE2B5}.Debug|Any CPU.ActiveCfg = Debug|Any CPU - {3D5637E3-94E5-4641-98FB-0FD8178CE2B5}.Debug|Any CPU.Build.0 = Debug|Any CPU - {3D5637E3-94E5-4641-98FB-0FD8178CE2B5}.Release|Any CPU.ActiveCfg = Release|Any CPU - {3D5637E3-94E5-4641-98FB-0FD8178CE2B5}.Release|Any CPU.Build.0 = Release|Any CPU + {BA8378C6-DDAD-473E-B4C2-27551A1996AA}.Debug|Any CPU.ActiveCfg = Debug|Any CPU + {BA8378C6-DDAD-473E-B4C2-27551A1996AA}.Debug|Any CPU.Build.0 = Debug|Any CPU + {BA8378C6-DDAD-473E-B4C2-27551A1996AA}.Release|Any CPU.ActiveCfg = Release|Any CPU + {BA8378C6-DDAD-473E-B4C2-27551A1996AA}.Release|Any CPU.Build.0 = Release|Any CPU EndGlobalSection GlobalSection(SolutionProperties) = preSolution HideSolutionNode = FALSE EndGlobalSection GlobalSection(ExtensibilityGlobals) = postSolution - SolutionGuid = {D96A9DB8-4E3E-42FC-BB0A-A8F18C5940B8} + SolutionGuid = {9410CE9C-F814-4659-A63D-36EE372D9FD3} EndGlobalSection EndGlobal diff --git a/src/hidex_rest_node.py b/src/hidex_rest_node.py index 11aaf6d..9e5a844 100644 --- a/src/hidex_rest_node.py +++ b/src/hidex_rest_node.py @@ -1,153 +1,233 @@ - - """ REST-based node that interfaces with WEI and provides various fake actions for testing purposes """ -import clr -clr.AddReference("C:\\Users\\rpl\\\source\\repos\\hidex_module\\hidex_node\\bin\\Debug\\HidexNode.dll") -import System.ServiceModel as SM -import System.ServiceModel.Channels as SMC -import HidexNode.HidexAutomation as HA -import System -import HidexNode as HN -import time -import glob -import os - - -from typing import Annotated - -from fastapi import UploadFile -from fastapi.datastructures import State -from wei.modules.rest_module import RESTModule -from wei.types import StepFileResponse, StepResponse, StepStatus -from wei.types.step_types import StepSucceeded -from wei.types.module_types import ( - LocalFileModuleActionResult, - Location, - ModuleState, - ValueModuleActionResult, - ModuleStatus, -) -from wei.types.step_types import ActionRequest - -# * Test predefined action functions +import os +import time +from pathlib import Path, WindowsPath +from typing import Annotated, ClassVar -hidex_rest_node = RESTModule( - name="hidex_node", - description="A module to control the Hidex plate reader", - version="1.0.0", - resource_pools=[], - model="Hidex", - actions=[], +import clr +from madsci.common.types.action_types import ( + ActionCancelled, + ActionSucceeded, ) -hidex_rest_node.arg_parser.add_argument( - "--output_path", - type=str, - help="The starting amount of foo", - default="C:\\Users\\rpl\\Desktop\\results", +from madsci.common.types.admin_command_types import AdminCommandResponse +from madsci.common.types.node_types import ( + NodeIntrinsicLocationDefinition, + NodeRepresentationTemplateDefinition, + RestNodeConfig, ) - - - - -@hidex_rest_node.startup() -def test_node_startup(state: State): - """Initializes the module""" - sbe = SMC.ReliableSessionBindingElement() - binding = SMC.CustomBinding() - binding.Elements.Add(sbe) - binding.Elements.Add(SMC.BinaryMessageEncodingBindingElement()) - binding.Elements.Add(SMC.NamedPipeTransportBindingElement()) - t = HA.HidexSenseAutomationServiceClient(SM.InstanceContext(HN.Callback_Wrapper()), binding, SM.EndpointAddress(System.Uri("net.pipe://localhost/HidexSenseAutomation/"))) - t.Connect(False) - c = t.GetState() - print(t.GetState() == c) - while t.GetState() == c: - print(t.GetState()) - time.sleep(0.5) - print(t.GetState()) - state.client = t - state.cancelled = False - - -@hidex_rest_node.state_handler() -def state_handler(state: State) -> ModuleState: - """Handles the state of the module""" - if state.client.GetState() == HA.InstrumentState.Idle: - state.status = ModuleStatus.IDLE - elif state.client.GetState() == HA.InstrumentState.Busy: - state.status = ModuleStatus.BUSY - return ModuleState(status=state.status) - - - - -@hidex_rest_node.action() -def open( - state: State, - action: ActionRequest, -) -> StepResponse: - """opens plate carrier""" - state.client.OpenPlateCarrier() - time.sleep(1) - return StepResponse.step_succeeded() - -@hidex_rest_node.action() -def close( - state: State, - action: ActionRequest, -) -> StepResponse: - """closes plate carrier""" - state.client.ClosePlateCarrier() - time.sleep(1) - return StepResponse.step_succeeded() - - - -@hidex_rest_node.action( - name="run_assay", - results=[ - LocalFileModuleActionResult(label="assay_result", description="result file from the assay"), - ], +from madsci.common.types.resource_types import Slot +from madsci.node_module.helpers import action +from madsci.node_module.rest_node_module import RestNode + +clr.AddReference( + str( + WindowsPath(__file__).parent + / "hidex_interface" + / "bin" + / "Debug" + / "HidexInterface.dll" + ) ) -def run_assay(state: State, action: ActionRequest, - assay_name: Annotated[str, "assay to run"], wait_for_result: Annotated[bool, "Whether we should wait for the results of the assay before returning"] = True) -> StepFileResponse: - """runs assay on the current sample""" - - list_of_files = glob.glob(state.output_path +'\\*') # * means all if need specific format then *.csv - latest_file = max(list_of_files, key=os.path.getctime) - prev_file = latest_file - print(latest_file) - state.client.SetAutoExportPath(state.output_path) - state.client.StartAssay(assay_name) - while state.client.GetState() == HA.InstrumentState.Busy: - pass - if bool(wait_for_result) and not state.cancelled: - while latest_file == prev_file: - list_of_files = glob.glob(state.output_path +'\\*') # * means all if need specific format then *.csv - latest_file = max(list_of_files, key=os.path.getctime) +import HidexInterface # type: ignore # noqa: E402 +import HidexInterface.HidexService as HidexService # type: ignore # noqa: E402, PLR0402 +import System # type: ignore # noqa: E402 +from System import ServiceModel # type: ignore # noqa: E402 +from System.ServiceModel import Channels # type: ignore # noqa: E402 + + +class HidexNodeConfig(RestNodeConfig): + """Configuration for the Hidex REST node""" + + output_path: Path = Path.home() / "Desktop" / "results" + """Path where the Hidex saves assay results""" + + +class HidexNode(RestNode): + """Hidex Node class for managing the Hidex plate reader""" + + hidex_interface: HidexService.HidexSenseAutomationServiceClient = None + """Interface to the Hidex plate reader service""" + config_model = HidexNodeConfig + """Configuration model used by the Hidex Node""" + config: HidexNodeConfig = HidexNodeConfig() + """Configuration for the Hidex Node""" + module_version = "1.2.0" + """Version of the Hidex Node module""" + + # Location representation templates — registered automatically by template_handler() + location_representation_templates: ClassVar[ + list[NodeRepresentationTemplateDefinition] + ] = [ + NodeRepresentationTemplateDefinition( + template_name="hidex_carriage_repr", + default_values={"carriage_type": "standard", "capacity": 1}, + schema_def={ + "type": "object", + "properties": { + "capacity": { + "type": "integer", + "minimum": 1, + "description": "Number of plates the carriage can hold", + }, + }, + }, + required_overrides=[], + tags=["plate_reader", "carriage"], + version="1.0.0", + description="Hidex Sense carriage representation with capacity", + ), + ] + + # Intrinsic locations — auto-created on startup with '{node_name}.' prefix + intrinsic_locations: ClassVar[list[NodeIntrinsicLocationDefinition]] = [ + NodeIntrinsicLocationDefinition( + location_name="hidex_carriage", + description="Hidex Sense plate reader carriage.", + representation_template_name="hidex_carriage_repr", + resource_template_name="hidex.nest", + allow_transfers=True, + ), + ] + + def startup_handler(self) -> None: + """Called to (re)initialize the node. Opens a connection to the Hidex.""" + self.initialize_resource_templates() + self.create_resources() + + sbe = Channels.ReliableSessionBindingElement() + binding = Channels.CustomBinding() + binding.Elements.Add(sbe) + binding.Elements.Add(Channels.BinaryMessageEncodingBindingElement()) + binding.Elements.Add(Channels.NamedPipeTransportBindingElement()) + self.hidex_interface = HidexService.HidexSenseAutomationServiceClient( + ServiceModel.InstanceContext(HidexInterface.Callback_Wrapper()), + binding, + ServiceModel.EndpointAddress( + System.Uri("net.pipe://localhost/HidexSenseAutomation/") + ), + ) + self.hidex_interface.Connect(False) + state = self.hidex_interface.GetState() + self.logger.log_debug(self.hidex_interface.GetState() == state) + while self.hidex_interface.GetState() == state: + self.logger.log_debug(self.hidex_interface.GetState()) time.sleep(0.5) - return StepFileResponse( - StepStatus.SUCCEEDED, - files={"assay_result": latest_file}, + self.logger.log_debug(self.hidex_interface.GetState()) + self.cancelled = False + self.logger.log("Hidex node initialized!") + + def initialize_resource_templates(self) -> None: + """Initialize the resource templates for the Hidex Node Module""" + self.resource_client.create_template( + template_name="hidex.nest", + description="Plate nest for a Hidex Sense Plate Reader", + resource=Slot( + resource_description="Plate nest for a Hidex Node", + ), + version="1.0.0", ) - else: - state.cancelled = False - return StepSucceeded() -@hidex_rest_node.cancel() -def cancel(state: State): - state.client.StopAssay() - state.cancelled = True - state.status = ModuleStatus.IDLE + def create_resources(self) -> None: + """Create or attach to the resources for this node""" + self.resource_client.create_resource_from_template( + template_name="hidex.nest", + resource_name=f"{self.node_info.node_name}.nest", + ) -@hidex_rest_node.shutdown() -def shutdown(state: State): - state.client.Disconnect() + def shutdown_handler(self) -> None: + """Called to shutdown the node. Should be used to close connections to devices or release any other resources.""" + self.logger.log("Shutting down") + self.hidex_interface.Disconnect() + self.hidex_interface = None + self.logger.log("Hidex node shutdown successfully!") + + def state_handler(self) -> None: + """Handles the state of the Hidex node""" + if not self.hidex_interface or self.node_status.initializing: + return + + if self.hidex_interface.GetState() == HidexService.InstrumentState.Idle: + self.node_state = { + "hidex_status_code": "READY", + } + elif self.hidex_interface.GetState() == HidexService.InstrumentState.Busy: + self.node_state = { + "hidex_status_code": "BUSY", + } + self.logger.info("BUSY") + else: + self.node_state = { + "hidex_status_code": "UNKNOWN", + } + self.logger.info("UNKNOWN") + + @action(name="open", description="Open the plate carrier") + def open(self) -> None: + """Opens the plate carrier""" + self.hidex_interface.OpenPlateCarrier() + time.sleep(3) + return ActionSucceeded() + + @action(name="close", description="Closes the plate carrier") + def close(self) -> None: + """Closes the plate carrier""" + self.hidex_interface.ClosePlateCarrier() + time.sleep(5) + return ActionSucceeded() + + @action( + name="run_assay", description="Runs the specificed assay on the current sample" + ) + def run_assay( + self, + assay_name: Annotated[str, "Name of the assay to run"], + wait_for_result: Annotated[ + bool, "Whether we should wait for the results of the assay before returning" + ] = True, + ) -> Annotated[Path, "The assay result"]: + """Runs assay on the current sample""" + + self.cancelled = False + pre_submit_time = time.time() + self.hidex_interface.SetAutoExportPath(str(self.config.output_path)) + self.hidex_interface.StartAssay(assay_name) + while self.hidex_interface.GetState() == HidexService.InstrumentState.Busy: + pass + if bool(wait_for_result): + while not self.cancelled: + time.sleep(1) + files = list(Path(self.config.output_path).glob("*")) + if files: + latest_file = max(files, key=os.path.getctime) + if ( + latest_file.is_file() + and latest_file.stat().st_birthtime > pre_submit_time + ): + break + else: + self.logger.log_debug("Assay cancelled before completion") + return ActionCancelled(errors=["Assay cancelled before completion"]) + return ActionSucceeded(files={"assay_result": latest_file}) + self.cancelled = False + + return None + + def cancel(self) -> AdminCommandResponse: + """Cancels the current assay""" + try: + self.hidex_interface.StopAssay() + self.cancelled = True + return AdminCommandResponse( + success=True, + ) + except Exception as e: + self.logger.log_error(f"Error cancelling assay: {e}") + return AdminCommandResponse(success=False, errors=[e]) if __name__ == "__main__": - hidex_rest_node.start() - + hidex_node = HidexNode() + hidex_node.start_node() diff --git a/test/run_test.py b/test/run_test.py deleted file mode 100755 index d150ba5..0000000 --- a/test/run_test.py +++ /dev/null @@ -1,20 +0,0 @@ -#!/usr/bin/env python3 - -from pathlib import Path - -from wei import ExperimentClient - - -def main(): - # The path to the Workflow definition yaml file - wf_path = Path("./test_hidex_workflow.yaml") - # This defines the Experiment object that will communicate with the server for workflows - exp = ExperimentClient("127.0.0.1", "8000", "Test_Hidex_Application") - # This initializes the connection to the server and the logs for this run of the program. - exp.register_exp() - # This runs the workflow and returns once the workflow is complete - exp.start_run(wf_path.resolve(), simulate=False, blocking=True) - - -if __name__ == "__main__": - main() diff --git a/test/run_wei_server.sh b/test/run_wei_server.sh deleted file mode 100755 index 591ebce..0000000 --- a/test/run_wei_server.sh +++ /dev/null @@ -1,34 +0,0 @@ -#!/bin/bash - -session="WEI" - -folder="$( cd -- "$(dirname "$0")" >/dev/null 2>&1 ; pwd -P )" - -tmux new-session -d -s $session -tmux set -g mouse on - -window=0 -tmux rename-window -t $session:$window 'redis' -tmux send-keys -t $session:$window 'cd ' $folder C-m -# Start the redis server, or ping if it's already up -if [ "$(redis-cli ping)" != "PONG" ]; then - tmux send-keys -t $session:$window 'redis-server' C-m -fi - -window=1 -tmux new-window -t $session:$window -n 'server' -tmux send-keys -t $session:$window 'cd ' $folder C-m -tmux send-keys -t $session:$window 'python3 -m wei.server --workcell ./test_hidex_workcell.yaml' C-m - -window=2 -tmux new-window -t $session:$window -n 'engine' -tmux send-keys -t $session:$window 'cd ' $folder C-m -# Uncomment the following for ROS support -# tmux send-keys -t $session:$window 'source ~/wei_ws/install/setup.bash' C-m -tmux send-keys -t $session:$window 'python3 -m wei.engine --workcell ./test_hidex_workcell.yaml' C-m - -window=3 -tmux new-window -t $session:$window -n 'test_application' -tmux send-keys -t $session:$window 'python3 run_test.py' - -tmux attach-session -t $session diff --git a/test/test_hidex_workcell.yaml b/test/test_hidex_workcell.yaml deleted file mode 100644 index 5fa444b..0000000 --- a/test/test_hidex_workcell.yaml +++ /dev/null @@ -1,21 +0,0 @@ -name: Hidex_Test_Workcell - -#Info about data processing and location of the workcell -config: - funcx_local_ep: "" - globus_local_ep: "" - globus_search_index: "" - globus_portal_ep: "" - globus_group: "" - workcell_origin_coordinates: [0, 0, 0, 0, 0, 0] - -#List of all components accessible in this workcell -modules: - - name: hidex - model: hidex_platereader - interface: wei_rest_node - config: - rest_node_address: "http://wendy.cels.anl.gov:2005" - workcell_coordinates: [0, 0, 0, 0, 0, 0] - -locations: {} diff --git a/test/test_hidex_workflow.yaml b/test/test_hidex_workflow.yaml deleted file mode 100644 index 26e7900..0000000 --- a/test/test_hidex_workflow.yaml +++ /dev/null @@ -1,29 +0,0 @@ -name: Test Hidex -metadata: - author: Doga Ozgulbas, Ryan D. Lewis - info: Test workflow for Hidex - version: 0.1 - -modules: - - name: hidex - -flowdef: - - name: Open Hidex - module: hidex - action: open - checks: null - comment: Open Hidex - - - name: Close Hidex - module: hidex - action: close - checks: null - comment: Close Hidex - - - name: Plate Assay - module: hidex - action: run_assay - args: - assay_name: "Absorbance" - checks: null - comment: Run Hidex Plate Assay diff --git a/tests/node_tests.ipynb b/tests/node_tests.ipynb new file mode 100644 index 0000000..7220933 --- /dev/null +++ b/tests/node_tests.ipynb @@ -0,0 +1,37 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0", + "metadata": {}, + "source": [ + "## Test the Hidex Node " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "1", + "metadata": {}, + "outputs": [], + "source": [ + "from madsci.client.node.rest_node_client import RestNodeClient\n", + "\n", + "client = RestNodeClient(url=\"http://localhost:3022\")" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": ".venv", + "language": "python", + "name": "python3" + }, + "language_info": { + "name": "python", + "version": "3.12.9" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +}