Merge pull request #1271 from Sage-Bionetworks/develop

Schematic 23.7.1

Author: GiaJordan

.github/workflows/docker_build.yml

@@ -8,6 +8,7 @@ on:
   push:
     tags:
       - 'v[0-9]+.[0-9]+.[0-9]+'
+      - 'v[0-9]+.[0-9]+.[0-9]+-[A-Za-z0-9]+'
 
 env:
   REGISTRY: ghcr.io

.github/workflows/test.yml

@@ -96,7 +96,7 @@ jobs:
         run: |
           # ran only on certain files for now
           # add here when checked
-          poetry run black schematic/configuration.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py --check
+          poetry run black schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py --check
 
       #----------------------------------------------
       #             type checking/enforcement
@@ -105,9 +105,9 @@ jobs:
         run: |
           # ran only on certain files for now
           # add here when checked
-          poetry run mypy --install-types --non-interactive schematic/configuration.py
+          # poetry run mypy --install-types --non-interactive
           # add here when enforced
-          poetry run mypy --disallow-untyped-defs --install-types --non-interactive schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
+          poetry run mypy --disallow-untyped-defs --install-types --non-interactive schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
 
       #----------------------------------------------
       #             linting
@@ -116,7 +116,7 @@ jobs:
         run: |
           # ran only on certain files for now
           # add here when checked
-          poetry run pylint schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
+          poetry run pylint schematic/configuration/*.py schematic/exceptions.py schematic/help.py schematic/loader.py schematic/version.py
 
       #----------------------------------------------
       #              run test suite

.gitignore

@@ -172,4 +172,11 @@ tests/data/mock_manifests/valid_test_manifest_censored.csv
 tests/data/mock_manifests/Rule_Combo_Manifest_censored.csv
 
 # Pickle file
-tests/data/schema.gpickle
+tests/data/schema.gpickle
+
+# Created during testting
+Example*
+manifests/*
+
+# schematic config file
+config.yml

CONTRIBUTION.md

@@ -8,7 +8,7 @@ Please note we have a [code of conduct](CODE_OF_CONDUCT.md), please follow it in
 
 ### Reporting bugs or feature requests
 
-You can use the [`Issues`](https://github.com/Sage-Bionetworks/schematic/issues) tab to **create bug and feature requests**. Providing enough details to the developers to verify and troubleshoot your issue is paramount:
+You can use [Sage Bionetwork's FAIR Data service desk](https://sagebionetworks.jira.com/servicedesk/customer/portal/5/group/8) to **create bug and feature requests**. Providing enough details to the developers to verify and troubleshoot your issue is paramount:
 - **Provide a clear and descriptive title as well as a concise summary** of the issue to identify the problem.
 - **Describe the exact steps which reproduce the problem** in as many details as possible.
 - **Describe the behavior you observed after following the steps** and point out what exactly is the problem with that behavior.

README.md

@@ -88,45 +88,69 @@ editor of your choice and edit the `username` and `authtoken` attribute under th
 
 <strong>Configure config.yml File</strong>
 
-*Note*: Below is only a brief explanation of some attributes in `config.yml`. <strong>Please use the link [here](https://github.com/Sage-Bionetworks/schematic/blob/develop/config.yml) to get the latest version of `config.yml` in `develop` branch</strong>.
-
-Description of `config.yml` attributes
-
-    definitions:
-        synapse_config: "~/path/to/.synapseConfig"
-        service_acct_creds: "~/path/to/service_account_creds.json"
-
-    synapse:
-        master_fileview: "syn23643253" # fileview of project with datasets on Synapse
-        manifest_folder: "~/path/to/manifest_folder/" # manifests will be downloaded to this folder
-        manifest_basename: "filename" # base name of the manifest file in the project dataset, without extension
-        service_acct_creds: "syn25171627" # synapse ID of service_account_creds.json file
-
-    manifest:
-        title: "example" # title of metadata manifest file
-        # to make all manifests enter only 'all manifests'
-        data_type: 
-          - "Biospecimen"
-          - "Patient"
-
-    model:
-        input:
-            location: "data/schema_org_schemas/example.jsonld" # path to JSON-LD data model
-            file_type: "local" # only type "local" is supported currently
-    style: # configuration of google sheet
-        google_manifest:
-          req_bg_color:
-            red: 0.9215
-            green: 0.9725
-            blue: 0.9803
-          opt_bg_color:
-            red: 1.0
-            green: 1.0
-            blue: 0.9019
-          master_template_id: '1LYS5qE4nV9jzcYw5sXwCza25slDfRA1CIg3cs-hCdpU'
-          strict_validation: true
-
-*Note*: Paths can be specified relative to the `config.yml` file or as absolute paths.
+There are some defaults in schematic that can be configured. These fields are in ``config_example.yml``:
+
+```text
+
+# This is an example config for Schematic.
+# All listed values are those that are the default if a config is not used.
+# Save this as config.yml, this will be gitignored.
+# Remove any fields in the config you don't want to change
+# Change the values of any fields you do want to change
+
+
+# This describes where assets such as manifests are stored
+asset_store:
+  # This is when assets are stored in a synapse project
+  synapse:
+    # Synapse ID of the file view listing all project data assets.
+    master_fileview_id: "syn23643253"
+    # Path to the synapse config file, either absolute or relative to this file
+    config: ".synapseConfig"
+    # Base name that manifest files will be saved as
+    manifest_basename: "synapse_storage_manifest"
+
+# This describes information about manifests as it relates to generation and validation
+manifest:
+  # Location where manifests will saved to
+  manifest_folder: "manifests"
+  # Title or title prefix given to generated manifest(s)
+  title: "example"
+  # Data types of manifests to be generated or data type (singular) to validate manifest against
+  data_type:
+    - "Biospecimen"
+    - "Patient"
+
+# Describes the location of your schema
+model:
+  # Location of your schema jsonld, it must be a path relative to this file or absolute
+  location: "tests/data/example.model.jsonld"
+
+# This section is for using google sheets with Schematic
+google_sheets:
+  # The Synapse id of the Google service account credentials.
+  service_acct_creds_synapse_id: "syn25171627"
+  # Path to the synapse config file, either absolute or relative to this file
+  service_acct_creds: "schematic_service_account_creds.json"
+  # When doing google sheet validation (regex match) with the validation rules.
+  #   true is alerting the user and not allowing entry of bad values.
+  #   false is warning but allowing the entry on to the sheet.
+  strict_validation: true
+```
+
+If you want to change any of these copy ``config_example.yml`` to ``config.yml``, change any fields you want to, and remove any fields you don't.
+
+For example if you wanted to change the folder where manifests are downloaded your config should look like:
+
+```text
+
+manifest:
+  manifest_folder: "my_manifest_folder_path"
+```
+
+_Note_: `config.yml` is ignored by git.
+
+_Note_: Paths can be specified relative to the `config.yml` file or as absolute paths.
 
 6. Login to Synapse by using the command line
 On the CLI in your virtual environment, run the following command: 
@@ -264,7 +288,7 @@ docker run -v %cd%:/schematic \
 If you install external libraries by using `poetry add <name of library>`, please make sure that you include `pyproject.toml` and `poetry.lock` file in your commit.
 
 ## Reporting bugs or feature requests
-You can use the [`Issues`](https://github.com/Sage-Bionetworks/schematic/issues) tab to **create bug and feature requests**. Providing enough details to the developers to verify and troubleshoot your issue is paramount:
+You can **create bug and feature requests** through [Sage Bionetwork's FAIR Data service desk](https://sagebionetworks.jira.com/servicedesk/customer/portal/5/group/8). Providing enough details to the developers to verify and troubleshoot your issue is paramount:
 - **Provide a clear and descriptive title as well as a concise summary** of the issue to identify the problem.
 - **Describe the exact steps which reproduce the problem** in as many details as possible.
 - **Describe the behavior you observed after following the steps** and point out what exactly is the problem with that behavior.

certificate.conf

@@ -4,7 +4,9 @@ server {
     include     /etc/nginx/conf.d/self-signed.conf;
     include     /etc/nginx/conf.d/ssl-params.conf;
     server_name 127.0.0.1;
-
+    proxy_read_timeout 300;
+    proxy_connect_timeout 300;
+    proxy_send_timeout 300;
     location / {
         try_files $uri @app;
     }

config.yml

@@ -0,0 +1,45 @@
+# This is an example config for Schematic.
+# All listed values are those that are the default if a config is not used.
+# Save this as config.yml, this will be gitignored.
+# Remove any fields in the config you don't want to change
+# If you remove all fields from a section, the entire section should be removed including the header.
+# Change the values of any fields you do want to change
+
+
+# This describes where assets such as manifests are stored
+asset_store:
+  # This is when assets are stored in a synapse project
+  synapse:
+    # Synapse ID of the file view listing all project data assets.
+    master_fileview_id: "syn23643253"
+    # Path to the synapse config file, either absolute or relative to this file
+    config: ".synapseConfig"
+    # Base name that manifest files will be saved as
+    manifest_basename: "synapse_storage_manifest"
+
+# This describes information about manifests as it relates to generation and validation
+manifest:
+  # Location where manifests will saved to
+  manifest_folder: "manifests"
+  # Title or title prefix given to generated manifest(s)
+  title: "example"
+  # Data types of manifests to be generated or data type (singular) to validate manifest against
+  data_type:
+    - "Biospecimen"
+    - "Patient"
+
+# Describes the location of your schema
+model:
+  # Location of your schema jsonld, it must be a path relative to this file or absolute
+  location: "tests/data/example.model.jsonld"
+
+# This section is for using google sheets with Schematic
+google_sheets:
+  # The Synapse id of the Google service account credentials.
+  service_acct_creds_synapse_id: "syn25171627"
+  # Path to the synapse config file, either absolute or relative to this file
+  service_acct_creds: "schematic_service_account_creds.json"
+  # When doing google sheet validation (regex match) with the validation rules.
+  #   true is alerting the user and not allowing entry of bad values.
+  #   false is warning but allowing the entry on to the sheet.
+  strict_validation: true