Merge pull request #3689 from kbase/develop

Merge to main for v5.4.3 release

Author: briehl

.github/dependabot.yml

@@ -21,6 +21,11 @@ updates:
       patterns:
         - "*"
   open-pull-requests-limit: 20
+  ignore:
+    - dependency-name: "bootstrap"
+    - dependency-name: "bowser"
+    - dependency-name: "d3"
+    - dependency-name: "jquery"
 - package-ecosystem: "docker"
   directory: "/"
   schedule:

Dockerfile

@@ -23,8 +23,8 @@ ARG SKIP_MINIFY
 EXPOSE 8888
 
 # Set the default environment to be CI, can be overridden by passing new CONFIG_ENV setting at container start
-ENV CONFIG_ENV ci
-ENV DOCKER_CONTAINER true
+ENV CONFIG_ENV=ci
+ENV DOCKER_CONTAINER=true
 
 # Copy in the narrative repo
 ADD ./kbase-logdb.conf /tmp/kbase-logdb.conf
@@ -59,8 +59,6 @@ RUN mkdir -p /kb/deployment/ui-common/ && \
     # Generate a version file that we can scrape later
     ./src/scripts/kb-update-config -f src/config.json.templ -o /kb/deployment/ui-common/narrative_version && \
     rm -r .git && \
-    # install core Python necessities + KBase scientific computing packages
-    pip install -r ./src/requirements-general.txt && \
     # install jupyter notebook and the narrative interface
     /bin/bash scripts/install_narrative_docker.sh && \
     chown -R nobody:www-data /tmp/narrative /kb/dev_container/narrative && \
@@ -70,7 +68,7 @@ RUN mkdir -p /kb/deployment/ui-common/ && \
 # into the location to check for a new narrative version. Normally we would put this in the template itself
 # but since the raw template is consumed at build time as a JSON file, a template with a default string would
 # cause JSON parsing to fail - GRRRRR!!!
-ENV VERSION_CHECK /narrative_version
+ENV VERSION_CHECK=/narrative_version
 
 USER nobody
 

RELEASE_NOTES.md

@@ -2,7 +2,83 @@
 
 The Narrative Interface allows users to craft KBase Narratives using a combination of GUI-based commands, Python and R scripts, and graphical output elements.
 
-This is built on the Jupyter Notebook v6.5.6 and IPython 8.26.0 (more notes will follow).
+This is built on the Jupyter Notebook v6.5.7 and IPython 8.28.x (more notes will follow).
+
+## Version 5.4.3
+URO-363 - add note to the sharing panel to contact KBase about DOIs
+
+- Python `requirements-general.txt` and `requirements.txt` merged into a single file so that all runtime deps are installed in one place.
+
+- Python dependencies updated to the following versions:
+  - coverage: 7.6.12
+  - pytest: 8.3.4
+  - pytest-cov: 6.0.0
+  - ruff: 0.9.9
+  - vcrpy: 7.0.0
+  - beautifulsoup4: 4.13.3
+  - biopython: 1.85
+  - bokeh: 3.6.2
+  - certifi: 2025.1.31
+  - cryptography: 44.0.1
+  - decorator: 5.2.1
+  - idna: 3.10
+  - markupsafe: 3.0.2
+  - networkx: 3.4.2
+  - numpy: 2.2.3
+  - pillow: 11.1.0
+  - plotly: 5.24.1
+  - pyasn1: 0.6.1
+  - pycurl: 7.45.4
+  - pygments: 2.19.1
+  - pyopenssl: 25.0.0
+  - python-daemon: 3.1.2
+  - scipy: 1.15.2
+  - setuptools: 75.8.2
+  - six: 1.17.0
+  - sympy: 1.13.3
+  - wordcloud: 1.9.4
+  - ipython: 8.33.0
+  - jinja2: 3.1.5
+  - pandas: 2.2.3
+  - pymongo: 4.11.1
+  - scikit-learn: 1.6.1
+  - statsmodels: 0.14.4
+  - tornado: 6.4.2
+
+- Javascript dependency updates
+  - dompurify 3.1.6 -> 3.2.4
+  - plotly.js-dist-min 2.35.0 -> 2.35.3  (note: next is 3.0.1, with breaking changes)
+  - @babel/traverse 7.25.6 -> 7.26.9
+  - @eslint/eslintrc 3.1.0 -> 3.3.0
+  - @eslint/js 9.11.1 -> 9.21.0
+  - @wdio/browserstack-service 9.0.9 -> 9.10.1
+  - @wdio/cli 9.0.9 -> 9.10.1
+  - @wdio/local-runner 9.0.9 -> 9.10.1
+  - @wdio/mocha-framework 9.0.8 -> 9.10.1
+  - @wdio/spec-reporter 9.0.8 -> 9.10.1
+  - axios 1.7.7 -> 1.8.1
+  - chromedriver 128.0.3 -> 133.0.3
+  - commander 12.1.0 -> 13.1.0
+  - eslint 9.11.1 -> 9.21.0
+  - eslint-config-prettier 9.1.0 -> 10.0.2
+  - expect-webdriverio 5.0.2 -> 5.0.5
+  - glob 11.0.0 -> 11.0.1
+  - globals 15.9.0 -> 16.0.0
+  - husky 9.1.6 -> 9.1.7
+  - jasmine-core 5.3.0 -> 5.6.0
+  - jquery-ui 1.14.0 -> 1.14.1
+  - lint-staged 15.2.10 -> 15.4.3
+  - postcss 8.4.47 -> 8.5.3
+  - prettier 3.3.3 -> 3.5.2
+  - puppeteer 23.4.0 -> 24.3.0
+  - sass 1.79.3 -> 1.85.1
+  - selenium-standalone 10.0.0 -> 10.0.1
+  - selenium-webdriver 4.25.0 -> 4.29.0
+  - string.prototype.startswith 1.0.0 -> 1.0.1
+  - stylelint 16.9.0 -> 16.15.0
+  - stylelint-config-recommended 14.0.1 -> 15.0.0
+  - stylelint-config-standard 36.0.1 -> 37.0.0
+  - terser 5.33.0 -> 5.39.0
 
 ## Version 5.4.2
 - UIP-52 - repair integration tests, get WebDriverIO up to date
@@ -77,7 +153,7 @@ This is built on the Jupyter Notebook v6.5.6 and IPython 8.26.0 (more notes will
   - stylelint-config-standard 36.0.0 -> 36.0.1
   - terser 5.31.1 -> 5.31.6
   - webdriverio 8.38.2 -> 9.0.9
-  
+
   - dompurify 2.5.5 -> 3.1.6
   - follow-redirects 1.15.6 -> 1.15.9
   - jquery-ui 1.13.2 -> 1.14.0
@@ -110,11 +186,11 @@ This is built on the Jupyter Notebook v6.5.6 and IPython 8.26.0 (more notes will
   - ruff 0.4.7 -> 0.5.5
 
 - JavaScript dependency updates
-  - @wdio/mocha-framework  8.38.2 -> 8.39.0 
-  - chrome-launcher  1.1.1 -> 1.1.2 
-  - chromedriver  126.0.0 -> 126.0.4 
-  - postcss  8.4.38 -> 8.4.39 
-  - selenium-webdriver  4.21.0 -> 4.22.0 
+  - @wdio/mocha-framework  8.38.2 -> 8.39.0
+  - chrome-launcher  1.1.1 -> 1.1.2
+  - chromedriver  126.0.0 -> 126.0.4
+  - postcss  8.4.38 -> 8.4.39
+  - selenium-webdriver  4.21.0 -> 4.22.0
 
 ## Version 5.4.0
 -   UIP-43

kbase-extension/scss/all_concat.scss

@@ -59,6 +59,7 @@
 @import "partials/renderJSON";
 @import "partials/reportViewer";
 @import "partials/select2";
+@import "partials/sharePanel";
 @import "partials/stagingTable";
 @import "partials/ui";
 @import "partials/userMenu";

kbase-extension/scss/partials/_sharePanel.scss

@@ -0,0 +1,134 @@
+.kb-share-panel {
+    text-align: center;
+
+    // .kb-share-panel__global_read_status
+    &__global_read_icon {
+        margin-right: 10px;
+    }
+
+    // .kb-share-panel__global_read_status
+    &__global_read_status {
+        margin: 5px;
+        padding: 10px;
+    }
+
+    // .kb-share-panel__my_access
+    &__my_access {
+        margin: 20px 5px 5px;
+    }
+
+    // .kb-share-panel__tabs
+    &__tabs {
+        margin: 0px 5px;
+
+        &__share {
+            width: 50%;
+            display: inline-block;
+            padding: 10px;
+            border: solid;
+            border-width: 1px 1px 0px;
+            cursor: pointer;
+            background-color: #d8d8d8;
+            border-bottom: 1px solid;
+            padding-bottom: 9px;
+        }
+
+        .left {
+            border-top-left-radius: 2px;
+            border-right: none;
+        }
+
+        .right {
+            border-top-right-radius: 2px;
+        }
+
+        .selected {
+            background-color: white;
+            border-bottom: none;
+            padding-bottom: 10px;
+        }
+
+        &__content {
+            border: solid;
+            border-width: 0px 1px 1px 1px;
+            border-radius: 0px 0px 2px 2px;
+            padding: 25px 15px 15px;
+            margin: 0px 5px;
+
+            .select2-selection--single {
+                min-height: 32px;
+            }
+
+            .select2-container {
+                margin-left: 5px;
+                margin-right: 5px;
+            }
+        }
+    }
+
+    &__btn_apply_orgs {
+        margin-left: 10px;
+    }
+
+    &__orgs_table {
+        border: 1px solid rgb(170, 170, 170);
+        border-radius: 4px;
+        text-align: left;
+        width: 51%;
+        padding: 10px;
+        margin: auto;
+        margin-top: 10px;
+    }
+
+    &__org_owner_message {
+        margin-top: 18px;
+    }
+
+    &__org_icon {
+        width: 40px;
+        margin: 8px;
+    }
+
+    &__shared_users_table {
+        margin-top: 15px;
+        max-height: 250px;
+        overflow-y: auto;
+        overflow-x: hidden;
+        display: flex;
+        justify-content: center;
+
+        tr {
+            .user_icon {
+                text-align: left;
+
+            }
+            .user_name {
+                text-align: left;
+                padding: 6px 4px 4px;
+            }
+            .user_perm_select {
+                text-align: right;
+            }
+            .user_remove_btn {
+                text-align: left;
+            }
+        }
+    }
+
+    &__share_user_selected {
+        width: 100%;
+
+        &__name {
+            white-space: normal;
+        }
+    }
+
+    // these two are used to override Select2 template selection text.
+    &__wrap {
+        white-space: normal;
+    }
+
+    &__nowrap {
+        white-space: nowrap;
+    }
+}