ini -> yml

galaxyproject · Jan 19, 2018 · 8d1a499 · 8d1a499
2 parents 1c2bd5f + 33bd540
commit 8d1a499
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diff --git a/.ci/jenkins/selenium/run_tests.sh b/.ci/jenkins/selenium/run_tests.sh
@@ -16,6 +16,8 @@ fi
 mkdir -p "$GALAXY_TEST_ERRORS_DIRECTORY"
 mkdir -p "$GALAXY_TEST_SCREENSHOTS_DIRECTORY"
 
+docker run -v `pwd`:`pwd`:rw -w `pwd` -u $UID node /bin/bash -c 'make client-production-maps'
+
 # Start Selenium server in the test Docker container.
 DOCKER_RUN_EXTRA_ARGS="-e USE_SELENIUM=1 -e GALAXY_TEST_SELENIUM_RETRIES=${GALAXY_TEST_SELENIUM_RETRIES} -e GALAXY_TEST_ERRORS_DIRECTORY=${GALAXY_TEST_ERRORS_DIRECTORY} -e GALAXY_TEST_SCREENSHOTS_DIRECTORY=${GALAXY_TEST_SCREENSHOTS_DIRECTORY} ${DOCKER_RUN_EXTRA_ARGS}"
 export DOCKER_RUN_EXTRA_ARGS

diff --git a/.gitignore b/.gitignore
@@ -133,6 +133,9 @@ client/galaxy/scripts/libs/*
 # Documentation build files.
 doc/build
 doc/schema.md
+doc/source/admin/config_logging_default_yaml.rst
+doc/source/api/api.rst
+doc/source/api/ts_api.rst
 doc/source/dev/schema.rst
 
 # Misc

diff --git a/.travis.yml b/.travis.yml
@@ -30,7 +30,7 @@ matrix:
 
 install:
   - pip install tox
-  - if [ "$TOX_ENV" == "first_startup" ]; then bash -c "bash scripts/common_startup.sh && wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite && mv db_gx_rev_0127.sqlite database/universe.sqlite && bash manage_db.sh -c ./config/galaxy.ini.sample upgrade"; fi
+  - if [ "$TOX_ENV" == "first_startup" ]; then bash -c "bash scripts/common_startup.sh && wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite && mv db_gx_rev_0127.sqlite database/universe.sqlite && bash manage_db.sh -c ./config/galaxy.yml.sample upgrade"; fi
 
 script: tox -e $TOX_ENV
 

diff --git a/Makefile b/Makefile
@@ -93,6 +93,24 @@ reports-config-lint: ## lint reports YAML configuration file
 reports-config-rebuild-rst: ## Rebuild sample reports RST docs
 	$(CONFIG_MANAGE) build_rst reports > doc/source/admin/reports_options.rst
 
+config-validate: ## validate galaxy YAML configuration file
+	$(CONFIG_MANAGE) validate galaxy
+
+config-convert-dry-run: ## convert old style galaxy ini to yaml (dry run)
+	$(CONFIG_MANAGE) convert galaxy --dry-run
+
+config-convert: ## convert old style galaxy ini to yaml
+	$(CONFIG_MANAGE) convert galaxy
+
+config-rebuild-sample: ## Rebuild sample galaxy yaml file from schema
+	$(CONFIG_MANAGE) build_sample_yaml galaxy --add-comments
+
+config-lint: ## lint galaxy YAML configuration file
+	$(CONFIG_MANAGE) lint galaxy
+
+config-rebuild-rst: ## Rebuild sample galaxy RST docs
+	$(CONFIG_MANAGE) build_rst galaxy > doc/source/admin/galaxy_options.rst
+
 release-ensure-upstream: ## Ensure upstream branch for release commands setup
 ifeq (shell git remote -v | grep $(RELEASE_UPSTREAM), )
 	git remote add $(RELEASE_UPSTREAM) git@github.com:galaxyproject/galaxy.git

diff --git a/client/galaxy/scripts/components/Citations.vue b/client/galaxy/scripts/components/Citations.vue
@@ -57,7 +57,10 @@ export default {
     },
     computed: {
         formattedReferences: function() {
-            return this.citations.reduce((a, b) => a.concat(`<p class="formatted-reference">${this.formattedReference(b)}</p>`), "");
+            return this.citations.reduce(
+                (a, b) => a.concat(`<p class="formatted-reference">${this.formattedReference(b)}</p>`),
+                ""
+            );
         }
     },
     created: function() {
@@ -187,16 +190,16 @@ export default {
 };
 </script>
 <style>
-.citations-formatted{
+.citations-formatted {
     word-wrap: break-word;
 }
 
-.citations-bibtex-text{
+.citations-bibtex-text {
     width: 100%;
     height: 500px;
 }
 
-.citation-padding{
-    padding:5px 10px;
+.citation-padding {
+    padding: 5px 10px;
 }
 </style>
diff --git a/client/galaxy/scripts/components/HistoryImport.vue b/client/galaxy/scripts/components/HistoryImport.vue
@@ -60,4 +60,4 @@ export default {
 .ui-message {
     display: block;
 }
-</style>
+</style>
diff --git a/client/galaxy/scripts/components/Message.vue b/client/galaxy/scripts/components/Message.vue
@@ -4,17 +4,16 @@
 
 <script>
 export default {
-  name: 'Message',
-  props: {
-    message: {
-      type: String,
-      required: true
-    },
-    status: {
-      type: String,
-      default: 'done'
+    name: "Message",
+    props: {
+        message: {
+            type: String,
+            required: true
+        },
+        status: {
+            type: String,
+            default: "done"
+        }
     }
-  }
-}
+};
 </script>
-
diff --git a/client/galaxy/scripts/components/admin/BaseGrid.vue b/client/galaxy/scripts/components/admin/BaseGrid.vue
@@ -25,19 +25,19 @@
 
 <script>
 export default {
-  props: {
-    isLoaded: {
-      type: Boolean
-    },
-    title: {
-      type: String
-    },
-    columns: {
-      type: Array
-    },
-    rows: {
-      type: Array
+    props: {
+        isLoaded: {
+            type: Boolean
+        },
+        title: {
+            type: String
+        },
+        columns: {
+            type: Array
+        },
+        rows: {
+            type: Array
+        }
     }
-  }
-}
+};
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataManagerGrid.vue b/client/galaxy/scripts/components/admin/DataManagerGrid.vue
@@ -24,24 +24,24 @@
 
 <script>
 export default {
-  props: {
-    dataManagerTableName: {
-      type: String,
-      required: true
+    props: {
+        dataManagerTableName: {
+            type: String,
+            required: true
+        },
+        dataManagerColumns: {
+            type: Array,
+            required: true
+        },
+        dataManagerItems: {
+            type: Array,
+            required: true
+        }
     },
-    dataManagerColumns: {
-      type: Array,
-      required: true
-    },
-    dataManagerItems: {
-      type: Array,
-      required: true
-    }
-  },
-  methods: {
-    handleReloadButtonClick(event) {
-        this.$emit('reloaddatamanager', this.dataManagerTableName);
+    methods: {
+        handleReloadButtonClick(event) {
+            this.$emit("reloaddatamanager", this.dataManagerTableName);
+        }
     }
-  }
-}
+};
 </script>
diff --git a/client/galaxy/scripts/components/admin/DataTables.vue b/client/galaxy/scripts/components/admin/DataTables.vue
@@ -12,106 +12,109 @@
 </template>
 
 <script>
-import axios from 'axios';
-import Message from '../Message.vue';
-import DataTablesGrid from './DataTablesGrid.vue';
-import DataManagerGrid from './DataManagerGrid.vue';
+import axios from "axios";
+import Message from "../Message.vue";
+import DataTablesGrid from "./DataTablesGrid.vue";
+import DataManagerGrid from "./DataManagerGrid.vue";
 
 export default {
-  data() {
-    return {
-      currentView: 'data-tables-grid',
-      isLoaded: false,
-      dataTables: [],
-      dataManagerTableName: '',
-      dataManagerColumns: [],
-      dataManagerItems: [],
-      message: '',
-      status: ''
-    }
-  },
+    data() {
+        return {
+            currentView: "data-tables-grid",
+            isLoaded: false,
+            dataTables: [],
+            dataManagerTableName: "",
+            dataManagerColumns: [],
+            dataManagerItems: [],
+            message: "",
+            status: ""
+        };
+    },
 
-  components: {
-    message: Message,
-    'data-tables-grid': DataTablesGrid,
-    'data-manager-grid': DataManagerGrid
-  },
+    components: {
+        message: Message,
+        "data-tables-grid": DataTablesGrid,
+        "data-manager-grid": DataManagerGrid
+    },
 
-  computed: {
-    currentProps() {
-      let props;
+    computed: {
+        currentProps() {
+            let props;
 
-      if (this.currentView === 'data-tables-grid') {
-        props = {
-          isLoaded: this.isLoaded,
-          rows: this.dataTables
-        };
-      } else {
-        props = {
-          dataManagerTableName: this.dataManagerTableName,
-          dataManagerColumns: this.dataManagerColumns,
-          dataManagerItems: this.dataManagerItems
-        };
-      }
+            if (this.currentView === "data-tables-grid") {
+                props = {
+                    isLoaded: this.isLoaded,
+                    rows: this.dataTables
+                };
+            } else {
+                props = {
+                    dataManagerTableName: this.dataManagerTableName,
+                    dataManagerColumns: this.dataManagerColumns,
+                    dataManagerItems: this.dataManagerItems
+                };
+            }
 
-      return props;
-    }
-  },
+            return props;
+        }
+    },
 
-  methods: {
-    showDataManager(dataManagerTableName) {
-      axios.get(`${Galaxy.root}data_manager/tool_data_table_items`, {
-          params: {
-            table_name: dataManagerTableName
-          }
-        })
-        .then((response) => {
-          this.message = response.data.message;
-          this.status = response.data.status;
+    methods: {
+        showDataManager(dataManagerTableName) {
+            axios
+                .get(`${Galaxy.root}data_manager/tool_data_table_items`, {
+                    params: {
+                        table_name: dataManagerTableName
+                    }
+                })
+                .then(response => {
+                    this.message = response.data.message;
+                    this.status = response.data.status;
 
-          if (response.data.status !== 'error' && response.data.status !== 'warning') {
-            this.dataManagerTableName = dataManagerTableName;
-            this.dataManagerColumns = response.data.data.columns;
-            this.dataManagerItems = response.data.data.items;
-            this.currentView = 'data-manager-grid';
-          }
-        })
-        .catch((error) => {
-          console.error(error);
-        });
-    },
+                    if (response.data.status !== "error" && response.data.status !== "warning") {
+                        this.dataManagerTableName = dataManagerTableName;
+                        this.dataManagerColumns = response.data.data.columns;
+                        this.dataManagerItems = response.data.data.items;
+                        this.currentView = "data-manager-grid";
+                    }
+                })
+                .catch(error => {
+                    console.error(error);
+                });
+        },
 
-    reloadDataManager(dataManagerTableName) {
-      axios.get(`${Galaxy.root}data_manager/reload_tool_data_table`, {
-          params: {
-            table_name: dataManagerTableName
-          }
-        })
-        .then((response) => {
-          this.message = response.data.message;
-          this.status = response.data.status;
+        reloadDataManager(dataManagerTableName) {
+            axios
+                .get(`${Galaxy.root}data_manager/reload_tool_data_table`, {
+                    params: {
+                        table_name: dataManagerTableName
+                    }
+                })
+                .then(response => {
+                    this.message = response.data.message;
+                    this.status = response.data.status;
 
-          if (response.data.status !== 'error' && response.data.status !== 'warning') {
-            this.dataManagerItems = response.data.data.items;
-          }
-        })
-        .catch((error) => {
-          console.error(error);
-        });
-    }
-  },
+                    if (response.data.status !== "error" && response.data.status !== "warning") {
+                        this.dataManagerItems = response.data.data.items;
+                    }
+                })
+                .catch(error => {
+                    console.error(error);
+                });
+        }
+    },
 
-  created() {
-    axios.get(`${Galaxy.root}admin/data_tables_list`)
-      .then((response) => {
-        this.isLoaded = true;
-        this.dataTables = response.data.data;
-        this.message = response.data.message;
-        this.status = response.data.status;
-      })
-      .catch((error) => {
-        console.error(error);
-      });
-  }
-}
+    created() {
+        axios
+            .get(`${Galaxy.root}admin/data_tables_list`)
+            .then(response => {
+                this.isLoaded = true;
+                this.dataTables = response.data.data;
+                this.message = response.data.message;
+                this.status = response.data.status;
+            })
+            .catch(error => {
+                console.error(error);
+            });
+    }
+};
 </script>