{"action":"created","comment":{"url":"https://api.github.com/repos/molgenis/molgenis.org/pulls/comments/44778352","id":44778352,"diff_hunk":"@@ -270,26 +223,350 @@ Go to the Upload menu. You now should see something like this:\n \n ![Importer first screen](images/importer_first_screen.png?raw=true, \"importer\")\n \n-To keep it simple, all you need to do is click the 'select a file' button, select your newly made EMX file, and press the next button until it starts importing. Don't worry about all the options you are skipping, we will handle those [later in this document](#importing-advanced). After your import is done, you can view your data in the data explorer. Go there by clicking the 'Data Explorer' link in the menu.\n+To keep it simple, all you need to do is click the 'select a file' button, select your newly made EMX file, and press the next button until it starts importing. Don't worry about all the options you are skipping, we will handle those [upload section](#upload). After your import is done, you can view your data in the data explorer. Go there by clicking the 'Data Explorer' link in the menu.\n \n Congratulations! You have now deployed MOLGENIS either locally or on a server, and you have made the first steps on getting your data into the MOLGENIS database. Play around a bit with the different data explorer filters to get a feel on how MOLGENIS works.\n \n-Of course, simply uploading and showing data is not the only thing you can do with the MOLGENIS software. In the following [section](#from-user-to-expert), we will take you from being a simple user, and teach you on how to be an expert.\n-\n----\n----\n+Of course, simply uploading and showing data is not the only thing you can do with the MOLGENIS software. In the following MOLGENIS step-by-step section, we will take you from being a simple user, and teach you on how to be an expert.\n \n-## <a name=\"from-user-to-expert\"></a> From user to expert, MOLGENIS step-by-step\n+## <a name=\"molgenis-step-by-step\"></a> MOLGENIS step-by-step\n In this section you will learn about all the different modules MOLGENIS has to offer, step-by-step. Every module will be explained through a simple use case, going from a light explanation into a an example using every module at its full capabilities. Let us not wait any longer! We will start off with the most basic step, importing your data.\n \n-### <a name=\"importing-advanced\"></a> Becoming an expert MOLGENIS data importer\n-<!--\n-TODO: Put Jonathan his text here\n--->\n+### <a name=\"terminology\"></a> Terminology of Molgenis\n+In this section we introduce and explian the terminolegy of MOLGENIS\n+\n+| Term     |Explanation       |Example |Comments|\n+|----------|------------------|--------|--------|\n+| Package  | A namespace item. Multiple packages can create a namspace where entities can live in || The default namespace in molgenis is called \"default\"|\n+| Data set | A collections of entities that are contextual related| An file can contain multiple entities  | |\n+| Entity | An entity is the template and collection of a subject | Like a table in a database| |\n+| Entity | An entity is the actual data that is collected based on the template from an entity (Term above)| Like a row in a database| In the future we will change this term to \"instance\" to avoid complicity and double use of the same term|\n+| Attribute| An attribute describes the charcteristics of a data item in a entity |Like a column in a database||\n+\n+### <a name=\"upload\"></a> Data upload\n+The upload module is the place in MOLGENIS where you can upload your data into the MOLGENIS application. When you have the permissions, you will see the upload menu item.\n+\n+![Upload menu item](images/upload/upload-menu-item.png?raw=true, \"upload menu item\")\n+\n+#### <a name=\"upload-possibilities\"></a>Upload possibilities\n+The MOLGENIS upload module supports the following file formats and data:\n+\t\n+|file format\t\t|file extention             |data formats|\n+||\n+|CSV              \t|\".csv\" \".txt\" \".tsv\" \".zip\"|EMX|\n+|Excel            \t|\".xls\" \".xlsx\"             |EMX|\n+|OWL              \t|\".owl.zip\"                 |OWL|\n+|VCF (version 4.0)\t|\"vcf\" \".vcf.gz\"            |VVCF (version 4.0)|:\n+\n+##### <a name=\"upload-possibilities-abbreviations\"></a>Abbreviations:\n+\n+* CSV: Comma Seperated Value\n+* OWL: Web Ontology Language\n+* VCF: Variant Call Format\n+* EMX: Entity Model Extensible\n+\n+#### <a name=\"upload-screens\"></a>Upload pages\n+The different pages will be explained by uploading the<a name=\"advanced-data-example\"></a> \"Advanced data example\" ([download](data/advanced_data_example_v20151104.xlsx)) example data set.\n+\n+The pages are: \n+\n+1. Upload file\n+2. Options\n+3. Packages\n+4. Validation\n+5. Result\n+\n+Navigation buttons at the bottom of the pages:\n+\n+* Previous: Go to the previous page.\n+* Next: Go to the next page.\n+* Restart: Push this button when you want to start importing a new data set. It will redirect you to the start of this wizard. Pushing this button will kill the session but not the importing job.\n+* Finish: The same as Restart.\n+\n+\n+##### <a name=\"upload-screens-upload-file\"></a>Upload file page\n+\n+###### <a name=\"upload-screens-options-steps\"></a>Steps\n+\n+1. Select a file to upload.\n+2. Click on the next button.\n+\n+![Upload file screen](images/upload/upload-file-screen.png?raw=true, \"Upload file\")\n+\n+##### <a name=\"upload-screens-options\"></a>Options page\n+Select a data upload option. On this page you can select the rules of how to upload your data into MOLGENIS. Because this dataset is an new data set to the application we leave the default option \"Add entities\" selected. In tabular data sets, the term entities refers to data-rows.\n+It is important to understand that this selection is about the data and not the meta data of the data set.\n+\n+###### <a name=\"upload-screens-options-options\"></a>Options\n+\n+1. Add entities: Importer adds new entities or fails if entity exists.\n+2. Add entities / update existing: Importer adds new entities or updates existing entities.\n+3. Update entities: Importer updates existing entities or fails if entity does not exist.\n+\n+###### <a name=\"upload-screens-options-steps\"></a>Steps\n+\n+1. Click on the next Button.\n+\n+![Upload file screen](images/upload/options-screen.png?raw=true, \"Options\")\n+\n+##### <a name=\"upload-screens-packages\"></a>Packages page\n+Because the entity (table) persons has no package defined, we get the option to choose another package then the MOLGENIS default package. The select options are generated from the available packages in the data set.\n+\n+###### <a name=\"upload-screens-packages-steps\"></a>Steps\n+\n+1. Click on the next Button.\n+\n+![Upload file screen](images/upload/packages-screen.png?raw=true, \"Packages\")\n+\n+##### <a name=\"upload-screens-validation\"></a>Validation page\n+When you see this page the validation is already done. This page validates the structure of the meta data.\n+\n+\"Entities\" table where all the entities (tables) are defined.\n+\n+* Name: Name of entity\n+* Importable: Is this entity inportable or not. Two options (Yes, No) \n+\n+\"Entity fields\" table that will contain information about the fields of a entity (Columns of the table)\n+\n+* Name: Name of entity\n+* Detected: A comma separated list of fields that were found for this entity\n+* Required: Are there required fields defined in the meta data that are missing in the entity?\n+* Available: Are there fields in the meta data that are optionel and were not found in the entity?\n+* Unknown: Are there fields defined in the entity that were undefined in the meta data?\n+\n+###### <a name=\"upload-screens-validation-steps\"></a>Steps\n+\n+1. Click on the next Button.\n+\n+![Upload file screen](images/upload/validation-screen.png?raw=true, \"Validation\")\n+\n+##### <a name=\"upload-screens-result\"></a>Result page\n+\n+When this page is shown with the \"import succes\" message, than you know that your data and metadata are uploaded correctly.\n+\n+After the data is uploaded into MOLGENIS, you can change some permissions for the entities.\n+\n+In the permissions view you can:\n+\n+1. Select a group: which user group will get these permissions.\n+2. Select permission for a entity (table). You can choose between: Edit, View, Count and None. For more information about permissions visit this section: [Setting permissions](#permissions)\n+\n+###### <a name=\"upload-screens-result-steps\"></a>Steps\n \n-### <a name=\"molgenis-interface-modules\"></a> How to use MOLGENIS user interface modules (Hairball)\n+1. [Optional] Select the view permission for the root_hospital_cities entity.\n+2. [Optional] Click on the save button.\n+3. Click on the finish button.\n+\n+![Upload file screen](images/upload/result-screen.png?raw=true, \"Result\")\n+\n+### <a name=\"molgenis-interface-modules\"></a> How to use MOLGENIS user interface modules\n MOLGENIS is a web-based application with many different modules allowing you to approach your data in different ways. One module focuses on showing you how a certain data set is modeled, one focuses purely on filtering and querying your data, while another module allows for filling in questionnaires created in EMX. This diversity can be confusing at times, so the following sections will take you through each module one by one, showing you the how they work and what you can do with them.\n \n+#### <a name=\"data-explorer\"></a> Data Explorer\n+\n+One of the central plugins for many of the MOLGENIS databases is the data explorer, as the name suggests this is the plugin to use if you wish to take a closer look at the data.\n+\n+Note that some of the compoments described below are only shown if they are enabled in the application settings and to people with the appropriate permissions.\n+\n+##### Description of the different components on the screen:\n+On the top of the data explorer the name of the currently selected entity is shown as well as the description.\n+\n+At the right side at the top a dropdown is shown which can be used to select the entity you wish to display.\n+For admins a delete button is shown at the right side of the entity select, clicking it will allow you to choose if you which to delete only the data or also the metadata for the currently selected entity.\n+  \n+![Dataexplorer entity select](images/dataexplorer/entitySelect.png?raw=true, \"dataexplorer/entitySelect\")\n+\n+In the upper left corner of the data explorer is a search box, this search box can be used to search all your data for a certain search term.\n+  \n+![Dataexplorer search](images/dataexplorer/searchbox.png?raw=true, \"dataexplorer/searchbox\")\n+\n+Directly below the search box the currently active attribute filters are shown. By clicking on them they can be edited. The cross trailing every filter can be used to delete this filter. Filters can be set from the attribute selection tree which is described below.\n+Using the checkbox in front of each attribute the visibilty of this attribute in the table can be managed. This filter icon can be used to set filters for this specific attribute.\n+  \n+![Dataexplorer active filters](images/dataexplorer/active_filters.png?raw=true, \"dataexplorer/active_filters\")\n+\n+In the area with the active filters you will also find the button to open the filter wizard, this is a popup screen that allows you to add filters for different attributes in one go.\n+\n+![Dataexplorer filter wizard](images/dataexplorer/filterwizard.png?raw=true, \"dataexplorer/filterwizard\")\n+\n+##### mods\n+    \n+![Dataexplorer tabs](images/dataexplorer/dataexplorer_tabs.png?raw=true, \"dataexplorer/dataexplorer_tabs\")\n+\n+The data explorer consists of multiple modules to view or process the data in different ways. These modules are described below:\n+\n+##### Data mod\n+The data mod shows the data in a table, the table can be sorted by clicking on the headers.\n+If your data contains references to other entities, an icon is shown to expand this reference to show the data from the referenced entity.\n+\n+Every line starts, depening on your permissions with some action icons:\n+  \n+![Dataexplorer action buttons](images/dataexplorer/action_buttons.png?raw=true, \"dataexplorer/action_buttons\")\n+\n+- Add row:\n+Using this button will open a popup with inputs for all the attributes in the entity, allowing you to create a new 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