diff --git a/.github/mkdocs/mkdocs.yaml b/.github/mkdocs/mkdocs.yaml index fc3555b..c8a9dd7 100644 --- a/.github/mkdocs/mkdocs.yaml +++ b/.github/mkdocs/mkdocs.yaml @@ -5,7 +5,7 @@ docs_dir: ../../docs nav: - Home: index.md - SciCat User Guide: - - user-manual/index.md + - user-guide/index.md - Login: - login/index.md - Anonymous: login/Anonymous.md @@ -14,15 +14,16 @@ nav: - datasets/index.md - Publishing data: datasets/Publishing.md - Publishing data Advanced: datasets/PublishingAdvanced.md + - Data Retrieval: datasets/jobs.md - Proposals: - proposals/index.md - Samples: samples/index.md - - Instruments: instruments.md + - Instruments: instruments/index.md - Troubleshooting: - troubleshoot/index.md - SciCat Operator Guide: - - operator-manual/index.md + - operator-guide/index.md - swagger/index.md - backendconfig/index.md - backendconfig/authorization/index.md diff --git a/docs/backendconfig/authorization/authorization_datasets.md b/docs/backendconfig/authorization/authorization_datasets.md index bfe648c..aae63fe 100644 --- a/docs/backendconfig/authorization/authorization_datasets.md +++ b/docs/backendconfig/authorization/authorization_datasets.md @@ -1,4 +1,4 @@ -# Datasets Authoorization +# Datasets Authorization ## CASL ability actions This is the list of the permissions methods available for datasets and all their endpoints and more fine-grained instance authorization. diff --git a/docs/backendconfig/authorization/index.md b/docs/backendconfig/authorization/index.md index 753a1ca..aaaba7c 100644 --- a/docs/backendconfig/authorization/index.md +++ b/docs/backendconfig/authorization/index.md @@ -2,43 +2,30 @@ ## General For how authorization is handled in SciCat, see [general](./authorization.md) description. - Developers information, see [github](https://github.com/SciCatProject/documentation/blob/master/Development/v4.x/backend/authorization/authorization.md). - ## Authorization Datasets -Summary of how authorization for Datasets are handeld [better visible](./authorization_datasets.md) displayed. Developers information, see [github](https://github.com/SciCatProject/documentation/blob/master/Development/v4.x/backend/authorization/authorization_datasets.md). ## Authorization OrigDatablocks -Summary of how authorization for OrigDatablocks are handeld [better visible](./authorization_origdatablocks.md) displayed. - Developers information, see [github](https://github.com/SciCatProject/documentation/blob/master/Development/v4.x/backend/authorization/authorization_origdatablocks.md). ## Authorization Jobs -Summary of how authorization for OrigDatablocks are handeld [better visible](./authorization_jobs.md) displayed. - Developers information, see [github](https://github.com/SciCatProject/documentation/blob/master/Development/v4.x/backend/authorization/authorization_jobs.md). ## Authorization Users -Summary of how authorization for Users are handeld [better visible](./authorization_users.md) displayed. - Developers information, see [github](https://github.com/SciCatProject/documentation/blob/master/Development/v4.x/backend/authorization/authorization_users.md). ## Authorization Proposals -Summary of how authorization for proposals are handeld [better visible](./authorization_proposals.md) displayed. - Developers information, see [github](https://github.com/SciCatProject/documentation/blob/master/Development/v4.x/backend/authorization/authorization_proposals.md). ## Authorization Intruments -Summary of how authorization for instruments are handeld [better visible](./authorization_instruments.md) displayed. - Developers information, see [github](https://github.com/SciCatProject/documentation/blob/master/Development/v4.x/backend/authorization/authorization_instruments.md). diff --git a/docs/datasets/PublishingAdvanced.md b/docs/datasets/PublishingAdvanced.md index 38909b7..b46da43 100644 --- a/docs/datasets/PublishingAdvanced.md +++ b/docs/datasets/PublishingAdvanced.md @@ -4,13 +4,16 @@ The previously described options to [publish datasets](Publishing.md) in SciCat ## Implementation workflow target -This diagram shows the essential steps in the workflow to be implemented. Please note, that SciCat datasets are *always* only *meta datasets*, SciCat has no direct to the storage system there is no default coupling to such systems. +Please note only metadata is stored in SciCat, there is no direct coupling between the software and the storage system. If you wish to publish both the metadata and data, please speak to your operator or consult the developer documentation for examples. ### 1. Create a list of selected datasets -User can select datasets to create a **dataset list**; more datasets can be added and removed in several sessions. He can cancel the process at any time. New will be that while examining single datasets he can directly add or remove them to or from the selection in the cart. +You can select datasets to create a **dataset list**; more datasets can be added and removed in several sessions. You can cancel the process at any time. New will be that while examining single datasets he can directly add or remove them to or from the selection in the cart. Before proceeding, you will be asked to verify the selection of datasets. You as user have finalized the dataset selection for which you want to register the dataset with a DOI. + +##### Internal review (to be implemented) +Some institutions may introduce an internal review step at this point: other authenticated user (as part of a dedicated reviewer-group) review the selected datasets. If OK, proceed to next form and the initial you can continue the DOI minting process. ### 2. Fill the form for this dataset selection -The user will be forwarded to a form where one can **provide metadata specific to this selection** which can e.g. match site specific information about e.g. grants, associated projects, etc. All selected datasets will be made public. You will be asked to verify the selection of datasets. Owners and Admins are allowed to update this form. Again this shall be possible within several sessions. +You will be forwarded to a form where you provide **metadata specific to this selection** already conform to DataCite metadata fields to match site specific information about e.g. grants, associated projects, etc. All selected datasets will be made public. Owners (and Admins) are allowed to update this form. Again, this shall be possible within several sessions. ### 3. Publish the selection After hitting button all selected datasets become publicly visible: not only the owner can view all the metadata of the data, date of creation, associated files names, location, PI, etc. This is **prerequisite** for DOI registration. diff --git a/docs/datasets/img/dataset_details.png b/docs/datasets/img/dataset_details.png new file mode 100644 index 0000000..93bd61f Binary files /dev/null and b/docs/datasets/img/dataset_details.png differ diff --git a/docs/datasets/img/datasets_SearchBar.png b/docs/datasets/img/datasets_SearchBar.png new file mode 100644 index 0000000..9befcf8 Binary files /dev/null and b/docs/datasets/img/datasets_SearchBar.png differ diff --git a/docs/datasets/img/datasets_detailedView.png b/docs/datasets/img/datasets_detailedView.png new file mode 100644 index 0000000..986bf50 Binary files /dev/null and b/docs/datasets/img/datasets_detailedView.png differ diff --git a/docs/datasets/img/datasets_filterNConditions_1.png b/docs/datasets/img/datasets_filterNConditions_1.png new file mode 100644 index 0000000..8afe064 Binary files /dev/null and b/docs/datasets/img/datasets_filterNConditions_1.png differ diff --git a/docs/datasets/img/datasets_filterNConditions_2.png b/docs/datasets/img/datasets_filterNConditions_2.png new file mode 100644 index 0000000..3ed816c Binary files /dev/null and b/docs/datasets/img/datasets_filterNConditions_2.png differ diff --git a/docs/datasets/index.md b/docs/datasets/index.md index fda3263..3a92635 100644 --- a/docs/datasets/index.md +++ b/docs/datasets/index.md @@ -1,21 +1,44 @@ # Datasets -SciCat datasets are sets of meta data and can include several files which e.g. comprise a self-contained measurement - which is fully customizeable during ingestion of meta data. Users can search, view, list the meta data of a dataset. +SciCat datasets are sets of metadata and can include several files which e.g. comprise a self-contained measurement - which is fully customizeable during ingestion of metadata. Users can search and view different formats (e.g. in tree, tables or as JSON) of the dataset and list them. -To group and tag datasets is depicted [here](grouping_tagging_ds.md). Datasets can also be issued to be **published**: either removing the restricted view or triggering the process of obtaining a DOI for the selected datasets, see description of [publication of SciCat datasets](Publishing.md). +## Features +A very handy feature is to **group and tag** datasets. Find [here](grouping_tagging_ds.md) more details how to group them using tags. -### How to query datasets +Datasets can also be selected for **several actions**: +One such action is the *publication* of that selection. For more details see [publication of SciCat datasets](Publishing.md). +Generally, actions depend on what is implemented at your site and can cover a wide range from +comprising them into a *new datacollection of a custom type* [(see advanced documentation)](../datasets/datasetTypes.md) to +using that selection of datasets to *run an analysis* on them. +## How to search for datasets +Datasets can be queried in several places: + +* The search bar at the top of the page provides a quick free text search. +* The filter & conditions column on the left allow you to customize your filters and conditions, adjust the filters to those that you find interesting and define your own conditions making use of your specific scientific metadata. + +The bar looks like this: +![search bar](img/datasets_SearchBar.png) + +Filtering by conditions can be applied through the option box on the left. + +![filterColumn](img/datasets_filterNConditions_1.png) + +If you chose "More Filters" a pop-up window appears where you can chose which of the filters you want to display. You can also add your own conditions as well (visible in the background under conditions): +![apply filters and conditions](../datasets/img/datasets_filterNConditions_2.png) + +## Dataset details +The main tab shows the details of a dataset. + +![example of dataset details page](img/dataset_details_PSI.png) ## Dataset file listing -Here is the view of files belonging to a dataset: Below the PID on the top, one finds the tab **Datafiles**: +A dataset can have several associated files to it. They can be listed by clicking on the tab **Datafiles** just right to the Details tab: ![list](img/dataset_details_filelist.png) - ## Dataset attachments -What kind of attachement can be saved? Will they be searchable? Can also other formats be attached than pngs? +Another tab is for the attachements of a dataset, e.g. PNG or TIFF images. -On the dataset details page, you can click on the Attachments tab ![Choose an image file, must be under 16 MB limit](img/dataset_attachments_PSI.png) Simply follow the instructions to upload an image. The size is restricted to be below 16 MB. @@ -30,13 +53,6 @@ Scientific meta data is shown in JSON under its section and looks like this: One can also get the JSON file via the swagger API. If set up, one can directly access the API endpoints of SciCat backend. Usually the address is in the form: ```my-scicat-instance.country/explorer```, swagger is accessible via the explorer. One needs to authenticate by copying the token from the GUI into the field **authorize**, then find the dataset of interest, by trying it out it will display you dataset and you can download it in JSON format. ## Edit Scientific meta data -// WARNING: this is the old text! -If enabled, fields in the scientific metadata can be modified and edited by the owner of the data by hitting the "Edit" Icon. The user can add,remove or change metadata fields, every change will create a new record in the databse with it's history. +If enabled, fields in the scientific metadata can be modified and edited by any member of the [Owner Group](../backendconfig/authorization/authorization_datasets.md) of the data by hitting the "Edit" Icon. The user can add, remove or change metadata fields, every change will create a new record in the databse with it's history [feature is soon available again from 2025-07-02]. ![Image edit metadata](img/editMetadata.png) - - -## New developments on dataset types -Generalize datatypes to remove restrictions of ```raw``` and ```derived``` types (difference was a set of dataset properties). - -[datasetTypes](datasetTypes.md) \ No newline at end of file diff --git a/docs/datasets/jobs.md b/docs/datasets/jobs.md new file mode 100644 index 0000000..3e14145 --- /dev/null +++ b/docs/datasets/jobs.md @@ -0,0 +1,6 @@ +# Archival and retrieval of experimental data + +SciCat can be setup to interconnect to your local storage system which allows you to do the following: +* Send datasets to your site's archive via a click of a button +* Retrieve your datasets asynchronously via a button click. +For more information please contact your site administrators. diff --git a/docs/index.md b/docs/index.md index dc746f4..d711027 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,4 +1,4 @@ # Welcome to SciCat Documentation -Find [**SciCat USERS Guide**](user-manual/index.md) or [**SciCat Operator's Guide**](operator-manual/index.md). -Developers can read long the ```READMEs``` in github of the [projects page](https://www.scicatproject.org) and in both guides as well. +Find [**SciCat USERS Guide**](user-guide/index.md) or [**SciCat Operator's Guide**](operator-guide/index.md). +Developers can read along the ```READMEs``` in github of the [projects page](https://www.scicatproject.org) and in both guides as well. diff --git a/docs/instruments/index.md b/docs/instruments/index.md index e69de29..4dcd95b 100644 --- a/docs/instruments/index.md +++ b/docs/instruments/index.md @@ -0,0 +1,3 @@ +## Instruments + +Instruments contains the metadata of the different instruments available at the facility. \ No newline at end of file diff --git a/docs/login/Dashboard.md b/docs/login/Dashboard.md index 1fdf32d..9aef31f 100644 --- a/docs/login/Dashboard.md +++ b/docs/login/Dashboard.md @@ -1,9 +1,27 @@ # Dashboard -The dashboard is the first page that you see when you are logged in. When set to datasets as main access point, it will show an overview of all datasets that you have access to. +SciCat's Dashboard or also sometimes called Landing Page is the first page that you see independent of whether you are logged in or not. If you want to login click *Sign in* on the top right button, see [here](./index.md) for more information. When set to datasets as main access point, it will show an overview of all datasets that you have access to. If you do not login you see those that are public. ![dashboard](img/dashboard.png) +SciCat offers now new features for viewing metadata as you like with adjustable columns. + +![dashboard_adjustableColumns](img/dashboard_adjustableColumns_rk.png) + +You can change the columns to be shown by chosing from the three right dots "Column setting" and select those you would like. You can also drag columns by hovering over dots that appear just next to the label, click and pull it where you want to place it, then release. + +![dashboard_newFeatures](img/dashboard_optionsPerColumn.png) + +You can + +1. sort columns (click on the name and pull) +2. adjust width of columns (left block of dots) +3. remove or add columns (selection from Column settings) +4. invert order of display (click arrow next to the name) +5. apply a filter directly on that dataset with various options ("contains", "equals", "startsWith", "endsWith", "empty", "notEmpty") and either add (+), or (||) and exclude (x) another filter. + +![Overall Menu](img/dashboard_filterOnColumns.png) + ## Menu access to different information pages You can always navigate to other parts of the application, simply by clicking on the user icon on the top right corner @@ -11,11 +29,11 @@ You can always navigate to other parts of the application, simply by clicking on ![Overall Menu](img/menu_dropdown.png) ## Finding Datasets -SciCat provides several possibilities for finding the right datasets. One can use the tob search bar, one can narrow down your selection by applying filters and/or conditions and the user can search on his scientific metadata as well. +SciCat provides several possibilities for finding the right datasets. You can use the top search bar, you can narrow down your selection by applying filters and/or conditions and the user can search on scientific metadata as well. ### Using Filters and Conditions -On the left one can apply most common filters. Currently there are +On the left you can apply most common filters. Currently there are 1. Location: location of creation of the dataset. 2. PID: Identifier of the dataset. @@ -29,20 +47,11 @@ The text fields provide an auto completion, which becomes visible as you type. You can click on the date calendar to select the start date and a second to select end date. Make sure you select 2 dates. -One can configure the selection of filters and add specific _conditions_. An example shows two additional conditions added: +You can configure the selection of filters and add specific _conditions_. An example shows two additional conditions added: ![filters](./img/dashboard_filters.png) -## Searching - -The text field at the top of the navigation bar allows you to search the metadata for any word contained in the metadata (but not arbitrary substrings). The search starts automatically when to start to type in this textfield, so better type fast ;-) - -## Configure table columns - -The cog wheel symbol on the top right allows to define the columns, that you want to see in the table - ## View Details - -To view a dataset simply click on it in the table and a more detailed view will load (this is covered in the next section) +To view a dataset simply click on it in the table and a more detailed view will load (this is covered in the datasets section) diff --git a/docs/login/img/dashboard.png b/docs/login/img/dashboard.png index 4d84bb3..e779983 100644 Binary files a/docs/login/img/dashboard.png and b/docs/login/img/dashboard.png differ diff --git a/docs/login/img/dashboard_adjustableColumns_rk.png b/docs/login/img/dashboard_adjustableColumns_rk.png new file mode 100644 index 0000000..f6f34c1 Binary files /dev/null and b/docs/login/img/dashboard_adjustableColumns_rk.png differ diff --git a/docs/login/img/dashboard_filterOnColumns.png b/docs/login/img/dashboard_filterOnColumns.png new file mode 100644 index 0000000..5e787ad Binary files /dev/null and b/docs/login/img/dashboard_filterOnColumns.png differ diff --git a/docs/login/img/dashboard_optionsPerColumn.png b/docs/login/img/dashboard_optionsPerColumn.png new file mode 100644 index 0000000..783d578 Binary files /dev/null and b/docs/login/img/dashboard_optionsPerColumn.png differ diff --git a/docs/login/index.md b/docs/login/index.md index ed26518..6383761 100644 --- a/docs/login/index.md +++ b/docs/login/index.md @@ -2,17 +2,14 @@ To get access to **all** the data, for which you have read access, you first have to login. Otherwise you can browse only public datasets, see [anonymous browsing](Anonymous.md). -To login hit the "Sign in" Icon at the top right corner. +To login hit the "Sign in" icon at the top right corner. ![Login to ESS](img/login.png) -There are two types of account associated with the DataCatalog: *Functional* and *User*. A *functional* account will primarily be used by software and system administrators to deal with backups and other tasks. - -*User* accounts are tied into the login system that is used by your institution, for example: Active Directory. You are able to log in to the system using the same credentials you use on that account. This process is called *authenitication* in IT tech terminology +User accounts are tied into the login system that is used by your institution, for example: Active Directory. You are able to log in to the system using the same credentials you use on that account. This process is called *authenitication* in IT tech terminology. When you login as a user your user management system will assign groups to the logged in user. Each dataset is also assigned to one such group (via the so called ownerGroup field), and you can view the datasets only, if you are member of the corresponding group. The logic that defines, what parts of the data you can see, is called "authorization" in IT terminology. The first page you'll see after login is the ["Dashboard"](Dashboard.md). Another example login page from PSI is here - ![Login to PSI](img/login-psi.png) diff --git a/docs/operator-manual/img/DacatDataflowV3.png b/docs/operator-guide/img/DacatDataflowV3.png similarity index 100% rename from docs/operator-manual/img/DacatDataflowV3.png rename to docs/operator-guide/img/DacatDataflowV3.png diff --git a/docs/operator-manual/img/job-assembler.png b/docs/operator-guide/img/job-assembler.png similarity index 100% rename from docs/operator-manual/img/job-assembler.png rename to docs/operator-guide/img/job-assembler.png diff --git a/docs/operator-manual/index.md b/docs/operator-guide/index.md similarity index 78% rename from docs/operator-manual/index.md rename to docs/operator-guide/index.md index c219c3e..a9f9f26 100644 --- a/docs/operator-manual/index.md +++ b/docs/operator-guide/index.md @@ -1,14 +1,21 @@ -# Welcome to SciCat Operator's Manual +# Welcome to SciCat Operator's Guide ## Overview +SciCat is a flexible metadata catalogue designed to be easily interfaced in to most existing infrastructure. The following guide will introduce the configuration required to integrate SciCat into common technologies. -Getting SciCat up and running at your site should be rather straight forward for a test deployment. However turning into a production ready system may involve a bit more work, because different existing systems will need to be interfaced to SciCat. +How to ingest metadata, set SciCat up to deploy it is best covered by understanding its core systems, backend and frontend, its features, configurations, and what else one could do to fully exploit all of SciCat's capabilities. -## Understanding the Components +SciCat consists of a backend application, that is connected to the database - a MongoDB - and a frontend client exposing database content through a GUI to a user. At large scale facilities SciCat handles about 30 PB of data. -For the subsequent sections it will be useful to have a "helicopter" overview of the various components that need to play together seamlessly. The following diagram shows these components and also shows potentially existing components at your site, that you would likely want to interface to SciCat. The specific diagram reflects essentially the situation at PSI as of Sept. 2020. Of course your situation may look different. The diagram should therefore be seen as an example, which you need to adapt to your situation. +## Features + +SciCat covers these core aspects in a flexible way: + +1. Searchable metadata fields, most common and highly specific ones. SciCat was developed by the PaNoSc community and has been successfully used more widely. This is because SciCat is highly configurable. +2. Provision of unique persistent identifiers not only for the internal catalogue, but also connecting to the global DOI system through e.g. ready pathway to publication via [DataCite](https://datacite.org/). + +SciCat is an open source project can can be developed in accordance with our (license)[https://github.com/SciCatProject/scicat-backend-next?tab=BSD-3-Clause-1-ov-file#readme]. -![ToDo: Updated schematic view of SciCat components](img/DacatDataflowV3.png) ## Up-to-date operator's information Generally, the [**scicatlive**](https://www.scicatproject.org/scicatlive/latest/) documentation contains an up-to-date information how to set up and run the system ```SciCat``` interfacing it with various external, site-specific services. For troublshooting issues, please refer [the User's Guide](../troubleshoot/index.md). @@ -45,9 +52,7 @@ See [here](https://github.com/SciCatProject/frontend/blob/master/SITE-LOGO-CONFI SciCat strength is to intergrate into almost any existing infrastructure because **messaging systems** can be easily interfaced to SciCat that take over the communication to other services and systems. -In particular RabbitMQ (used at PSI) and Apache Kafka are in use. Such systems can e.g. be used to interface to an tape archive system. To add the specific business logic you can e.g. add your own scripting layer. At PSI however a Node-RED based solution proved to be a stable and flexible platform for this purpose. Node-RED is a A NodeJS based visual programming tool to handle flows of data from one source to another. The following shows the Nod-RED flow used for communicating job requests to the PSI archive system. - -![Node-RED](img/job-assembler.png) +A detailed description of jobs in for the new backend can be found [here](https://github.com/SciCatProject/documentation/blob/master/Development/v4.x/backend/configuration/jobconfig.md). ### Different entry points to SciCat diff --git a/docs/operator/datasetsv4/index.md b/docs/operator/datasetsv4/index.md deleted file mode 100644 index 9fb1243..0000000 --- a/docs/operator/datasetsv4/index.md +++ /dev/null @@ -1,44 +0,0 @@ -# How to run new dataset endpoint in v4 - -For now one can run and play with the new version of dataset endpoints v4. Here is how to set it up: - -1. Pre-requisits: admin rights, git, docker, nodejs (v.20.18.2) and npm (v10.8.2). -2. For frontend to run, install angular like this: "npm install -g @angular" -3. Git clone frontend and backend repository. -4. Launch "npm install" in each dir by entering "npm install", respectively. -5. Configuration of backend: add "loggers.json", "functionalAccounts.json", -"proposalTypes.json", "datasetTypes.json" und ".env" files (there are examples named *.example). -6. Start MongoDB: I do it using docker container. Recipe is get the image, e.g. bitnami/mongodb:latest, attach volume to it, e.g. "mongodb", mount it, e.g. to /bitnami/mongodb, port 27017. Open in host on 27017. -7. Optional -8. Start backend: in dir of backend run "npm run start". After about 10s you should be able to view the APIs from "localhost:3000/explorer" in the browser. -9. Start frontend: in dir of frontend run "npm run start". After about 40s one should see under "localhost:4200" to SciCat frontend. - -1. Voraussetzungen: Adminrechte, Git, Docker, NodeJS (ich habe es jetzt -mit v.20.18.2 laufen) inkl. npm (bei mir v10.8.2). -2. Wenn Frontend laufen soll: Über npm angular installieren via "npm -install -g @angular". -3. Front- und Backend Repositories von GitHub klonen. -4. Jeweils im Verzeichnis von Backend und Frontend einmal "npm install" -um die Dependencies zu installieren. -5. Backendkonfiguration: Das Backend braucht fünf zusätzliche Dateien um -richtig zu laufen: "loggers.json", "functionalAccounts.json", -"proposalTypes.json", "datasetTypes.json" und ".env". Für alle davon ist -eine Beispieldatei schon vorhanden (die .env.example ist allerdings -Mist, ich habe mal meine momentane angehängt mit der es läuft). -6. MongoDB starten: Mache ich über einen Docker-Container. Rezept: Image -bitnami/mongodb:latest, Volumen "mongodb" anlegen und im Container auf -/bitnami/mongodb mounten, Port 27017 im Container auf 27017 im Host -öffnen. -7. (Optional?) MongoDB anlegen: Über Docker in den laufenden mongodb -Container einloggen. Auf der Shell "mongosh dacat" ausführen, das legt -die DB "dacat" an (andere name geht auch, dann muss das nur auch in der -.env anders!). Laut der alten Dokumentation muss man dann in der mongosh -den Befehl "db.Dataset.createIndex( { "$**" : "text" } )" ausführen, um -Textindexing zu bekommen. Nicht 100% sicher ob das noch aktuell ist, -musst du mal Max zu fragen. -8. Backend starten: Im Backendverzeichnis "npm run start", sollte dann -nach ca. 10s laufen. Testen, indem "localhost:3000/explorer" im Browser -geöffnet wird - wenn Swagger zu sehen ist, läuft es. -9. Frontend starten: Nachdem das Backend läuft, wieder "npm run start" -im Frontendverzeichnis ausführen. Frontend sollte nach Kompilierung (ca. -30s) auf "localhost:4200" zu sehen sein. \ No newline at end of file diff --git a/docs/operator/index.md b/docs/operator/index.md deleted file mode 100644 index 1ff4d93..0000000 --- a/docs/operator/index.md +++ /dev/null @@ -1,9 +0,0 @@ -# Welcome to SciCat Manual for Admins - -This is a short guide containing most of how SciCat can be operated. Many technical aspects are already described in the [scicatlive](https://www.scicatproject.org/scicatlive/latest/) documentation. - -We highlight in more detail aspects for someone exploring core SciCat software. - -* How to set up development versions of the new version of [dataset endpoints](datasetsv4/index.md). -* How to configure SciCat to mint DOIs. -* How to integrate SciCat with other systems. \ No newline at end of file diff --git a/docs/proposals/img/proposallist.png b/docs/proposals/img/proposallist.png new file mode 100644 index 0000000..c406e80 Binary files /dev/null and b/docs/proposals/img/proposallist.png differ diff --git a/docs/proposals/index.md b/docs/proposals/index.md index a397d75..4a63b90 100644 --- a/docs/proposals/index.md +++ b/docs/proposals/index.md @@ -1,3 +1,7 @@ ## Proposals -Here shall be a description of all meta data fields describing the proposal and how they are or can be related to datasets and samples. \ No newline at end of file +Proposals if entered can be listed as well (select from your login icon on top right *Proposals*). Now *parent proposals* can be handled and associated to your run number ID or beamtime id as *proposal ID* which is the child proposal of the parent proposal. + +With the new adjustable configurable table view one can select what to display and sort as well just like in datasets. + +![proposals](./img/proposallist.png) \ No newline at end of file diff --git a/docs/samples/img/sampleDetails.png b/docs/samples/img/sampleDetails.png new file mode 100644 index 0000000..b0739a2 Binary files /dev/null and b/docs/samples/img/sampleDetails.png differ diff --git a/docs/samples/img/sample_linkedFromDataset.png b/docs/samples/img/sample_linkedFromDataset.png new file mode 100644 index 0000000..2fbe350 Binary files /dev/null and b/docs/samples/img/sample_linkedFromDataset.png differ diff --git a/docs/samples/img/sample_popUp.png b/docs/samples/img/sample_popUp.png new file mode 100644 index 0000000..9142636 Binary files /dev/null and b/docs/samples/img/sample_popUp.png differ diff --git a/docs/samples/index.md b/docs/samples/index.md index 93e4378..b1424e0 100644 --- a/docs/samples/index.md +++ b/docs/samples/index.md @@ -1,4 +1,12 @@ ## Samples -A dscription of which meta data fields can be expected in SciCats sample description will follow. +If set up at your site you can list, search and view samples that have been entered into SciCat. This screenshot shows how to filter for specific characteristics of a sample: +![samples](./img/sample_popUp.png) + + +When selecting a such sample one sees the details +![samples](./img/sampleDetails.png) + +Once a sample entry exist in SciCat one can link datasets to it. It appears under "related information" +![samples](./img/sample_linkedFromDataset.png) diff --git a/docs/user-guide/index.md b/docs/user-guide/index.md new file mode 100644 index 0000000..895d0db --- /dev/null +++ b/docs/user-guide/index.md @@ -0,0 +1,42 @@ +# Welcome to SciCat Users Guide + +Scicat, a scientific metadata catalogue, allows your to explore your datasets through their metadata. SciCat has mechanisms to interact with the related datasets through its flexible integration with most storage systems. + +SciCat is a data management tool accompanying some critical steps during the entire data life cycle which are: getting an overview of datasets for data analysis, for re-analysis, for publishing datasets, and in particular for publication. + +Advantages of SciCat: + +* It can be integrated to almost any other service that has REST APIs. Therefore, site-specific applications can be easily integrated. +* The Data Model of SciCat forsees a schemaless fields for quite different use cases. This concept has been implemented for the main class, Datasets, but is extended to function in the same way for the other classes e.g. Proposlas, Samples, Intstruments and Published Data. +* Its components are based on OpenSource software projects and state of the art technologies using MongoDB as backbone database, nestjs as backend basis. + +In the past 5 years SciCat has undergone major improvements in key areas for better user experience and re-structuring to meet the various different needs of photon science labs. The collaboration has grown and governance will be soon established. + +## How to run SciCat +More detailed information on how to run scicat, see [scicatlive documentation](https://www.scicatproject.org/scicatlive/latest/). For more details on how to ingest, setup and deploy information from SciCat, see the [operator's guide](../operator-guide/index.md). + +## How to use SciCat +Once metadata is ingested into SciCat, the user can login and view, edit the metadata, list, filter and make a selection of interesting datasets using also scientific metadata. There are four main areas of SciCat where metadata can be explored: + +1. [Datasets](../datasets/index.md): Metadata in SciCat is ideally sorted according to a dataset. It can have several associated files attached which have the same metadata like a thumbnail or most common image files. +2. [Proposals](../proposals.md): are used to link datasets to the proposal under which beamtime was granted. +3. [Instruments](../instruments.md): Instruments is a library of instruments available at your institute, which can be linked to datasets. +4. [Samples](../samples.md): Here you can add metadata describing a physical sample which can be linked to it’s experimental use captured in datasets. + +For many the SciCat datasets are the entry point to the catalogue, but soon it will be possible to start with samples or published data records (registered metadata sets). +You can just browse what's in the catalogue for any published datasets. Else one can list all datasets that I either own or have access to. Here is how to find more on how to proceed: + +## How-Tos for Users (Quick-links) + +* [Login](../login/index.md) +* Search and find your data, see [Datasets How to query](../datasets/index.md#how-to-query-datasets) +* How to change some fields after ingestion +* How to view history of changes to a dataset +* How to [group and tag datasets](../datasets/grouping_tagging_ds.md). +* How to group and tag grouped datasets + +## A few more How-To's for users and site-admins +* Where to find the version of the deployed SciCat Frontend? Check [here](../about/operatorHowTos.md). + + + diff --git a/docs/user-manual/index.md b/docs/user-manual/index.md deleted file mode 100644 index 73a3d62..0000000 --- a/docs/user-manual/index.md +++ /dev/null @@ -1,40 +0,0 @@ -# Welcome to SciCat Users Manual - -This is a short guide to most common questions users of SciCat can face. First of all: What is SciCat? And what are its features, how can I use it? SciCat, a _science catalogue_, should serve you to find back your data through its **metadata**. Genrally all datasets in SciCat are a priori datasets of _metadata_. In a further step, SciCat can handle access to the actual the experimental data. - -SciCat is a bookkeeping tool accompanying some critical steps during the entire data life cycle which are: getting an overview of datasets for data analysis, for re-analysis, for publishing datasets, and in particular for publication. - -SciCat has several strong points: - -* It can be integrated to almost any other service that has REST APIs. Therefore, site-specific applications can be easily integrated. -* The Data Model of SciCat forsees a schemaless fields for quite different use cases. This concept has been implemented for the main class, Datasets, but is extended to function in the same way for the other classes e.g. Proposlas, Samples, Intstruments and Published Data. -* Its components are based on OpenSource software projects and state of the art technologies. - - -For more detailed information on how to run scicat, see [scicatlive documentation](https://www.scicatproject.org/scicatlive/latest/). For more details on how to ingest, setup and deploy information from SciCat, see the [site admin manual](operator/index.md). - -## Features: Quick links to How-To's for users - -You can just browse what's in the catalogue for any published datasets. Else one can list all datasets that I either own or have access to. Here is how to find more on how to proceed: - -* [Login](../login/index.md) -* Search and find your data, see [Datasets How to query](datasets/index.md#how-to-query-datasets) -* How to change some fields after ingestion -* How to view history of changes to a dataset -* How to [group and tag datasets](../datasets/grouping_tagging_ds.md). -* How to group and tag grouped datasets - -## A few more How-To's for users and site-admins -* Where to find the version of the deployed SciCat Frontend? Check [here](about/operatorHowTos.md). - - - -## Structure of SciCat - -These main classes determine the functionality of SciCat: - -1. [Datasets](datasets/index.md): This class is the most elaborated one. -2. [Proposals](proposals.md): are used to link datasets to the proposal under which beamtime was granted. -3. [Instruments](instruments.md): Depending on the science background `instruments` can mean something different. -4. [Samples](samples.md): -