diff --git a/files/export/.gitignore b/files/export/.gitignore old mode 100755 new mode 100644 diff --git a/files/processed_images/resized/.gitignore b/files/processed_images/resized/.gitignore old mode 100755 new mode 100644 diff --git a/files/uploads/.gitignore b/files/uploads/.gitignore old mode 100755 new mode 100644 diff --git a/openatlas/database/link.py b/openatlas/database/link.py index fad43fd51..4e3bb4bf7 100644 --- a/openatlas/database/link.py +++ b/openatlas/database/link.py @@ -174,11 +174,10 @@ def get_all_links_for_network( FROM model.link l JOIN model.entity de ON l.domain_id = de.id JOIN model.entity re ON l.range_id = re.id - WHERE de.openatlas_class_name IN %(system_classes)s - AND re.openatlas_class_name IN %(system_classes)s; + WHERE de.openatlas_class_name IN %(system_classes)s + AND re.openatlas_class_name IN %(system_classes)s; """, {'system_classes': tuple(system_classes)}) - # Todo: return list(g.cursor) would be better but triggers an API error return [dict(row) for row in g.cursor.fetchall()] @@ -202,5 +201,4 @@ def get_links_by_id_network(ids: list[int]) -> list[dict[str, Any]]: WHERE l.range_id IN %(ids)s OR l.domain_id IN %(ids)s; """, {'ids': tuple(ids)}) - # Todo: return list(g.cursor) would be better but triggers an API error return [dict(row) for row in g.cursor.fetchall()] diff --git a/openatlas/static/manual/.doctrees/environment.pickle b/openatlas/static/manual/.doctrees/environment.pickle index b97a95654..a8b1b97a3 100644 Binary files a/openatlas/static/manual/.doctrees/environment.pickle and b/openatlas/static/manual/.doctrees/environment.pickle differ diff --git a/openatlas/static/manual/.doctrees/faq.doctree b/openatlas/static/manual/.doctrees/faq.doctree index 23550c85c..c8225a152 100644 Binary files a/openatlas/static/manual/.doctrees/faq.doctree and b/openatlas/static/manual/.doctrees/faq.doctree differ diff --git a/openatlas/static/manual/.doctrees/features.doctree 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Tag: technical
-There are two main approaches how to deal with multiple projects or case -studies.
+There are two main approaches on how to deal with multiple projects or case +studies:
If every project has their own instance (installation) of OpenAtlas than you +
If every project has their own instance (installation) of OpenAtlas then you don’t have to worry about separating the data later. But it would also mean that data can’t be used together, at least not directly.
Tag: design decision
-In OpenAtlas it can be chosen if and when to make data public but:
+If and when data saved in OpenAtlas is shared can be chosen at any point, but:
All registered users have access to all model data
Either all data is made public via the API or none
Presentation sites can filter which data (e.g. which case study) to show +
Presentation sites can filter which data (e.g. which case study) is shown via the API
Showing images is a special case because it also depends on licenses and the IIIF server
There is no option (or plans to add one) to hide parts of the data for -specific users. Reasons for this is that it would conflict with one of our core -values (open) but there are also practical reasons, e.g. to avoid duplicates. -If a strict separation is needed, using multiple OpenAtlas instances would -likely be a better alternative.
+specific users as that conflicts with one of our core value - to be open. +Furthermore, there are practical reasons, e.g. to avoid duplicates. +If a strict separation is needed, using multiple OpenAtlas instances might +be a better solution.In case it is planned to share files with the public, e.g. at a presentation -site or a public archive, several criteria have to be met.
+If you plan on sharing files with the public, e.g. on a presentation +site or a public archive, several criteria have to be met:
The file must exist
A license has to be specified
It has to be marked with public sharing allowed
The file has to be marked with public sharing allowed
In case these criteria aren’t met, a file won’t be:
+In case these criteria aren’t met, a file:
Shared via the API
Won’t show up on presentation sites developed by the OpenAtlas team
Won’t be included in case the long time archiving -system ARCHE is used
Will not be shared via the API
Will not show up on presentation sites developed by the OpenAtlas team
Will not be included in long-term archiving via +ARCHE
But be aware that although the file itself won’t be shared, the file -information (e.g. filename) will still be available (e.g. shown on a +
Be aware that although the file itself won’t be shared, the file +information (such as filenames, etc.) will still be available (e.g. shown on a presentation site).
-At file -> list at the top you find counts for:
+At file -> list you find counts for:
public files
public files with a missing license
public files with a license but without creator (which many licenses require)
Public files
Public files with a missing license
Public files with a license but without creator (which many licenses require)
A free text entry field would lead to lots of unstructured data. Unstructured data can not be processed automatically and would result in it -not being presented nor searchable in the OpenAtlas system as well as in a -presentation site that presents your data. Therefore, we made the decision, not -to include free text types into the OpenAtlas system. Solutions to this problem -are very case specific, but you could:
+neither being presented nor searchable in the OpenAtlas system as well as in a +presentation site. Therefore, we made the decision, not to include free text +types into the OpenAtlas system. Solutions to this problem are very case +specific, but you could:use the already provided description fields to enter any type of free text -(keep in mind that this also comes with restrictions on how to present this -data at a presentation site)
create a new tree of project specific types for as many cases as possible +
Use the provided description field to enter any type of free text +(keep in mind that this also comes with restrictions on how to present the +data on a presentation site)
Create a new tree of project specific types for as many cases as possible and structure your data with them – for a step by step tutorial how to create new types, click here.
Another reason is that these formats might change over time. All in all it is -more important for us that acquired data is as interoperable, as long as +more important that acquired data is as interoperable for as long as possible.
-Of course the situation is different for e.g. presentation sites for OpenAtlas -data. There it would be possible to e.g. add manual formatted texts where -needed.
+For presentation sites and the alike it is possible to add e.g. manually +formatted texts, etc. where needed.
The data model specifies the structure in which the information is stored -within the database. The use of an ontology, for example, allows the data to be +within the database. The use of an ontology allows the data to be combined more easily with information from other projects and is consistent with the FAIR principles.
The OpenAtlas Model is based on the international standard of @@ -118,8 +118,8 @@
Types can be used to adapt for specific research topics
Reference Systems for -Linked Open Data (LOD)
Reference Systems help create Linked Open +Data (LOD)
Archaeological finds @@ -130,7 +130,7 @@
The user interface allows for easy and quick entry of information into the +
The user interface (UI) allows for easy and quick entry of information into the database, while the data is mapped in the background according to the specifications of the data model (see above). Due to the use of types, this can be designed @@ -188,8 +188,8 @@
The User Management Features allows the activation of users for the own -OpenAtlas instance. These can also be divided into different user groups with +
The User Management Features allows the activation of users for your +OpenAtlas instance. They can be divided into different user groups with different permissions. In addition, the user interface can be adapted to the user’s own preferences via settings.
The overview page can be reached when clicking on the logo at the upper left. -When logged in following is displayed:
+The overview page can be reached by clicking on the logo in the upper left +corner. When logged in following information is displayed:
An overview table of already entered entities
Links to manual, Model and Network visualization
Glabella (W = 3)
-2 to -0.7: female
The image annotation feature allows for marking areas on an image and adding -a text and/or link it to an entity. E.g. a person on a group picture or an -artifact at an excavation site image.
+a text and/or link to an entity. In that way a person in a group picture +or an artifact on an excavation photo can be linked to the entity in OpenAtlas.Prerequisite for image annotation is an enabled and configured IIIF server.
At a File detail view click on the Enable IIIF view button -below the image if it wasn’t converted already.
-Once the image was converted you can click on the Annotate link below the +
In a File’s detail view, click the Enable IIIF view button +below the image, if it is not converted already. +Once the image is converted click the Annotate link below the image and the annotation view will open in a new tab.
-In the image annotation view you can see the image in an IIIF viewer and a form -for new annotations and a list of already entered annotations with links to -edit or delete them.
+In the image annotation view you can see the image in an IIIF viewer as +well as a form for new annotations including a list of already saved +annotations. Links to edit or delete previous annotations are als porvided.
Form fields
IIIF image view - here you can use the rectangle draw button on the left -side to mark an area.
Annotation - you can enter a description here
Entity - you can link an entity here
IIIF image view - click the button on the left to draw a rectangle +to mark the desired area.
Annotation - enter a description
Entity - link to an entity
Be aware that the Entity selection only offers entities that are already -linked to the file. This is to guarantee that the entity is also linked via -the model (which the image annotation is not part of).
+linked to the file. This guarantees that each selectable entity is also +linked to the file via the model. Immage annotation does not create new +model links in the background!The interactive map (based on Leaflet) is a tool -to present and enter the location of places. PostGIS -is used for creating and manipulating spatial data.
+to present and enter a place’s location. +PostGIS is used for creating and manipulating +spatial data.With the magnifying glass icon in the upper left you can search for (current) -places at GeoNames.
+Press the magnifying glass icon on the left side to search for +a places. The search filters data on +GeoNames and provides a list of places with +the same name. Choosing the desired places allows to import the geonames ID +and/or the coordinates of said place into the OpenAtlas place form (see below).
With the icon a WKT text can be imported. +
With the icon WKT text can be imported. Clicking this button will open a new popup where a WKT geometry can be entered. If the geometry is valid, the draw geometry button will be enabled. By clicking this button the geometry will be drawn on the map and the respective @@ -139,33 +143,32 @@
When in insert or update mode of a place you have following options available -(can be combined):
+When in insert or update mode of a place you have the following options +(more than one can be used):
Set a marker/point at the position where the physical thing is located.
Draw a line connected to a physical objects spatial characteristics, e.g. -the course of a road.
Draw the shape of a physical thing if the precise extend is known.
Draw the area in which the physical thing is located. E.g. if its precise -shape is not known but known to be within a certain area.
Set a marker/point at the position where the physical thing is located
Draw a line connected to a physical object’s spatial characteristics, e.g. +the course of a road or the bed of a river
Draw the shape of a physical thing if the precise extend is known
Draw an area in which the physical thing is located with 100% certainty
The GeoNames ID field can either be manually entered or imported from a map -search result.
-The checkbox exact match can be used if there is a high -degree of confidence that the concepts can be used interchangeably. By default -it is a close match, which means that the concepts are sufficiently similar +
The GeoNames ID field can either be entered manually or imported +from the map’s search result
+Exact match should be used if there is a high degree of confidence that +the concepts can be used interchangeably. By default it is a +close match, which means that the concepts are sufficiently similar that they can be used interchangeably in some information retrieval applications. Please refer to SKOS for further information.
If you have the module map overlay activated in your Profile, added +
If the module map overlay is activated in the Profile settings, added overlays for places will be visible on the map by default and can be toggled -at map layer button at the upper right corner.
+with the map layer button at the upper right corner.To insert new overlays (only available for editors and admins) go to the view of a specific place. After adding an image file in the file tab you can click link in the overlay column to enter coordinates (Easting and Northing) for:
@@ -175,7 +178,7 @@With the integration of D3.js data can be visualized as -a network graph available at the Network visualization button at the -Overview or as an egocentric network at the entity detail view.
-Classic is the default but it can be switched to other types at the top of -the visualization pages.
+With the integration of D3.js, data can be visualized as +a network graph. The graph, specific for each OpenAtlas instance, is available +via the Network visualization button at the Overview or as an +egocentric network at the entity detail view.
+Three different layouts are provided. Classic is the default setting but +it can be switched to other types at the top of the visualization pages.
Default map zoom - define the lowest zoom level to include all +features in a Map view
Max map zoom - adjust how far you can zoom into a Map.
Show icons in tables - if activated small images of files are shown in tables
After then pressing the Radiocarbon dating button, you can add and/or edit +
After pressing the Radiocarbon dating button, you can add and/or edit the following information:
Laboratory ID - an alphanumerical abbreviation of the lab that conducted the analyses, e.g. VERA for Vienna Environmental Research Accelerator
Specimen ID - a numeric ID given to the sample by the conducting laboratory
Radiocarbon year - Result if the analysis in years, e.g. 1015
Radiocarbon year - Result of the analysis in years, e.g. 1015
Range - Accounts for the possible error of the measurement and is stated in the result as +/- value in years, e.g. +/- 30. In the form you only state the amount of years, adding +/- into the form field is not necessary
To allow quick navigation, even in a big data set, the global full-text search -can find entities containing the search term in their name or aliases. It is:
+To allow quick navigation even in big data sets, the global full-text search +can find entities containing the search term in their name or aliases. The +search is:
Not case sensitive, e.g. aDa lovelacE will find Ada Lovelace
Full text, e.g. da Love will find Ada Lovelace
Unaccented, e.g. Lovē will find Love and vice-versa
You can use % as a placeholder, e.g. Ada L%ce will +
Not case sensitive, so aDa lovelacE will find Ada Lovelace
Full text, therefore da Love will find Ada Lovelace
Unaccented, Lovē will find Love and vice-versa
You can use % as a placeholder, so Ada L%ce will find Ada Lovelace
Additionally, a refined advanced search can be used to filter the results -where more options are available:
+Additionally, an advanced search can be used to filter the results when more +than one option is available:
Only entities edited by me - show only entities which you have created or -edited.
Only entities edited by me - shows only entities which you have +created or edited.
Also search in description - searches in description and date comments
Classes - search only in selected classes, e.g. Place
Classes - searches only in selected classes, such as place or actor
Dates
This filter is only active if at least the from or to year is filled out.
If only a year is provide the from date will be YYYY-01-01, the to date will be YYYY-12-31
If only a year and a month is provided it will be the last of this month.
If only a year and a month is provided it will show data from the first +to the last day of the month
If the option Include dateless entities is checked, entities without -dates will be found too.
Because entities can have up to 4 date values (time span for begin and time span for end) they will be added to the result if at least one date meets the -criteria. E.g. a person that lived from 1540 to 1560 will be found when -the from year value is 1550.
+criteria. Therefore, a person that lived from 1540 to 1590 will be found +when the from year value is 1550. diff --git a/openatlas/static/manual/troubleshooting/display.html b/openatlas/static/manual/troubleshooting/display.html index 6f42630dd..a762c4f08 100644 --- a/openatlas/static/manual/troubleshooting/display.html +++ b/openatlas/static/manual/troubleshooting/display.html @@ -100,31 +100,34 @@This is a general topic in case there are display errors like elements are out -of place, missing or not working as intended. There can be many reasons for -these errors and they have probably nothing to do with you but here are some -suggestions you can try on your side to fix them.
+This is a general topic in case there are display errors such as out of place +elements, missing or not working items. Many reasons can cause errors +and a malfunction most likely was not caused by you but here are +some suggestions what you can try on your side to fix them.
Make sure your browser is up to date. We try to support all major browsers but -because OpenAtlas uses advanced features a current version may be required.
+due to OpenAtlas using advanced features a current version may be required.Sometimes browser cache (remember) older content. A refresh should solve this -problem. E.g. in Firefox you can do this with the F5 key.
+problem. For example, in Firefox this can be done by pressing the +F5 key.JavaScript is required for advanced features to work. In case you haven’t -activated JavaScript you should see a warning message at the top of the site.
+activated JavaScript in our browser settings, a warning message will be +displayed.If none of the above solutions work please report this bug. There is a -Feedback link on the start page after you logged in. It would be very +
If none of the above solutions work, please report the bug to us. There is a +Feedback link at the start page after you logged in. It would be very helpful if you provide which browser/version you are using and a screenshot -showing the problem.
+showing the problem. You can also go to +redmine directly and report the issue there.Here are some explanations for error codes you may encounter. Please let us know if you think you -encountered a bug.
+Here are some explanations for error codes you may encounter. Please let us +know if you think you encountered a bug. The best way to report an issue is +via out issuetracker at redmine
You are trying to access a page that you don’t have permissions for. E.g. trying to edit an entity -as user with a read only group. The user interface shouldn’t provide you with links to sites -that are restricted for your user. Maybe you used an obsolete link or bookmark.
+You are trying to access a page that you don’t have permissions to access. +This can happen if you try to edit an entity as user with read only +status. The user interface shouldn’t provide you with links to sites +that are restricted for your user, so maybe you used an obsolete link or +bookmark. If this happens regularly, please report the issue.
The site you requested cannot be found. Maybe you used an obsolete link or bookmark.
+The site you requested cannot be found. Maybe you used an obsolete link or +bookmark.
You see this message if you tried to access an entity with an id that doesn’t exist (anymore). -Maybe you used an obsolete link or bookmark.
+This message is displayed if you tried to access an entity with an ID that +doesn’t exist (anymore). Maybe you used an obsolete link or bookmark.
Here you find help and suggestions for common issues. In case this doesn’t solves the -problem please report the issue.
+Here you find help and suggestions for common issues. In case this doesn’t +solves the problem please report the issue.
Proceed according to the error message.
+Depending on the issue, please try the following solutions to log in.
You can activate the show password checkbox to see the entered password and make sure that the -problem isn’t keyboard related, e.g. capslock is turned on.
-You can request a new password when clicking -Forgot your password? which is located under login button if email was set up.
+You can activate the show password checkbox to see the entered password +and make sure that the problem isn’t keyboard related, e.g. if capslock is +turned on.
+You can request a new password by clicking the +Forgot your password? link. It is directly located underneath the login +button. This is only possible if an email address was provided in the +profile settings previously.
Either you misspelled the username or the user doesn’t exist (anymore).
-If there is a Forgot your password? link below the login you can request a new password with -the email you are registered with. With the new password you’ll also receive your username.
+If there is a Forgot your password? link below the login button you can +request a new password. The information will be sent to the provided email. +A new username is provided together with the password.
Your user was deactivated. If you think this to be a mistake please contact your project manager.
+Your user was deactivated. If you think this was done by mistake, please +contact your project manager.
For security reasons (e.g. automatic attacks) the login gets locked after a few failed attempts. -Number of failed attempts and minutes to wait until you can try again depend on project specific -settings but in most cases you can try again after a few minutes.
+For security reasons (e.g. automatic attacks) the login gets locked after a +few failed attempts. The number of failed attempts and minutes to wait until +you can try again depend on project specific settings. If you can’t try +again after a few minutes, please contact your project manager.
CIDOC based OpenAtlas shortcuts: OA8 (begins in) and OA9 (ends in)
-Date input fields in forms are initially hidden and can be shown with -clicking on Show beside the Date label.
-To manage uncertainty in time up to 4 dates can be used: a time span for the -beginning and a time span for the ending. You find detailed examples here: +
Date input fields in forms are initially hidden and can be shown after +clicking on the Show button next to the Date label.
+To manage uncertainty in time up to four dates can be used: a time span for the +beginning with start and end date as well as and a time span for the end, +also with a beginning and end date. Find detailed examples here: Time Spans
Exact date
-For example if you knew the exact birth of an actor you could enter -1356-12-23 in the first row.
+If you know the exact birth of an actor you could enter +1356-12-23 in the first row of the date field.
Time span
-If you are unsure e.g when a Church was destroyed you could use both end -dates. Chose a wide enough -span where you are sure it had happened, e.g. the fist decade of 1800.
-enter in the first end year: 1800
enter in the second end year: 1809
Missing days and months are filled out so that the result will be -1800-01-01 to 1809-12-31.
+If you are unsure when e.g. a Church was destroyed, you can use both end +dates to enter a timespan. Chose a wide enough range to make sure the event +lies in between those dates with 100% certainty. So, to record a date within +the fist decade of 1800, enter: +* 1800 into the first end row of the date field +* 1809 into the second end row of the date field
+Days and months are filled in automatically if not stated by you. The result +will therefor be 1800-01-01 to 1809-12-31.
Autocomplete dates
-If not an exact date was entered, the system automatically creates -a time span. For example, if only the first year is entered, it will be -converted to a timespan of this year. For example:
+If a date but not an exact date was entered into the form, the system +automatically creates a time span. For example, if only a year is +entered in the first row, a timespan of this year will be saved. +For example:
800 will generate: 800-1-1 to 800-12-31.
800-5 will generate 800-5-1 to 800-5-31
Year: -4713 to 9999 but not zero
Month: 1 to 12
Day: 1 to 31
Comment: a text field for additional information for begin or end
Comment: add additional information for begin or end
Additional fields if the time module is activated in Profile or -a time was already entered:
+Additional fields for hour, minute and second appear if the time module is +activated in the Profile or if that information was already +entered for that entity:
+Possible values:
Hour: 0 to 23
Minute: 0 to 59
A description can be searched for in the advanced Search.
Almost all special characters are supported like e.g. Cyrillic characters or -mathematical symbols.
Almost all special characters are supported like Cyrillic characters or +mathematical symbols for example.
There are no formatting options (except line breaks) to keep data usable for different systems.
Keep in mind that as much information as possible should be covered by +using types for facilitating presentation on a presentation site
Forms are used for data entry. asterisk. Required fields are marked with an asterisk *.
+Forms are used for data entry. Required fields are marked with an asterisk *.
The name field is one of the few required fields which are marked with an asterisk.
-It’s quite important since it is used to find entries in tables or with the global Search.
-Duplicate names are allowed but if they don’t differ in e.g. the standard type, it could be -difficult to find the right one in a table.
+The name field is one of the few required fields which are marked with an +asterisk. +It’s important to choose a fitting name for every entry as it is used to +find data in tables and within the global Search.
+Duplicate names are allowed but if they don’t differ in e.g. the standard +type, it will become difficult to differentiate them from each other.
diff --git a/openatlas/static/manual/ui/table.html b/openatlas/static/manual/ui/table.html index 0560a7987..143ba118b 100644 --- a/openatlas/static/manual/ui/table.html +++ b/openatlas/static/manual/ui/table.html @@ -92,19 +92,25 @@Tables are used to show multiple entries at a glance. To navigate quickly multiple tools are available:
+Tables are used to show multiple entries at a glance. To navigate quickly +multiple tools are available:
Sorting - click on the header to sort the entries, click a second time for invert sorting
Search - type into the search field on top right to filter entries containing the term
Paging - if there are multiple pages you can navigate with the buttons below
Mouse over - long names or descriptions that are cut off can be read with mouse over
Sorting - click on the header to sort entries, click a second time to +invert sorting
Search - type into the search field in the top right to filter entries +containing the search term
Paging - if there are multiple pages you can navigate with the buttons +below
Mouse over - long names or descriptions that are cut off can be read +with mouse over
You can configure the display of tables in your Profile
+You can configure the display of tables in your Profile +Available settings:
amount of entries per page
whether to show aliases
Amount of entries per page
Show aliases