Institute of Mathematics and Computer Science
European Bioinformatics Institute
User Guide
Version 2.05
AIMS
Accessing AIMS system
To access Assay Information Management System you need a valid login name and a
password. If you think that you should have access to this page, but don't have login
name/password you should contact the System Administrator.
Different user s might have different access rights . Currently acce ss rights are managed at
technology level (the user can access only these Technologies access to which have been
granted to him) and at entry ownership level - depending from ownership particular entries
could be available either fully or partially or be hidden for a particular user. Also the access
rights determine whether the user will be able to create new entries. If user has access to
several Technologies, his access rights for different Technologies might be different.
There are several pages or other functionality of the system that might be unavailable or
partially available to users without sufficient access rights.
Changing user settings
User settings page allows to modify a number of user-specific settings. The modified values
are activated immediately in the current session as well as saved and used in subsequent
sessions. The settings that currently can be modified are the following:
Page size. This value specifies the number of entries that are displayed in single page in
either of 1st level (Views), 2nd level (Samples), 3rd level (Assays) pages. The default value (if
not modified by user) depends from the configuration of particular AIMS instance.
Start with welcome page. This specifies whether after login in the system the first page that
is displayed is " W el co m e pa ge " . Th e main purpose of this pa g e is sh ow ing which user grou p is
used as default group in current session, and consequently, what access rights other users will
have to entries created by user within a particular session.
Default user group. This allows to change a user group that will be used as as default in
current session, and consequently, what access rights other users will have to entries created
within this particular session. The access rights specific to the selected default group are
shown in table below.
Change password. Allows user to change password.
Welcome page
Welcome page can be displayed as a first page after login in the system. Whether this is the
case depends from the settings of user account and can be modified by user by clicking on
User settings tab. In addition, the page will be unconditionally displayed to users with
administrator rights if there are some external tasks that need to be performed.
The main functionality of this page is the option to see and change if necessary the default
group that will be used in current session, and consequently, what access rights other users
will have to entries created within this particular session. The access rights specific to the
selected default group are shown in table below.
Study level
List of Studies page allows to view/edit/delete data either for all Studies currently in
database, which are attributed to particular Technology, or Studies contained within a
particular View (if Views are configured for the given Technology). If your access rights don't
allow to access a particular Experiment even in view only mode, only the value of Study ID will
be shown, all other values will be replaced by **.
Selection of Technology
If no Technology is selected, as a first step you must select a particular Technology you will be
working with. To do this, click on Select Technology tab, select a Technology from drop-down
list and click on Change button. Technology can be changed at later stage using Select
Technology tab. Note that when Technology is changed all settings made for this Technology
during the current session (such that configurations of Views/Study/Assays pages or filter
settings) are lost.
Creating/viewing/editing/deleting Studies
- To add a new Study to database click on New Study tab. If you are viewing Studies
attributed to one particular Study then new Study will be defined for that group. Otherwise the
new Study will be created together with a new Study.
- To edit data about a Study click on the corresponding edit icon
access rights one of the following icons will be shown instead:
in view only mode, you can also view data and supplementary files for the particular Study),
(the Edit dialog is available in view only mode, you cannot access data and supplementary
files),
- To create a new Study with the parameters copied from the existing one click on the
corresponding clone icon
will be replaced by
- To delete entry about a particular Study click on the corresponding edit icon
press Delete button. If there are Assays attributed to the given Study the button will be
replaced with * Delete. This allows deleting of Study and all Assays belonging to it. Since this
is a potentially dangerous operation, you will need to reconfirm the intention to delete as well
as to provide the exact number of Assays belonging to this Study.
- To change simultaneously the values of some properties for several Studies click on Batch
edit tab. You will have the option to select Studies for editing and then, after pressing Edit
Selected button, will be directed to edit dialog which allows to change properti e s of selected
Studies.
Add/Edit/View Study dialog allows you correspondingly to e nter data about a new Study or
to edit/view (depending of your access rights) data for already existing Study.
The values of Study Ids are generated automatically, these va lues depend from T echnology
and user who is creating Study. Ids of Studies are unique.
Data files and Supplementary files allow you to link to Study and upload data files obtained
from experiments as well as supplementary information files. Depending from AIMS
configuration you have the option of just uploading files from your local computer, or choice
between uploading files from your local computer or selection of files already pre-uploaded via
FTP. Depending from technology configuration you also may have the option to associate file
type with each of the files, however currently this is treated just as informal comment.
It is possible t o link several Data or Supplementar y files with each Study, howe ver you ne ed
to press Update button after linking each of the files and re-open Edit dialog for linking
(you don't have access to Study).
. If you don't have access rights to a particular Study, the icon
.
. If you have limited
(the Edit dialog is available
and then
another one.
Technically there is no difference between treatment of Data files and Supplementary files,
however it is recommended that Data files are used for files obtained from experiments and
Supplementary files for providing additional information which can't be entered via Edit dialog
fields.
The meaning of other fields hopefully should be self-apparent. The datatypes for each of the
fields are shown on the right side (position mouse over datatype names for some additional
information).
In Batch edit mode there is a checkbox for each of Studies' fields. Check the boxes for fields
values of which you wish to change. Fields are displayed in white, if its values for all Studies
selected for batch editing is the same, and gray if there are different values. Name fields
cannot be changed in Batch edit mode.
Navigation
To navigate to List of Assays page showing Ass ay s of a pa rti c ul ar S tudy click on
Associating Studies with Views
This functionality is available if Views are configured for the given Technology and Studies
associated with a particular View are currently listed.
To change which Studies are includes in a given View click on Define View tab. All Studies will
be listed with a checkbox on a right side (checked for Studies belonging to the given View).
You can freely modify the values of checkboxes and either click on OK Define View (the
Studies associated with this View will be redefined) or on link Cancel Define View (the previous
set of Studies for this View will be kept).
icon.
Batch edit
In Batch edit mode there is a checkbox for each of entries' fields. Check the ones you wish to
change for all entries in the batch. The fields left unchecked (displayed gray) can hold different
values for each entry and the checked ones (displayed white) will hold the changed value for
all entries.
Batch uploading
Upload 1st level (Studies) page allows to upload multiple entries from a single tab-
delimited file. The file must contain a header row with recognized column names (these
consist of a level prefix followed by ".", "Parameter group" (defined in Parameters table) and
the value corresponding to "Upload name" field in in Parameters table - e.g. Study.Software
details.Version) followed by rows corresponding to uploadable entries. Upload names of fields
that are configured in (defined in Common parameters table) are not configurable in Common
parameters table, but specified in "systemConst.xml" file (and in future will be shown in this
table in read-only mode). Usually these names consist only of two components, e.g. Study.ID.
Also, there is extended syntax options for columns describing uploadable files (see below).
Level prefixes (e.g. View, Study, Assay) are also specified in specified in "systemConst.xml"
file.
To obtain a correct header for a particular level, you can download tab-delimited files
containing only this header by clicking on Download ... header or Download ... he ader
(minimal) links; these will provide correspondingly either a header containing all recognized
column names, or a "minimal" he ader containing only names of mandatory columns.
There are three "checkbox" options that you can select for batch uploads at all levels:
- Generate identifiers automatically. If checked, automatic id generation of IDs will be
used and the corresponding column, e.g. Studies.ID, either ignored or disallowed (depending
from Allow unrecognized columns setting. ID generation will not work at 1st level (View), if
the ID generation at this level is not configured for a particular Technology. If unchecked,
column with IDs (e.g. Study.ID) is mandatory and it is required that IDs must be unique (but
see the next op ti o n ) .
- Allow duplicate rows. If checked, then entries with identical IDs are allowed in upload file,
however only a single (assume that randomly selected) entry will be uploaded in system.
Generally this option could be useful only in combination with unselected Generate identifiers
automatically and selected Allow unrecognized columns. The expected use case is upload i n g a
single file containing entries of all three levels - in this case the "whole collection" can be
uploaded by uplo ad i n g the same file corres po n d i n gl y a t 1s t, 2nd and 3rd level.
- Allow unrecognized columns. If checked, the upload file can contain arbitrary column
names that are not recognized by the system. The most typical usage could be uploading a file
with columns for all three AIMS levels (most of them of recognized only at their own level,
apart from parent level ID, which could be used also at child level).
In addition, at 2nd and 3rd levels there is a radio button allowing to specify one of the
following options:
- uploading all entries as child entries for parent entry shown (and selectable) in listbox;
- uploading each entry by specifying its own parent by its ID. In this case a column with
parent ID must be present in upload file (e.g. when uploading 3rd level entries (Assays) the
file must contain also column Study.ID);
- uploading each entry by specifying its own parent by its NAME. In this case a column with
parent NAME must be present in upload file (e.g. when uploading 3rd level entries (Assays)
the file must contain also column Study.NAME).
At 2nd level (Studies) there is also a checkbox Upload under view that activates/deactivates
radio button area. If deactivated, the entries will not be made children of any 1st level entry.
Note that whilst there is many-to-many relationship between 1st and 2nd level entries, via
data upload it is possible to make a 2nd level entry a child only of one 1st level entry.
Locations of upload files.
In all situations the page will contain the following two Browse buttons:
- Parameter file. This allows you to browse your local file system and select tab-delimited file
for upload.
- Local zipped data. This allows to pr ovide a zipped arc hi v e con t ai n ing all the files th at ar e
referenced in parameter file (if any). This ZIP archive is also uploaded form your local file
system. Whilst technically this is a simplest option for file upload, http protocol might impose
severe limitation of archive size that can be uploaded in this way.
If the system and you access rights are configured for pre-uploading files via FTP, two
additional options will be provided:
- FTP zipped data. Instead of uploading ZIP archive from your local system, you can browse
for archives that are already pre-uploaded on the server.
- FTP directory. This provides a similar pre-uploading option, however in this case you have
to specify a pre-uploaded directory containing all the referenced files. This option may be
more convenient for very large files that are hard to pack in a single archive. A notable
difference from the previous option is that in this case you shouldn't reference the same file
more than once. Ignoring this will result in a partially corrupt upload, requiring substantial
manual correction!
If data/supplementary files are pre-uploaded via FTP, there will be some delay before Assays
will be available for editing (
will be shown instead of edit icon). (Edit dialogs still will be
available for users with administrator rights, although note that data files still will not be
copied into repository and changi ng file references are likely to cause errors.) If icon is
shown, this means that there have been some problems with copying data and supplementary
files.
Referencing data and supplementary files.
The column names in header for referencing files that have to be uploaded are defined in
"systemConst.xml" file and will be shown in complete header obtainable via Download ...
header link. E.g., the column names might be Study.DATA_F, Study.DF_TYPE for data files,
and Study.SUPPL_F, Study.SF_TYPE for supplementary (protocol) files. The following features
have to be taken into account:
- columns for data or supplementary files will only be available (or recognized), if linking of
files to entries is configured for particular Collection and particular level;
- the file name (given e.g. in Study.DATA_F) must contain a full path to file either in ZIP
archive or in pre-u ploaded directory .
- the file type (given e.g. in Study.DF_TYPE) is a memo field describing the file. The list of
recognized values can be checked in Edit dialog that corresponds to uploaded entries (there
could be none).
- there is extended syntax allowing to upload multiple files for a single entry. The names of
columns that reference files can contain additional suffix of the form #file_number, where
"file_number" is an arbitrary string which distinguishes different columns. E.g. to upload two
files for a single entry two columns either headers Study.DATA_F#1, Study.DATA_F#2, or
headers Study.DATA_F#SS, Study.DATA_F#17 could be used. The same suffixes can be used
to specify corresponding file types, e.g. Study.DF_TYPE#1, Study.DF_TYPE#2.
Data Export and Transfer
Both data and metadata export (i.e. request made by user's specifications) and data/metadata
transfer (predefined export to a particular) data warehouse are accessible from the same tab
Data export/transfer. To access it from Views/Studies/Assays view pages, first click on Export
tab, select the entries you wish to export and click on Data export/transfer tab.
Depending from technology conf iguration and your access rights a page with a nonempty
subset from the following three sections will be displayed.
Data transfer (transfer name)
This allows to transfer selected entries to data warehouse for which such transfer is configured
for particular technology. Usually each entry should be transfered just once, thus transfered
entries are flagged and although a repeated transfer of flagged entries is possible, a warning
will be issued before doing so.
Note that configuration of data transfer for a given technology makes this option available only
from a single AIMS level (either from Views, Studies or Assays.
The only configurable option in this section is a field for entering email - in this case the
processing program will send the updates of processing status of transfers to this address.
Apart from that, a list of configuration files used for metadata transfer as well as a list of
transferred higher level entries (with num b e r of their children) are shown (depending from the
configuration a transfer may include either metadata or datafile transfer or both).
There is a choice to request transfer by pressing Transfer button and cancelling the operation.
When transfer has been requested the corresponding entries will be marked for processing
and files will be transferred later by an external program. The following flags will be used to
mark entries:
successfully completed),
the actual data transfer has failed, or data warehouse ha s reported tha t ther e are pr obl ems
(transfer has been requested), (the actual transfer of data has been
(a successful reception of data has been confirmed), (either
with transferred files). Some of these flags may not be available for soma data transfer
configurations.
Metadata export
This allows to export metadata according to configuration that is specified by XML template.
According from you access rights there may be only option to select from Configuration files
provided by system administrator, or also an option to Upload your own configuration file.
The syntax of configuration file is described in a separate document, but it allows to configure
meta data export in XML file in rather flexible format. Export can include metadata from the
aims AIMS level from which it has been requested, from all child levels as well as from all
SIMS levels that are referenced from these entries.
Export file can be generated in two formats: XML (native format) and TSV (a tab delimited file
that is obtained from "flattening" native XML file).
Data export
This allows to export data and supplementary files. For the option to functional you must
additionally setup the options how the data files will be delivered. This is done via XML
configuration file that should be set up by system administrator.
There are two options how transfers is being made (and these should be specified in
configuration file mentioned above): sending of files to FTP to a server of your choice (in this
case you should provide to administrator server location and login details), and copying files
on the same server to different directory (e.g. your account home directory). The configurable
options in this section are: providing Export name (this shoul d be obtained from administrator
and will be used to recognize that export is initiated by you and ned to be delivered to your
location) and email address for feedback (an email will be sent to this address after the export
will be completed). After the export is requested, the corresponding entries will be marked for
processing and files will be exported later by an external program.
Directories of XML configuration files
The root directory of configuration files is defined in web.xml file by <context-param> entry
data_transfer_configuration.directory. Within this directory the location of configuration
files are as follows:
Metadata export configuration files:
exports/[technology directory]/l1 (export at Assays level),
exports/[technology directory]/l2 (export at Studies level),
exports/[technology directory]/l3 (export at Views level),
where [technology directory] is defined by FTP directory entry in Technologies table.
Date transfer configuration files:
transfers/[technology directory]/[transfer directory],
where [technology directory] is defined as above and [transfer directory] corresponds to Data
directory entry in Transfer types table.
Assay level
List of Assays page allows to view/edit/delete data either for all Assays currently in
database, which are attributed to particular Technology, or Assays attributed to particular
Experiment. If your access rights don't allow to access a particular Assay even in view only
mode, only the value of Assay ID will be shown, all other values will be replaced by **.
Selection of Technology
If no Technology is selected, as a first step you must select a particular Technology you will be
working with. To do this, click on Select Technology tab, select a Technology from drop-down
list and click on Change button. Technology can be changed at later stage using the same
Select Technology tab. Note that when Technology is changed all se ttings made for this
Technology during the current session (such that configurations of Study/Experiment/Assay
pages or filter settings) are lost.
Creating/viewing/editing/deleting Assays
- To add a new Assay to database click on New Assay tab. If you are viewing Assays attributed
to one particular Experiment then new Assay will be defined for that group. Otherwise the new
Assay will be created together with a new Experiment.
- To edit data about a Assay click on the corresponding edit icon
access rights one of the following icons will be shown instead:
in view only mode, you can also view data and supplementary files for the particular Assay),
(the Edit dialog is available in view only mode, you cannot access data and supplementary
files),
- To create a new Assay with the parameters copied from the existing one click on the
corresponding clone icon
will be replaced by
- To delete entry about a particular Assay click on the corresponding edit icon
press Delete button.
- To change simultaneously the values of some properties for several Assays click on Batch
edit tab. You will have the option to select Assays for editing and then, after pressing Edit
Selected button, will be directed to edit dialog which allows to change properti e s of selected
Assays.
Add/Edit/View Assay dialog allows you correspondingly to enter data about a new Assay or
to edit/view (depending of your access rights) data for already existing Assay.
The values of Assay Ids are generated autom atically, these values depend from Technology,
Experiment and user who is creating Assay. Ids of Assays attributed to a particular Experiment
will be unique.
The Aliquot field should either be filled by using the prompting button (if available) and
selecting the referenced Aliquot from the list (in case when multiple Aliquots will be selected,
several Assays, one for each Aliquot, will be created); or can be filled with arbitrary string
value (including empty) if prompting button is unavailable. The requirement of Aliquot
prompting depends from AIMS configuration.
Data files and Supplementary files allow you to link to Assay and upload data files obtained
from experiments as well as supplementary information files. Depending from AIMS
configuration you have the option of just uploading files from your local computer, or choice
between uploading files from your local computer or selection of files already pre-uploaded via
FTP. Depending from technology configuration you also may have the option to associate file
(you don't have access to Assay).
. If you don't have access rights to a particular Assay, the icon
.
. If you have limited
(the Edit dialog is available
and then
type with each of the files, however currently this is treated just as informal comment.
It is possible t o link several Data or Supplementary files with each Assay, however you need
to press Update button after linking each of the files and re-open Edit dialog for linking
another one.
Technically there is no difference between treatment of Data files and Supplementary files,
however it is recommended that Data files are used for files obtained from experiments and
Supplementary files for providing additional information which can't be entered via Edit dialog
fields.
The meaning of other fields hopefully should be self-apparent. The datatypes for each of the
fields are shown on the right side (position mouse over datatype names for some additional
information).
Batch edit
In Batch edit mode there is a checkbox for each of Assays' fields. Check the boxes for fields
values of which you wish to change. Fields are displayed in white, if its values for all Assays
selected for batch editing is the same, and gray if there are different values. Name and Aliquot
fields cannot be changed in Batch edit mode.
Batch uploading
Upload Assays page allows to upload multiple entries from a single tab-delimited file. The file
must contain a header row with recognized column names (these consist of a level prefix
followed by ".", "Parameter group" (defined in Parameters table) and the value corresponding
to "Upload name" field in in Parameters table - e.g. Stu dy .Softwa re details. Version) foll owed
by rows corresponding to uploadable entries. Upload names of fields that are configured in
(defined in Common parameters table) are not configurable in Common parameters table, but
specified in " systemConst.xml" file (and in future will be sh own in this table in read-only
mode). Usually these names consist only of two components, e.g. Study.ID. Also, there is
extended syntax options for columns describing uploadable files (see below). Level prefixes
(e.g. View, Study, Assay) are also specified in specified in "systemConst.xml" file.
To obtain a correct header for a particular level, you can download tab-delimited files
containing only this header by clicking on Download ... header or Download ... he ader
(minimal) links; these will provide correspondingly either a header containing all recognized
column names, or a "minimal" he ader containing only names of mandatory columns.
There are three "checkbox" options that you can select for batch uploads at all levels:
- Generate identifiers automatically. If checked, automatic id generation of IDs will be
used and the corresponding column, e.g. Studies.ID, either ignored or disallowed (depending
from Allow unrecognized columns setting. ID generation will not work at 1st level (View), if
the ID generation at this level is not configured for a particular Technology. If unchecked,
column with IDs (e.g. Study.ID) is mandatory and it is required that IDs must be unique (but
see the next op ti o n ) .
- Allow duplicate rows. If checked, then entries with identical IDs are allowed in upload file,
however only a single (assume that randomly selected) entry will be uploaded in system.
Generally this option could be useful only in combination with unselected Generate identifiers
automatically and selected Allow unrecognized columns. The expected use case is upload i n g a
single file containing entries of all three levels - in this case the "whole collection" can be
uploaded by uplo ad i n g the same file corres po n d i n gl y a t 1s t, 2nd and 3rd level.
- Allow unrecognized columns. If checked, the upload file can contain arbitrary column
names that are not recognized by the system. The most typical usage could be uploading a file
with columns for all three AIMS levels (most of them of recognized only at their own level,
apart from parent level ID, which could be used also at child level).
In addition, at 2nd and 3rd levels there is a radio button allowing to specify one of the
following options:
- uploading all entries as child entries for parent entry shown (and selectable) in listbox;
- uploading each entry by specifying its own parent by its ID. In this case a column with
parent ID must be present in upload file (e.g. when uploading 3rd level entries (Assays) the
file must contain also column Study.ID);
- uploading each entry by specifying its own parent by its NAME. In this case a column with
parent NAME must be present in upload file (e.g. when uploading 3rd level entries (Assays)
the file must contain also column Study.NAME).
At 2nd level (Studies) there is also a checkbox Upload under view that activates/deactivates
radio button area. If deactivated, the entries will not be made children of any 1st level entry.
Note that whilst there is many-to-many relationship between 1st and 2nd level entries, via
data upload it is possible to make a 2nd level entry a child only of one 1st level entry.
Locations of upload files.
In all situations the page will contain the following two Browse buttons:
- Parameter file. This allows you to browse your local file system and select tab-delimited file
for upload.
- Local zipped data. This allows to pr ovide a zipped arc hi v e con t ai n ing all the files th at ar e
referenced in parameter file (if any). This ZIP archive is also uploaded form your local file
system. Whilst technically this is a simplest option for file upload, http protocol might impose
severe limitation of archive size that can be uploaded in this way.
If the system and you access rights are configured for pre-uploading files via FTP, two
additional options will be provided:
- FTP zipped data. Instead of uploading ZIP archive from your local system, you can browse
for archives that are already pre-uploaded on the server.
- FTP directory. This provides a similar pre-uploading option, however in this case you have
to specify a pre-uploaded directory containing all the referenced files. This option may be
more convenient for very large files that are hard to pack in a single archive. A notable
difference from the previous option is that in this case you shouldn't reference the same file
more than once. Ignoring this will result in a partially corrupt upload, requiring substantial
manual correction!
If data/supplementary files are pre-uploaded via FTP, there will be some delay before Assays
will be available for editing (
will be shown instead of edit icon). (Edit dialogs still will be
available for users with administrator rights, although note that data files still will not be
copied into repository and changi ng file references are likely to cause errors.) If icon
is
shown, this means that there have been some problems with copying data and supplementary
files.
Referencing data and supplementary files.
The column names in header for referencing files that have to be uploaded are defined in
"systemConst.xml" file and will be shown in complete header obtainable via Download ...
header link. E.g., the column names might be Study.DATA_F, Study.DF_TYPE for data files,
and Study.SUPPL_F, Study.SF_TYPE for supplementary (protocol) files. The following features
have to be taken into account:
- columns for data or supplementary files will only be available (or recognized), if linking of
files to entries is configured for particular Collection and particular level;
- the file name (given e.g. in Study.DATA_F) must contain a full path to file either in ZIP
archive or in pre-u ploaded directory .
- the file type (given e.g. in Study.DF_TYPE) is a memo field describing the file. The list of
recognized values can be checked in Edit dialog that corresponds to uploaded entries (there
could be none).
- there is extended syntax allowing to upload multiple files for a single entry. The names of
columns that reference files can contain additional suffix of the form #file_number, where
"file_number" is an arbitrary string which distinguishes different columns. E.g. to upload two
files for a single entry two columns either headers Study.DATA_F#1, Study.DATA_F#2, or
headers Study.DATA_F#SS, Study.DATA_F#17 could be used. The same suffixes can be used
to specify corresponding file types, e.g. Study.DF_TYPE#1, Study.DF_TYPE#2.
Data Export and Transfer
Both data and metadata export (i.e. request made by user's specifications) and data/metadata
transfer (predefined export to a particular) data warehouse are accessible from the same tab
Data export/transfer. To access it from Views/Studies/Assays view pages, first click on Export
tab, select the entries you wish to export and click on Data export/transfer tab.
Depending from technology conf iguration and your access rights a page with a nonempty
subset from the following three sections will be displayed.
Data transfer (transfer name)
This allows to transfer selected entries to data warehouse for which such transfer is configured
for particular technology. Usually each entry should be transfered just once, thus transfered
entries are flagged and although a repeated transfer of flagged entries is possible, a warning
will be issued before doing so.
Note that configuration of data transfer for a given technology makes this option available only
from a single AIMS level (either from Views, Studies or Assays.
The only configurable option in this section is a field for entering email - in this case the
processing program will send the updates of processing status of transfers to this address.
Apart from that, a list of configuration files used for metadata transfer as well as a list of
transferred higher level entries (with num b e r of their children) are shown (dpending from the
configuration a transfer may include either metadata or datafile transfer or both).
There is a choice to request transfer by pressing Transfer button and cancelling the operation.
When trasfer has been requested the corresponding entries will be marked for processing and
files will be transfered later by an external program. The f ollowing flags will be used to mark
entries:
successfully completed),
the actual data transfer has failed, or data warehouse ha s re porte d that ther e are pr obl ems
with transferred files). Some of these flags may not be available for soma data transfer
configurations.
Metadata export
This allows to export metadata according to configuration that is specified by XML template.
According from you access rights there may be only option to select from Configuration files
provided by system administrator, or also an option to Upload your own configuration file.
The syntax of configuration file is described in a separate document, but it allows to configure
meta data export in XML file in rather flexible format. Export can include metadata from the
aims AIMS level from which it has been requested, from all child levels as well as from all
SIMS levels that are referenced from these entries.
Export file can be generated in two formats: XML (native format) and TSV (a tab delimited file
that is obtained from "flattening" native XML file).
Data export
This allows to export data and supplementary files. For the option to functional you must
(transfer has been requested), (the actual transfer of data has been
(a successful reception of data has been confirmed), (either
additionally setup the options how the data files will be delivered. This is done via XML
configuration file that should be set up by system administrator.
There are two options how tranbfe r s is bei n g m a de ( a n d th e s e shou ld be specified in
configuration file mentioned above): sending of files bu FTP to a server of your choice (in this
case you should provide to administrator server location and login details), and copying files
on the same server to different directory (e.g. your account home directory). The configurable
options in this section are: providing Export name (this shoul d be obtained from administrator
and will be used to recognize that export is initiated by you and ned to be delivered to your
location) and emaila ddress for feedback (an email will be sent to this address after the export
will be completed). After the export is requested, the corresponding entries will be marked for
processing and files will be exported later by an external program.
Directories of XML configuration files
The root directory of configuration files is defined in web.xml file by <context-param> entry
data_transfer_configuration.directory. Within this directory the location of configuration
files are as follows:
Metadata export configuration files:
exports/[technology directory]/l1 (export at Assays level),
exports/[technology directory]/l2 (export at Studies level),
exports/[technology directory]/l3 (export at Views level),
where [technology directory] is defined by FTP directory entry in Technologies table.
Date transfer configuration files:
transfers/[technology directory]/[transfer directory],
where [technology directory] is defined as above and [transfer directory] corresponds to Data
directory entry in Transfer types table.
View level
List of Views page allows to vie w / e di t/de lete data eith er f or al l Vi ews currently in database,
which are attributed to particular Technology. This page is available only if Views are
configured for the given Technology. If your access rights don't allow to access a particular
View even in view only mode, only the value of View ID will be shown, all other values will be
replaced by **.
There is an important difference between Views and Studies/Assays levels. Whilst there is a
hierarchical one-to-many relation between Studies and Assays - each Assay belongs to exactly
one Study and will be deleted, if that Study will be deleted, there are possible many-to-many
relations between Views and Studies and Studies are not affected by creation or deletion of
Views. The association between Views and Studies are defined from List of Views page. For
more information see First level (Studies) help page.
Selection of Technology
Generally List of Views is available only if a technology is already selected. Technology can
be changed at later stage using the same Select Technology tab, selecting a Technology from
drop-down list and clicking on Change button. Note that when Technology is changed all
settings made for this Technology during the current session (such that configurations of
Views/Studies/Assays pages or filter settings) are lost.
Creating/viewing/editing/deleting Views
- To add a new View to database click on New View tab.
- To edit data about a View click on the corresponding edit icon
rights one of the following icons will be shown instead:
only mode, you can also view data and supplementary files for the particular View),
Edit dialog is available in view only mode, you cannot access data and supplementary files),
(you don't have access to View).
- To create a new View with the parameters copied from the existing one click on the
corresponding clone icon
be replaced by
- To delete entry about a particular View click on the corresponding edit icon
press Delete button. If there are Assays attributed to the given View the button will be
replaced with * Delete. This allows deleting of View and all Assays belonging to it. Since this is
a potentially dangerous operation, you will need to reconfirm the intention to delete as well as
to provide the ex ac t nu mbe r of Assays belongin g to thi s Vie w .
Add/Edit/View View dialog allows you correspondingly to enter data about a new View or to
edit/view (depending of your access rights) data for already existing View.
The values of View Ids are generated automatically, these values depend from Technology and
user who is creating View. Ids of Views are unique.
Data files and Supplementary files allows you to link to View and upload data files obtained
from Views as well as supplementary information files. Depending from AIMS configuration
you have the option of just uploading files from your local computer, or choice between
uploading files from your local computer or selection of files already pre-uploaded via FTP.
Depending from technology configuration you also may have the option to associate file type
with each of the files, however currently this is treated just as informal comment.
It is possible to link several Data or Supplemen tary files with each View, however you need to
press Update button after li nking each of the files and re - ope n Edit dialog for linkin g an other
one.
.
. If you don't have access rights to a particular View, the icon will
(the Edit dialog is available in view
. If you have limited access
(the
and then
Technically there is no difference between treatment of Data files and Supplementary files,
however it is recommended that Data files are used for files obtained from Views and
Supplementary files for providing additional information which can't be entered via Edit dialog
fields.
The meaning of other fields hopefully should be self-apparent. The datatypes for each of the
fields are shown on the right side (position mouse over datatype names for some additional
information).
Navigation
To navigate to List of Studies page showing Studies associated with a particular View click on
icon.
Batch edit
In Batch edit mode there is a checkbox for each of entries' fields. Check the ones you wish to
change for all entries in the batch. The fields left unchecked (displayed gray) can hold different
values for each entry and the checked ones (displayed white) will hold the changed value for
all entries.
Batch upload
Upload Views page allows to upload multiple entries from a single tab-delimited file. The file
must contain a header row with recognized column names (these consist of a level prefix
followed by ".", "Parameter group" (defined in Parameters table) and the value corresponding
to "Upload name" field in in Parameters table - e.g. Stu dy .Softwa re details. Version) foll owed
by rows corresponding to uploadable entries. Upload names of fields that are configured in
(defined in Common parameters table) are not configurable in Common parameters table, but
specified in " systemConst.xml" file (and in future will be sh own in this table in read-only
mode). Usually these names consist only of two components, e.g. Study.ID. Also, there is
extended syntax options for columns describing uploadable files (see below). Level prefixes
(e.g. View, Study, Assay) are also specified in specified in "systemConst.xml" file.
To obtain a correct header for a particular level, you can download tab-delimited files
containing only this header by clicking on Download ... header or Download ... he ader
(minimal) links; these will provide correspondingly either a header containing all recognized
column names, or a "minimal" he ader containing only names of mandatory columns.
There are three "checkbox" options that you can select for batch uploads at all levels:
- Generate identifiers automatically. If checked, automatic id generation of IDs will be
used and the corresponding column, e.g. Studies.ID, either ignored or disallowed (depending
from Allow unrecognized columns setting. ID generation will not work at 1st level (View), if
the ID generation at this level is not configured for a particular Technology. If unchecked,
column with IDs (e.g. Study.ID) is mandatory and it is required that IDs must be unique (but
see the next op ti o n ) .
- Allow duplicate rows. If checked, then entries with identical IDs are allowed in upload file,
however only a single (assume that randomly selected) entry will be uploaded in system.
Generally this option could be useful only in combination with unselected Generate identifiers
automatically and selected Allow unrecognized columns. The expected use case is upload i n g a
single file containing entries of all three levels - in this case the "whole collection" can be
uploaded by uplo ad i n g the same file corres po n d i n gl y a t 1s t, 2nd and 3rd level.
- Allow unrecognized columns. If checked, the upload file can contain arbitrary column
names that are not recognized by the system. The most typical usage could be uploading a file
with columns for all three AIMS levels (most of them of recognized only at their own level,
apart from parent level ID, which could be used also at child level).
In addition, at 2nd and 3rd levels there is a radio button allowing to specify one of the
following options:
- uploading all entries as child entries for parent entry shown (and selectable) in listbox;
- uploading each entry by specifying its own parent by its ID. In this case a column with
parent ID must be present in upload file (e.g. when uploading 3rd level entries (Assays) the
file must contain also column Study.ID);
- uploading each entry by specifying its own parent by its NAME. In this case a column with
parent NAME must be present in upload file (e.g. when uploading 3rd level entries (Assays)
the file must contain also column Study.NAME).
At 2nd level (Studies) there is also a checkbox Upload under view that activates/deactivates
radio button area. If deactivated, the entries will not be made children of any 1st level entry.
Note that whilst there is many-to-many relationship between 1st and 2nd level entries, via
data upload it is possible to make a 2nd level entry a child only of one 1st level entry.
Locations of upload files.
In all situations the page will contain the following two Browse buttons:
- Parameter file. This allows you to browse your local file system and select tab-delimited file
for upload.
- Local zipped data. This allows to pr ovide a zipped arc hi v e con t ai n ing all the files th at ar e
referenced in parameter file (if any). This ZIP archive is also uploaded form your local file
system. Whilst technically this is a simplest option for file upload, http protocol might impose
severe limitation of archive size that can be uploaded in this way.
If the system and you access rights are configured for pre-uploading files via FTP, two
additional options will be provided:
- FTP zipped data. Instead of uploading ZIP archive from your local system, you can browse
for archives that are already pre-uploaded on the server.
- FTP directory. This provides a similar pre-uploading option, however in this case you have
to specify a pre-uploaded directory containing all the referenced files. This option may be
more convenient for very large files that are hard to pack in a single archive. A notable
difference from the previous option is that in this case you shouldn't reference the same file
more than once. Ignoring this will result in a partially corrupt upload, requiring substantial
manual correction!
If data/supplementary files are pre-uploaded via FTP, there will be some delay before Assays
will be available for editing (
will be shown instead of edit icon). (Edit dialogs still will be
available for users with administrator rights, although note that data files still will not be
copied into repository and changing file references are likely to cause errors.) If icon
is
shown, this means that there have been some problems with copying data and supplementary
files.
Referencing data and supplementary files.
The column names in header for referencing files that have to be uploaded are defined in
"systemConst.xml" file and will be shown in complete header obtainable via Download ...
header link. E.g., the column names might be Study.DATA_F, Study.DF_TYPE for data files,
and Study.SUPPL_F, Study.SF_TYPE for supplementary (protocol) files. The following features
have to be taken into account:
- columns for data or supplementary files will only be available (or recognized), if linking of
files to entries is configured for particular Collection and particular level;
- the file name (given e.g. in Study.DATA_F) must contain a full path to file either in ZIP
archive or in pre-u ploaded directory .
- the file type (given e.g. in Study.DF_TYPE) is a memo field describing the file. The list of
recognized values can be checked in Edit dialog that corresponds to uploaded entries (there
could be none).
- there is extended syntax allowing to upload multiple files for a single entry. The names of
columns that reference files can contain additional suffix of the form #file_number, where
"file_number" is an arbitrary string which distinguishes different columns. E.g. to upload two
files for a single entry two columns either headers Study.DATA_F#1, Study.DATA_F#2, or
headers Study.DATA_F#SS, Study.DATA_F#17 could be used. The same suffixes can be used
to specify corresponding file types, e.g. Study.DF_TYPE#1, Study.DF_TYPE#2.
Data Export and Transfer
Both data and metadata export (i.e. request made by user's specifications) and data/metadata
transfer (predefined export to a particular) data warehouse are accessible from the same tab
Data export/transfer. To access it from Views/Studies/Assays view pages, first click on Export
tab, select the entries you wish to export and click on Data export/transfer tab.
Depending from technology conf iguration and your access rights a page with a nonempty
subset from the following three sections will be displayed.
Data transfer (transfer name)
This allows to transfer selected entries to data warehouse for which such transfer is configured
for particular technology. Usually each entry should be transfered just once, thus transfered
entries are flagged and although a repeated transfer of flagged entries is possible, a warning
will be issued before doing so.
Note that configuration of data transfer for a given technology makes this option available only
from a single AIMS level (either from Views, Studies or Assays.
The only configurable option in this section is a field for entering email - in this case the
processing program will send the updates of processing status of transfers to this address.
Apart from that, a list of configuration files used for metadata transfer as well as a list of
transferred higher level entries (with num b e r of their children) are shown (dpending from the
configuration a transfer may include either metadata or datafile transfer or both).
There is a choice to request transfer by pressing Transfer button and cancelling the operation.
When trasfer has been requested the corresponding entries will be marked for processing and
files will be transfered later by an external program. The following flags will be used to mark
entries:
successfully completed),
the actual data transfer has failed, or data warehouse ha s reported tha t ther e are pr obl ems
with transferred files). Some of these flags may not be available for soma data transfer
configurations.
Metadata export
This allows to export metadata according to configuration that is specified by XML template.
According from you access rights there may be only option to select from Configuration files
provided by system administrator, or also an option to Upload your own configuration file.
The syntax of configuration file is described in a separate document, but it allows to configure
meta data export in XML file in rather flexible format. Export can include metadata from the
aims AIMS level from which it has been requested, from all child levels as well as from all
SIMS levels that are referenced from these entries.
Export file can be generated in two formats: XML (native format) and TSV (a tab delimited file
that is obtained from "flattening" native XML file).
Data export
(transfer has been requested), (the actual transfer of data has been
(a successful reception of data has been confirmed), (either
This allows to export data and supplementary files. For the option to functional you must
additionally setup the options how the data files will be delivered. This is done via XML
configuration file that should be set up by system administrator.
There are two options how tranbfe r s is bei n g m a de ( a n d th e s e shou ld be specified in
configuration file mentioned above): sending of files bu FTP to a server of your choice (in this
case you should provide to administrator server location and login details), and copying files
on the same server to different directory (e.g. your account home directory). The configurable
options in this section are: providing Export name (this shoul d be obtained from administrator
and will be used to recognize that export is initiated by you and ned to be delivered to your
location) and emaila ddress for feedback (an email will be sent to this address after the export
will be completed). After the export is requested, the corresponding entries will be marked for
processing and files will be exported later by an external program.
Directories of XML configuration files
The root directory of configuration files is defined in web.xml file by <context-param> entry
data_transfer_configuration.directory. Within this directory the location of configuration
files are as follows:
Metadata export configuration files:
exports/[technology directory]/l1 (export at Assays level),
exports/[technology directory]/l2 (export at Studies level),
exports/[technology directory]/l3 (export at Views level),
where [technology directory] is defined by FTP directory entry in Technologies table.
Date transfer configuration files:
transfers/[technology directory]/[transfer directory],
where [technology directory] is defined as above and [transfer directory] corresponds to Data
directory entry in Transfer types table.
Data filtering
Filter settings page allows to search for Study Groups/Assays with values of selected fields
equal to the values defined in search page filters.
The fields, wh ich are available for filtering, are defined in parameters and
common_parameters tables. To define a filter for a particular field, enter a filtering
expression for this field. The syntax of filtering expressions is as follows:
- symbol "%" matches any substring (including empty substrings),
- symbol "_" matches any single symbol,
- all other symbols match themselves.
The filtering is done by SQL queries and for some particular datatypes (boolean, lists of
numbers, etc.) the syntax of "right" filtering expressions may not be intuitive.
For fields of fixed vocabulary types a drop-down list is provided instead of filtering expression.
Filters are conjunctive, i.e. if a field is included in search, database entries satisfying filter
values for this field AND filter values for all other fields will be found.
To display all databa se entries press Cancel filter button e ither on St udy Groups or on Assa ys
page.
Defining tabular views and reports
Configure columns
Configure ... columns page allows to select which columns and in which order will be
displayed in View, Study or Assay level pages in list (tabular) format. It also defines which
fields will be exported by Report function (which actually might be the main reason for
changing these settings). The level for which column display options can be changed
corresponds to the level from which Configure ... columns page has been entered (by using
Columns function).
To change the settings, enter numbers of columns in which the fields of interest should be
displayed. Columns are numbered by rational positive numbers which should be entered in
two adjacent textboxes containing correspondingly integer and fractional parts. On view pages
columns will be shown from left to right according to increasing ordering of column numbers.
Column number 0 means that the corresponding field will not be displayed.
To apply view settings press OK button. Pressing of Tune button will "normalize" the column
numbering, i.e. columns will be assigned consecutive integer numbers starting from 1. Also,
they will be re-ordered according to their numbers. Normalizing and re-ordering occurs also on
re-entering Configure ... columns page.
Settings are preserved only within the current session. After the nex t login the default settings
will be restored (the later can be configured from Configuration tables page by users having
sufficient access rights to do so).
Reports
This is the simplest way of data export, providing export of Studies in WYSIWYG mode. By
clicking on Report button you are able to save the data shown on Study page in tab-delimited
format. Included in the report are the same columns that are currently configured as visible in
Study page (see Column configuration). In the report you will get only the data you have
permission to view. You can manage the data you wish to include in your report either by
using filter first or by clicking on the “Export” link first and manually selecting the entries you
wish to see in the report. In both cases, the report will contain all selected data, even if the
entries are on several pages and not visible. Check the number of items on top of the list
(next to “Uncheck all” button if in batch export mode).
Vocabulary tables
Vocabulary tables page allows to view/add/edit/delete entries in fixed vocabularies.
Vocabularies that are available for editing depends from currently selected technology. Shown
are vocabularies that are defined for the particular technology (this is done in Configuration
tables page) as wel l as common vocabularies that are available for all technologies (these are
defined separately in Administrator tables page).
Editing options includ e adding new entries to the vocabulary, deleting existing entries,
renaming existing entries and changing the order in which entries will be available for
selection. To add a new entry click on a new link for a specific vocabulary. To edit/delete entry
click on edit icon
and icons.
Editing of vocabularies should be done with some care - deleting of an existing entry and
subsequent adding of new entry with the same name may lead to wrong values being
associated with data that are already stored in the system. However changing the order in
which entries are displayed for selection is safe operation in such context and doesn't affect
the data already stored in the system.
The length of vocabulary tables is limited by a 4000 character long encoding of vocabulary in
database.
Depending from your access rights you might hav e only view only access to Vocabulary
tables page or the page might be unavailable for you.
for a specific vocabulary. To change the display order use correspondingly
Technology configuration
Configuration tables page allows to access and (depending from your access rights) modify
configuration of currently selected technology. The tables shown on this page and their
meaning are descri be d b elow .
Table Parameter types
Contains data types that are available for the current Technology for use in configurable
parameter fields. There are 10 base types, some of which may be pa ra me tr ized by different
values of 2 attributes (currently, only Attribute 1 values is used practice). In database all
these datatypes are encoded in 200 byte character strings, which places some restrictions on
range of values that can be used in these data types. The available base types are:
- string string of up to 200 characters, shown in one line in edit dialogs,
- bigstring string of up to 200 characters, shown in multiple lines in edit dialogs,
- number integer (range likely depends from what is recognized as integers by java),
- float float (range likely depends from what is recognized as floats by java),
- boolean yes/no, represented by checkbox in edit pages,
- array of number list of 1 to 10 integers, shown adjacently in one row in edit pages, number
of integers given as value for Attribute 1,
- array of float list of 1 to 10 floats, shown adjacently in one row in edit pages, of integers
given as value for Attribute 1,
- table, values from controlled vocabulary defined in Vocabularies or Common
Vocabularies tables (the last can be found on Administrator tables page), the required
table should be selected in field Table name. Values from vocabularies are shown in edit
dialogs as drop-down lists.
- datatime data and time (if Attribute 1 value is 3), date (if Attribute 1 value is 2) or year (if
Attribute 1 value is 1).
- time time (duration) in format mm:ss if Attribute 1 value is 3), hh:mm (if Attribute 1 value
is 6) or hh:mm:ss (if Attribute 1 value is 7)
The table automatically lists all entries present in Common parameter types table (shown
on Administrator tables page), which are uneditable. In addition new entries can be created
and/or edited for a particular technology. Generally this is needed for creation of new
parameters of table and array of... types. The meaning of the table fields should be
apparent.
Table Common parameters
Table contains configuration of fixed datatype fields for cu r r en t Te c hn o l og y f or Views, Studies
and Assays. For each of these the following fixed type fields are available - indentifString
(normally used for Ids, string of up to 200 characters), visibleName (normally used for Names,
string of up to 200 characters), comment (string of up to 4000 characters), dataFiles (used for
associated data files), protocolFiles (used for supplementary files), creator (FK to Users
table), modifier (FK to Users table), createDate
aliquotId (string of up to 200 characters and (optionally) FK to referenced Aliquot).
Configuration options include visibility and column and row names in edit dialogs. Note that
(apart from a l iquotID, whi c h s hould be used only for Assays) there is exac tl y on e field of each
type available for Views, Studies and Assays. The configuration of fields creator, modifier,
createDate and modifDate is optional.
The table contains the following configurable fields (in this order):
- Parameter short name - name shown as column name in List of Views/Studies/Assays
pages,
- Parameter long name - name shown on th e left side of the field in Add/Edit/View di alogs,
- Parameter upload name - name used in header of batch upload file (this is currently provided
(datatime), modifDate (datatime) and
for reference purposes only - the upload names for common parameters are hard-coded in the
software),,
- Assay column name - the name of field which is configured (doesn't apply to Assays, if left
empty),
- Study column name - the name of field which is configured (doesn't apply to Studies, if left
empty),
- View column name - the name of field which is configured (doesn't apply to Views, if left
empty),
- Assay view column # - column number in List of Assays page (n ot shown, if 0),
- Sortable - if true, the entries in List of Assays can be shorted by the values of this
parameter,
- Study view column # - column number in List of Studies page (not shown, if 0),
- Sortable - if true, the entries in List of Studies can be shorted by the values of this
parameter
- View view column # - column number in List of Views page (not shown, if 0),
- Sortable - if true, the entries in List of Views can be shorted by the values of this
parameter,
- Show in filter - if true the parameter will be included in data filter,
- Comment - informal comment.
Table Parameters
Table contains configuration of Fxxx fields for current Technology for Views, Studies and
Assays. Currently up to 55 fields from F001 to F055are available for Views, Studies and
Assays. (to increase this, changes should be made in both, data base and program files).
Apart from configuration options what is available for Common parameters, additionally
"soft" data types used for these fields should be configured (available datatypes are these that
are given in Parameter types table).
The table contains the following configurable fields (in this order):
- Parameter short name - name shown as column name in List of Views/Studies/Assays
pages,
- Parameter group - parameter group (see Parameter groups table in Administrator tables
page) to which the para m e ter be l on gs . Pa rameter groups affe c t the upper level header in List
of Views/Studies/Assays pages and parameter position in Add/Edit/View dialogs (all
parameters from the same group are kept together),
Parameter type - parameter type from Parameter types table,
-
- Parameter long name - name shown on th e left side of the field in Add/Edit/View di alogs,
- Parameter upload name - name used in header of batch upload file,
- Assay column name - the name of field which is configured (doesn't apply to Assays, if left
empty),
- Study column name - the name of field which is configured (doesn't apply to Studies, if left
empty),
- View column name - the name of field which is configured (doesn't apply to Views, if left
empty),
- Required - if true the field can't be left empty,
- Assay view column # - column number in List of Assays page (n ot shown, if 0),
- Sortable - if true, the entries in List of Assays can be shorted by the values of this
parameter,
- Study view column # - column number in List of Studies page (not shown, if 0),
- Sortable - if true, the entries in List of Studies can be shorted by the values of this
parameter,
- View view column # - column number in List of Views page (not shown, if 0),
- Sortable - if true, the entries in List of Views can be shorted by the values of this
parameter,
- Assay row - order number of the field in Add/Edit/View dial og for Assays (within a parameter
group),
- Study row - order number of the field in Add/Edit/View dial og for Studies (within a
parameter group),
- View row - order number of the field in Add/Edit/View dialog for Views (within a parameter
group),
- Show in filter - if true the parameter will be included in data filter,
- Comment - informal comment.
Table Data types
Data types are labels for different types of data files that for current Technology can be
associated with Views, Studies and Assays. They are optional and for informal use only processing of data file doesn't depend from data type used for labelling it. The field Extension
is used for data transfer purposes only - it specifies extension that will be used for file when
being sent to target location.
Table Supplementary types
Supplementary types are labels for different types of supplementary files that for current
Technology can be associated with Views, Studies and Assays. They are optional and for
informal use only - processing of supplementary file doesn't depend from supplementary type
used for labelling it.
Table Vocabularies
Defines controlled vocabularies available for current Technology. The content of these
controlled voc abularies is accessible and can be modified from Vocabularies page. To use
these vocabularies, the corresponding parameter table types should be additionally configured
also in Parameter types table. The dialog for entries contains fields Table (the name to be
referenced in Parameter types table) and Long name (the name under which vocabulary is
shown in Vocabularies page) as well as informal Comment.
System administration
Administrative tables page allows to access and (depending from your access rights) modify
technology independent configuration tables of the system. Generally these tables can be
divided in two gr oup s : us e r an d th eir access rights ma nagement and settin g s th at ap ply to all
technologies. The tables shown on this page and their meaning are described below.
Table Technologies
Contains data about currently configured Technologies and allows to create new Technologies
and modify the existing ones. There is also an option of Technology import in XML format
(when doing the Technology name given in import file will be used unless it is already present,
in later case it will be modified to make it unique) as well as for Technology configuration
export in XML format. The import/export XML files generally contain information about the
particular entry in Technologies table as well as full contents of tables in Vocabularies and
Configuration pages for the particular Technology. Due to this importing of Technologies
should be done with some caution - if the Technology is undesired and needs to be deleted,
the contents of tables in Vocabularies and Configuration pages largely will need to be
deleted manually.
Also, when a new Technology is created, contents of tables Common parameter types and
Default common parameters are copied to configuration of new Technology.
The table contains the following fields:
- Technology - Technology name,
- Id prefix - a string which will be used as part of Id when creating new Studies or Assays,
- FTP directory - subdirectory from which data and supplementary files will be listed (if FTP
option is enabled for this AIMS configuration),
- Is public - if true, Technology is visible for all users, otherwise only for users configured in
Technology access rights table,
- Use ID generation - if true IDs will be generated automatically at all levels, otherwise they
can be entered manually (generated IDs will be offered, but can be changed),
- Show Views - if true, View level is available for this Technology,
- transfer type - if selected from a list (values are defined in Transfer types table), a data
and metadata transfer option to a specified data warehouse will b e available for this
Technology,
- Comment - informal comment.
Table Transfer types
Describes data transfers (usually to data warehouses) then can be configured for existing
technologies. For transfers to be fully configured, additional configuration (XML file defining
transfer location and protocol as well as date e n cryption/compression parameters and
feedback processing) must be set up. For this setup you should contact system administrator.
The table contains the following fields:
- Transfer type - Transfer type name, used for referring to Transfer when configuring
Technology,
- Abbreviation - name that is used by external transfer program, this should correspond to the
value in additional XML configuration file,
- Data directory - subdirectory for XML templates that ar e used to configure metadata export
(value should be supplied even if metadata export is not neede d),
- Transfer from level - specifies from w h ic h level (
- Comment - informal comment.
Table Parameter groups
Describes Parameter groups which are the upper level header in List of
View, Study, Assay transfer is a v ailable),
Studies/Experiments/Assays pages and parameter position in Add/Edit/View dialogs (all
parameters from the same group are kept together). Also largely informal, up to extent the
use of default groups provided with AIMS is recommended.
The table contains the following fields:
- Parameter group - Parameter group name, used in defining Parameter group in Parameters
table for particular technology,
- Short name - name show n in upper level header in List of Views/Studies/Assays pages,
- Position in Assay - the order number of fields of this Parameter group in Add/Edit/View
dialog for Assays,
- Position in Study - the order number of fields of this Parameter group in Add/Edit/View
dialog for Studies,
- Position in View - the order number of fields of this Parameter group in Add/Edit/View dialog
for Views,
- Comment - informal comment.
Table Common parameter types
Contains data types that are available for the all Technologies for use in configurable
parameter fields. There are 10 base types, some of which may be pa ra me tr ized by different
values of 2 attributes (currently, only Attribute 1 values is used practice). In database all
these datatypes are encoded in 200 byte character strings, which places some restrictions on
range of values that can be used in these data types. The available base types are:
- string string of up to 200 characters, shown in one line in edit dialogs,
- bigstring string of up to 200 characters, shown in multiple lines in edit dialogs,
- number integer (range likely depends from what is recognized as integers by java),
- float float (range likely depends from what is recognized as floats by java),
- boolean yes/no, represented by checkbox in edit pages,
- array of number lis t of 1 to 10 integers , shown adjacently in one row in edit pages, number
of integers given as value for Attribute 1,
- array of float list of 1 to 10 floats, shown adjacently in one row in edit pages, of integers
given as value for Attribute 1,
- table, values from controlled vocabulary defined in Vocabularies or Common
Vocabularies tables (the last can be found on Administrator tables page), the required
table should be selected in field Table name. Values from vocabularies are shown in edit
dialogs as drop-down lists.
- datatime data and time (if Attribute 1 value is 3), date (if Attribute 1 value is 2) or year (if
Attribute 1 value is 1).
- time time (duration) in format mm:ss if Attribute 1 value is 3), hh:mm (if Attribute 1 value
is 6) or hh:mm:ss (if Attribute 1 value is 7)
The meaning of the table fields should be apparent. The table entries are automatically
included in Parameter types table in Configuration page for all Technologies.
Table Default common parameters
Table is used as a template for Common Parameters table in Configuration page when a
new Technology is created.
Table contains configuration of fixed datatype fields for current Technology for Studies,
Experiments and Assays. For each of these the following fixed type fields are available indentifString (normally used for Ids, string of up to 200 characters), visibleName (normally
used for Names, string of up to 200 characters), comment (string of up to 4000 characters),
dataFiles (used for associated data files), protocolFiles (used for supplementary files), creator
(FK to Users table), modifier (FK to Users table), createDate (datatime), modifDate
(datatime), simsBottomRef, simsMiddleRef,simsTopRef, and simsCollectionName (referencing
entries in SIMS).
Configuration options include visibility and column and row names in edit dialogs. Note that
there is exactly one field of each type available for Views, Studies and Assays. Field
simsCollectionName should be configured if and only if at least one of the fields
simsBottomRef, simsMiddleRef,simsTopRef is configured (for particular level). The
configuration of fields creator, modifier, createDate and modifDate is optional.
The table contains the following configurable fields:
- Parameter short name - name shown as column name in List of
Studies/Experiments/Assays pages,
- Parameter long name - name shown on th e left side of the field in Add/Edit/View di alogs,
- Parameter upload name - name used in header of batch upload file (this is currently provided
for reference purposes only - the upload names for common parameters are hard-coded in the
software),
- Assay column name - the name of field which is configured (doesn't apply to Assays, if left
empty),
- Study column name - the name of field which is configured (doesn't apply to Studies, if left
empty),
- View column name - the name of field which is configured (doesn't apply to Views, if left
empty),
- Assay view column # - column number in List of Assays page (n ot shown, if 0),
- Sortable - if true, the entries in List of Assays can be shorted by the values of this
parameter,
- Study view column # - column number in List of Studies page (not shown, if 0),
- Sortable - if true, the entries in List of Studies can be shorted by the values of this
parameter
- View view column # - column number in List of Views page (not shown, if 0),
- Sortable - if true, the entries in List of Views can be shorted by the values of this
parameter,
- Show in filter - if true the parameter will be included in data filter,
- Comment - informal comment.
Table Common vocabularies
Defines controlled vocabularies available for all Tec hnologies. The content of these controlled
vocabularies is accessible and can be modified from Vocabularies page. To use these
vocabularies, the corresponding parameter table types should be additionally configured also
in Parameter types table for each Technology where it is used. The dialog for entries
contains fields Table (the name to be referenced in Parameter types table) and Long name
(the name under which vocabulary is shown in Vocabularies page) as well as informal
Comment.
Table Project partners
Each user can be associated with zero or one of project partners. Currently this serves a
memo purpose only (but can be used when creating reports by external software).
Table Users
Defines Users of the system.
The table contains the following fields:
- User description - informal User description,
- Login name - login name,
- Administrator rights - administrator level rights for this user, the options are are non-
accessible (no access to AdminTables page), view only, limited editing (actually meaning
almost full access, some configuration printouts and external task tables not shown) and full
editing,
- User password - password (shown in MD5 hashed form, but can be reset from this dialog),
- Id prefix - a string which will be used as part of Id when creating new Experiments or
Studies,
- Start with welcome page - if true, Welc o m e pa ge is shown after login into the system,
- FTP is allowed - if true, User can access files preuploaded via FTP (if FTP option is enabled for
this AIMS configuration),
- FTP directory - subdirectory from which data and supplementary files will be listed (if FTP
option is enabled for this AIMS configuration),
- Default user group - the User group, which owns Studies and Experiments created by this
user. When a new user is created all User groups is available in drop-down list and initially
default User group is selected. When data about already existing user is edited this list
contains only User groups the User is member of,
- Project partner - allows to specify entry from Project partners table with whom this user is
associated; currently memo purpose only,
- Comment - informal comment.
At least one User group must be present (and one User is created automatically when newly
installed AIMS is used for the first time). Users having Administrator rights at limited editing or
higher level automatically have full access to all entries and Vocabularies and Configuration
pages regardless of access rights configurations.
Table User rights
Defines granting of access rights at user level.
The table contains the following fields:
- Granted by - Use r to S tu d i e s an d Ex periments owned by whom the access is granted,
- Granted to - User to which the access is granted,
- User rights - the level of rights granted, options are non-accessible, view only, data files
non-accessible, view only, data files accessible and full access,
- Comment - informal comment.
Generally User has full access to entries owned by him, access to other entries depend from
configuration in User rights and User group rights tables. User doesn't automatically have
access to entries of user group he belongs to - this has to be configured in User group rights
table.
Table Technology access rights
Defines users that can access non-public Technologies.
The table contains the following fields:
- User - User to which access is given,
- Technology - Te chnology for which access is given,
- Can create Study - if true, can create new Studies,
- Can create View - if true, can create new Views (if configured for particular Technology),
- Vocabulary access rights - the access level to
Vocabularies page, options are non-
accessible, view only, limited editing (can edit existing entries but not delete them or create
new ones) and full editing,
- Configuration access rights - the access level to Configuration page, options are non-
accessible, view only, limited editing (can edit existing entries but not delete them or create
new ones) and full editing,
- Data export rights - specifies, what options of XML template based metadata export is
available, options are non-accessible, predefined (only from XML templates previously set up
by system administrator), user defined (upload of own templates is possible),
- Data file export rights - if true, can access data file export functionality (for this to work
additional export configuration must be set up with system administrator),
- Data transfer rights - if true, can initiate data transfer (if configured for particular
Technology),
- Comment - informal comment.
Table User groups
Defines User groups.
The table contains the following fields:
- Group name - name of User group,
- Is default - if true this is the User group the newly created user is assigned to as to his
default User group,
- Comment - informal comment.
At least one User group must be present (and one User group is created automatically when
newly installed AIMS is used for the first time). Exactly one User group should be default - to
facilitate this Is default checkbox can only be checked, not un-checked (when another User
group is made defa ul t, th e pr evious default Us e r gr ou p l o se s th a t sta t us) .
Table User group rights
Defines granting of access rights at user group level.
The table contains the following fields:
- Granted by - User group to Studies and Experiments owned by whom the access is granted,
- Granted to - User group to which the access is granted,
- User rights - the level of rights granted, options are non-accessible, view only, data files
non-accessible, view only, data files accessible and full access,
- Comment - informal comment.
Generally User has full access to entries owned by him, access to other entries depend from
configuration in User rights and User group rights tables. User doesn't automatically have
access to entries of user group he belongs to - this has to be configured in User group rights
table.
Table User group membership
Describes User groups to which User is a member.
The table contains the following fields:
- User - User for which membership is defined,
- User group - User group to which user belongs,
- Comment - informal comment.
When a new user is created, he is automatically assigned to default User group and the
corresponding entry is placed in this table. The user can't be deleted from his default group.
Table Pending tasks
Table shows information about data and protocol files associated with uploaded assays that
still have to be uploaded in repository. This table generally is for providing information only unless system errors have occurred, editing isn't recommended.
Table Pending exports
Table shows information about requested data transfers and e xports of data files. These
entries still needs to be processed by external program. This table generally is for providing
information only - unless system errors have occurred, editing isn't recommended.
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