GMQL WEB Interface
Home Page: http://www.bioinformatics.deib.polimi.it/geco/?home
License: Apache License 2.0
GMQL-WEB project is designed and implemented for make GMQL project publicly available and easy to use by biologists and bioinformaticians.
Please visit GMQL-WEB wiki page for further information.
In User jobs and Query logjob windows, if Elapsed time / Execution time is more than 60, express it in "minutes, seconds"; if it more than 3600, express it in "hours, minutes, seconds"
Add possibility for the user to change the maximum number of vertical lines displaied (before the vertical scroll appears) in the Query editor and Dataset areas
Make possible for any user to manage its queries, by deleting those not needed anymore, and saving on file on user laptop those to be backed-up (both for guest and registered users)
In uploadSampleUrls when it's set a schema type for the dataset, the system still expects the request to contain a schema file (error 406: Not Acceptable)
We need to have associated to each dataset the date of its creation.
This should be stored somewhere (possibly in the xml structure where Andrea store the dataset profiling information) at the time of the dataset creation, and then shown in the web interface (using a web service created for this aim).
Now, clicking on a sample in the repository, you enabled the possibility to view also the sample metadata in a popup window.
That very nice. Yet, the title of such window is "Region data of ..."; it has to be changed to "Metadata of ..." (probably a copy past error).
GMQL ace editor is not working.
left/start and right/stop must be reported in the schema section as in the dataset schema file, i.e. as LONG (now they are reported as DOUBLE)
In the GMQL web home page add:
the following sentence "This system is under active development, please forgive us for possible errors and send us your comments, criticisms and congratulations, if any."
the number of visit, as collected in Google Analytic
Add possibility to specify the logical operators to be used in the select predicate (also OR and NOT, besides AND), and in case possibly to specify parenthesis among logical sub-predicates.
Fix issues in visualizing datasets in UCSC Genome Browser, by adding unique ID-value pair in each "group" attribute (more test on this aspect should be done)
When a schema is selected (particularly, but possibly not only, in case of a not custom schema), show name and type of the selected schema attributes.
In particular, it should be clarified what are the attributes in the:
Enable connection to IGB by 1) exposing the repository for IGB "Quick load" (first public data, then possibly also private data of “upgraded” registered user); 2) establishing port connection to a local open instance of IGB in order to directly visualize results in it as in UCSC Genome Browser
Download service as zip file is starting very slowly and this leads to timeout in the network connection.
Double(or single) quotation mark between the double(or single) quotation needs to be escaped in metadata browser.
In the new metadata window, after closing the window (maybe due just to check which was the query ...), column visibility selection is lost.
Can it be made persistent till the dataset is changed?
Correctly report the Schema name for private datasets as for public ones (for private ones now it is reported "DatasetName_SCHEMAS")
During data upload check sample consistency vs. dataset schema; complete loading only if all lines of all samples of the uploaded dataset are compliant, whereas stop upload at the first line not compliant, and report the error, the line and sample where it occurs.
Rational and details as follows:
When a new dataset is created with samples that have less region attributes than those listed in the selected dataset schema, currently uploading ends with success, but then the processing of such dataset ends (successfully) with empty result!
If one or more of the uploaded samples include more attributes than those listed in the selected schema, currently the system manages this situation by loading only the values of a number of the first/leftmost sample attributes equal to the number of attributes listed in the schema; this is the only thing that can be done, but it is right only when the additional sample attributes are the last, i.e. the rightmost, ones in the sample.
Check correctness of selected schema for the uploaded samples while creating the new dataset, and accordingly provide a message to the user (either if any of their lines contain less or more region than expected), and stop loading, so that to avoid not conformant samples in the repository.
In top bar, add link to the Genomic Computing web page
Make possible to visualize the first K rows of a sample (possibly with a first heather row with schema column names)
Enable a structure where to incrementally store example queries (in case with their description), which can be clicked to be copied in the Query editor section to be run (for an example see http://147.8.174.16:9999/stql/queries/shared ), making easy for an administrator to add / modify example queries.
As Schema type of tab delimited output datasets use TAB (now is DEL)
In Metadata browser, make possible changing:
- Dataset without loosing all defined attribute-value predicates
- Any (not only the last one) selected attribute and/or value
- Now it is not possible to download a dataset different from the one selected for Metadata browser without loosing all the defined attribute-value predicates in the Metadata browser
Extend XML schema file adding new attributes for dataset content description.
It is important to associate with each datasets some info about it and the data it contains (e.g., type of contained data, where retrieved from, creation(update date, number of samples included, amount of bytes, etc. ...
Some of these information can be provided directly by the GMQL-Importer software, other should be provided through the solving of issue #2 and #28.
In the xml schema file of GMQL datasets it is important to define an" information" tag which includes several subtags, one for each info to provide (see above examples).
This implies changing the xsd associated with the xml schema and the implementation of both the web interface (in order to make this information accessible and display it properly) and the implementation, in order to parse the xml file and make the information available to the web interface.
It is important to make such changes to the implementation so that all subtags included in the information tag are parsed and displayed in the web interface, so that if new info are required to be displayed, it will be then enough to add them in the xml (in a proper subtag under the information tag) and change the xsd without any further change to the implementation.
To avoid giving a bad impression to the reviewers of our work, the execution log shown in the web interface should not include the current several lines of warnings which "appear as possible errors".
Such warnings can be useful, particularly for the developers, but not for the final web user.
I would provide to web user only a shorter log, including only INFO, ERROR, and others lines, and possibly a link to the current full log (including also WARN lines).
This can be done by generating in the core GMQL another log file with only the log lines tagged as INFO, ERROR, and others (by replicating what has been done for generating the current log files, without including the lines tagged as WARN).
The new log file will be shown in the web interface in place of the current one, together with a link to show, only if/when required, the current full log file in another window for more insights (having still the full log is useful when some issue occurs, in order to understand and fix it more easily/quickly).
Inform the user about the interface available features, e.g. about GMQL statement autocomplete in query editor, or about how to search in the window; this can be done, for example, by adding a note below the "Query editor" title, such as " *: Press CTRL + spacebar for GMQL command auto-complete support", or a note such as "Press CTRL + f key for text search", respectively, or with a better solution to be thought.
When a job is killed, show “EXEC_STOPPED” instead of “EXEC_FAILED”
Add a web service to change the name of a dataset
What's the issue in the 'enhancer' annotation sample which prevents its materialization when selected?
Running:
DATA_SET_VAR = SELECT(annotation_type == 'enhancer') HG19_BED_ANNOTATION;
MATERIALIZE DATA_SET_VAR INTO RESULT_DS;
the generated datest is empty (both in GTF and tab format)
Enable a user to request for an upgraded user category; consequently, an email should be sent to the user administrators listed (and easily updatable) in the system (but not publicly visible), and any of such administrator should be able to decide to accept or not the request and reply with a message to the user.
In the “Add” window for uploading personal datasets:
In the window title, change text “data set” to “dataset”
When an error occurs (e.g. a new dataset is created with the name of a data existing in the repository Private section), report why (now only “error” is reported); @akaitoua I thik this requires Abdulrahman fix
Add possibility to specify in Metadata browser (and then in the GMQL select) the request that the searched samples have null value for a specific metadata attribute (i.e. that they do not have any value for that attribute, that is they do not have that metadata attribute, as it is already possible in the GMQL select by specifying "NOT(attribute == '*')").
Enable visualization of dataset “vocabulary”.
It requires the vocabulary file to be stored in the repository
When uploading dataset samples some character encoding seams not working properly; in fact, when downloading metadata file some characters are not recognize in the local encoding system (e.g. ANSI - Latin1) resulting in some unreadable string (e.g. 17��-estradiol); can the encoding info be embedded in the uploaded/downloaded file?
Show if the generated personal dataset includes GTF or TAB files
It requires fixes in the back-end
Make possible to structure the content of the Datasets window in subbranches, within the current only Private/Public ones.
By clicking the “Execute” button, the query is executed without previously compiling it, so that if any syntax error is present, it generates a runtime error. Make the “Execute” button compiling the query before running it.
Enable the user to change the name of his/her datasets
Make possible searching within all values of all attributes, not only of the single selected attribute (related to datasets vocabulary visualization?).
Do not force changing dataset visualization in metadata browser when a new dataset is materialized as result of a running query
Provide information about the size (in byte), number of samples and the number of regions in a dataset (and the number of regions in a sample), besides the date of each dataset
In the new metadata window, for the column visibility, is it possible to add the option of disabling all columns?
This would be very useful when there are many columns and you want to view only very few (the most typical case).
When first a job is run, then after it is finished a new query is compiled, pressing the Compile_success (compile_failed) button open the log window with as content the log of the previous job run.
Add a button to enlarge/shorten the Query editor window also at the bottom of the window (not only on top); it is very useful in case of long text queries.
Add as keywords of the language, to be shown in different color in the query editor window, the following ones:
DIST, DG, DL BAGD
LEFT_DISTINCT, RIGHT_DISTINCT, BOTH
Make the Datasets area horizontally resizable (this can help when datasets have long names).
start adding a button as in query editor to enlarge the Datasets area
Show in the interface the entire size used by the user / out of the user disk quota
Make possible to easy visualize the query saved in a personal dataset, with following possibility of loading it in the Query editor
Define user categories (base/intermediate/advanced/admin) and manage the resources (disk space and computational power) assigned to each user category / specific user (this is very important for the correct use of the Cineca cluster)
Implement a limitation on resource usage for users who are not in the upgraded category (to be evaluated the differentiation of resource usage limitation between public and registered user, but not in the upgraded category)
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