CN111145855A - Automatic generation method and system for clinical PDF report - Google Patents
Automatic generation method and system for clinical PDF report Download PDFInfo
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Abstract
The invention relates to the field of PDF file processing, in particular to a method and a system for automatically generating clinical PDF reports, which comprise a clinical and knowledge data storage submodule, a report template hierarchy construction module, a report template configuration module, a report creation submodule, a report data information storage submodule, an HTML version report auditing module, a Tex version report auditing module and a PDF version report management module which are sequentially connected; by the technical scheme, the clinical PDF report can be automatically, quickly and accurately generated, the productivity is improved, and meanwhile, the authority and the reliability of hospitals and medical detection companies are improved due to low report error rate.
Description
Technical Field
The invention relates to the field of PDF file processing, in particular to a method and a system for automatically generating a clinical PDF report.
Background
With the progress and development of biomedical information technology, especially gene detection and NGS technology, a large number of clinical test reports in PDF format are required to be provided every day. Most of the reports provided by hospitals or medical testing companies at present are prepared by manually filling sample information, test results and interpretation results into a Word template, or by reading data from an Excel table and filling the data into the Word template in a semi-automatic manner at a higher level, so as to generate a Word report and finally converting the report into a PDF report. Whether purely manual or semi-automatic, a large amount of manual processing operations are involved, so that the efficiency is low, mistakes are easy to make, and the labor cost is greatly increased. The invention aims to realize the automatic generation of the clinical medical PDF report, and the report is generated by calling data from the database in one key mode, so that both hands are liberated, the productivity of a hospital and a medical detection company is improved, meanwhile, the error rate of the report caused by manual operation is reduced, and the authority and the reliability of the hospital and the medical detection company are improved.
Existing clinical medical report generation systems have the following disadvantages:
1. data storage: in the prior art, clinical sample information, detection result data and data interpretation knowledge information are mostly stored in a plurality of different Excel files, so that the data acquisition, recording and extraction processes are time-consuming and labor-consuming, errors are easy to occur, and persistent safe storage is not facilitated.
2. Report the template: the report template is almost made by Word, a set of templates must be made again for different units, different projects and even different samples, and both creation and management are time-consuming and labor-consuming;
3. report generation: most of report generation is to manually extract data items from an Excel table into a Word template, generate a Word version report and then convert the report into a PDF, which is not only very easy to make mistakes, but also extremely inefficient.
Disclosure of Invention
In view of the above, the present invention provides an automatic generation method and system for clinical PDF reports, which can solve the disadvantages of the existing clinical medical report generation system.
In order to achieve the above purpose, the invention provides the following technical scheme: the invention discloses an automatic generation system of clinical PDF reports, which comprises a clinical and knowledge data storage submodule, a report template hierarchy construction module, a report template configuration module, a report creation submodule, a report data information storage submodule, an HTML report auditing module, a Tex report auditing module and a PDF report management module which are sequentially connected;
the clinical and knowledge data storage submodule is used for storing various data such as sample information, sample detection result data, interpretation knowledge data and the like;
the report template level construction module develops a report template so as to realize the personalized requirements of different companies, different projects and even different samples on the report template;
the report template configuration module is used for filling data information which needs to be kept consistent in reports of the same company, the same project or the same sample type, and comprises report titles, unit logos, edition block titles and the like;
the report creating submodule is used for selecting sample information, selecting sample detection result data, selecting a report template, and then creating a PDF clinical report in a one-click mode;
the report data information storage submodule is used for storing the template, the corresponding report structure and the report data;
the HTML version report auditing module calls a report structure and data according to the report ID, displays the report structure and data in an HTML page and provides a data editing and auditing function;
the Tex version report auditing module calls a generated Tex version report according to the report ID and provides a data editing and auditing function and a preview function of corresponding PDF;
the PDF report management module provides unified management for the finally generated clinical PDF report.
Further, the clinical and knowledge data storage submodule adopts a relational database MySQL or a non-relational database MongoDB.
The invention also provides an automatic generation method of the clinical PDF report, which comprises the following steps:
the method comprises the following steps: creating a report template of a 'component-module-edition-frame-template' hierarchical framework by the report template hierarchical construction module;
step two: configuring a specific report template by the report template configuration module;
step three: the clinical and knowledge data storage submodule stores various data such as sample information, sample detection result data and interpretation knowledge data;
step four: calling sample information, detection result data, knowledge data and a report template through the report creating submodule, and creating a clinical PDF report;
step five: storing all levels of structures of the template, template data and report data through the report data information storage submodule;
step six: the report is audited through the HTML report auditing module and the Tex version report auditing module respectively;
step seven: the viewing, downloading and archiving of clinical PDF reports are realized through the PDF report management module.
Further, the template construction of the report template hierarchy construction module adopts Java object-oriented creation most basic structural components.
Furthermore, the report template configuration module provides a pull-down menu for the user to select the template frame, loads the frame structure in the form of HTML after selecting the frame, and provides the configuration of various basic information in the forms of text boxes, text fields, file fields and the like.
Further, the report creating submodule firstly enters an HTML page for displaying sample information; in the drop-down menu, the user selects a template configured in advance, and then creates a report.
Further, the HTML version report auditing module acquires the report structure and data information from the report data information storage submodule through the id field, displays the report structure and data information in an HTML page and provides an online editing and auditing function of the report information.
Further, the Tex version report auditing module reads a text code from the Tex version report created and generated by the report creating sub-module and provides an online editing and auditing function of the Tex code.
Compared with the prior art, the invention has the beneficial effects that:
1. firstly, sample information, detection results and knowledge data are stored in a database, so that the method is favorable for the persistent storage of all clinical relevant data information, and can realize the automatic extraction of target data by utilizing a query language carried by the database, thereby facilitating the accurate generation of report data;
2. secondly, the report template is constructed by adopting a hierarchical structure of 'component-module-layout-frame-template', so that the customizable capacity of the report template is greatly expanded, and the application field and the scene of the system are enriched;
3. by establishing the template, the report can be generated quickly, and the production speed of the report is greatly improved;
by the technical scheme, the clinical PDF report can be automatically, quickly and accurately generated, the productivity is improved, and meanwhile, the authority and the reliability of hospitals and medical detection companies are improved due to low report error rate.
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The invention is further described below with reference to the following figures and examples:
FIG. 1 is a block diagram of the system architecture of the present invention;
FIG. 2 is a flow chart of a method of the present invention;
FIG. 3 is a table of type A of the present invention: one line of the head tape carries a plurality of rows of data;
FIG. 4 is a table of type B, key-value pair type data, according to the present invention.
Detailed Description
As shown in fig. 1: the clinical PDF report automatic generation system comprises a clinical and knowledge data storage submodule, a report template hierarchy construction module, a report template configuration module, a report creation submodule, a report data information storage submodule, an HTML report auditing module, a Tex report auditing module and a PDF report management module which are sequentially connected;
the clinical and knowledge data storage submodule is used for storing various data such as sample information, sample detection result data, interpretation knowledge data and the like;
the report template level construction module develops a report template so as to realize the personalized requirements of different companies, different projects and even different samples on the report template;
the report template configuration module is used for filling data information which needs to be kept consistent in reports of the same company, the same project or the same sample type, and comprises report titles, unit logos, edition block titles and the like;
the report creating submodule is used for selecting sample information, selecting sample detection result data, selecting a report template, and then creating a PDF clinical report in a one-click mode;
the report data information storage submodule is used for storing the template, the corresponding report structure and the report data;
the HTML version report auditing module calls a report structure and data according to the report ID, displays the report structure and data in an HTML page and provides a data editing and auditing function;
the Tex version report auditing module calls a generated Tex version report according to the report ID and provides a data editing and auditing function and a preview function of corresponding PDF;
the PDF report management module provides unified management for the finally generated clinical PDF report.
As shown in fig. 2, an automatic generation method of a clinical PDF report of the present embodiment includes the steps of:
the method comprises the following steps: creating a report template of a 'component-module-edition-frame-template' hierarchical framework through a report template hierarchical construction module;
step two: configuring a specific report template through a report template configuration module;
step three: the clinical and knowledge data storage submodule stores various data such as sample information, sample detection result data and interpretation knowledge data;
step four: calling sample information, detection result data, knowledge data and a report template through a report creating submodule, and creating a clinical PDF report;
step five: storing each level structure of the template, template data and report data through the report data information storage submodule;
step six: the report is audited through an HTML report auditing module and a Tex version report auditing module respectively;
step seven: the viewing, downloading and archiving of clinical PDF reports are realized through a PDF report management module.
In an embodiment of the invention, the clinical and knowledge data storage submodule stores the basic information of the sample, the clinical information, the detection result data of the sample and the interpretation knowledge data of the detection result by adopting a relational database MySQL. The basic information and clinical information of the sample can be added singly, can be imported by an LIMS (laboratory information management system), and can be imported in batches through an Excel template designed in advance; the sample detection result data can be added singly, can also be directly imported by a biological information analysis cloud platform, and can also be imported in batches through an Excel template designed in advance; the detection result interpretation knowledge data can be submitted to a system on line, and batch import can also be carried out through an Excel template which is designed in advance; the data stored in the MySQL database are used for data retrieval in the subsequent report generation process through a powerful SQL query language;
in another embodiment of the invention, the report template hierarchy building module is implemented by adopting an innovative hierarchical structure, namely a hierarchical architecture of 'component-module-edition-framework-template'; the template construction uses the object-oriented idea of Java, first creating the most basic structure "component": the basic constituent units of clinical PDF reports are text, tables, pictures, etc., and based on the features of these units, several components are created:
for example, a picture, in addition to the URL of the picture itself, also includes a picture title, a picture description, some remark information, and so on, so an entity class named as comicinfo may be created, which contains four String types of private attributes: picitle, piciSrc, picisdesc and piccoments, get and set methods related to the attributes, constructors containing all four attributes and empty constructors not containing any attribute;
for another example, there are two tables, i.e. a key-value pair form table with a row header carrying multiple rows of data (as shown in fig. 3) or a left header and a right data (as shown in fig. 4), where both tables need to define a header and a data portion, such as a type a table, define two entity classes ComTabTitle and ComTabData for storing header and data information, respectively, and have private attributes of String types tbtNew 1-tbtNew 12 and dnew 1-tbdNew 12, respectively, and for a type B table, define two entity classes ComStrTitle and strdata for storing header and data information, respectively, and have private attributes of String types strnew 1-strtNew 30 and dnew 1-strew 30; the header and the data type of the A-type table define 12 attributes, because the number of fields of the table in a general clinical PDF report generally does not exceed 12, usually only 4-6 fields are provided, and 12 fields are almost certainly the upper limit, while for the B-type table, the number of key-value pairs appearing in different clinical PDF reports may be different, so the number of the defined field data is relatively large, and all the redundant designs are designed to better flexibly adapt to different clinical PDF report requirements for a template;
the combination of components and strings or the combination of different components with each other, etc. may form a plurality of different types of modules, for example, a B-type table in combination with a plurality of string types may create a very basic module modbaselnfo, which contains 5 private attributes: the basic structure includes only one B-type table, and the name, description and remark information of the module is recorded by three fields of the character string type, namely, fdModuleDesc, fdModuleCommment and the like;
for another example, in the clinical PDF report in the field of gene detection, there often occurs a combination of B-type tables and a-type tables, for example, a B-type table in a certain section records mutation information, medication guidance information, etc. related to a certain gene, and then a-type table of an ongoing clinical trial related to the certain gene is followed, since these two tables appear in pairs, for the convenience of designing the data structure, these two tables are integrated into a module modigeneanalysis withct, which contains 7 private attributes, namely fields fdGeneSymbol, fdalterationns, fdcollicatenaltrialstitle, 3 component objects comStrTitle, comStrData, comtaltitle, and a component object list tabdatalist, of 3 character string types;
different modules can be combined to generate a block of a clinical PDF report, where a block represents a large class of data information, such as basic information of a sample (name, gender, age, mobile phone number, etc.), clinical information of a sample (disease category, censorship hospital, censorship department, censorship doctor, sampling date, sample receiving date, etc.), sample detection results (such as detected gene mutation, gene fusion, chromosome structure variation, etc.), clinical interpretation results (such as medication interpretation results, germ line mutation interpretation results, chemical medication guidance results, immune efficacy prediction results, etc.), and the like, and this block is often composed of one or more modules, such as a sample information block, which includes basic information and clinical information of a sample, and the basic information and the clinical information are key-value pair data, so the block should be composed of two ModBasicInfo modules corresponding to the two data sets and fields of several character string types, that is, SecSampleInfo contains 5 fields: sectionName, sectionDesc, sectionCommissions and modBasicinfoPatient and modBasicinfoSample of string type;
a plurality of different layout blocks form a report template framework, the construction mode of the report template framework is similar to that of the layout blocks and the modules, and the report template framework comprises a plurality of layout block objects, character strings and Date objects, such as a framework TemLung27, the report template framework is designed and built for a certain lung cancer gene detection product and comprises 13 fields: 4 String types (id, temName, temDesc, temStatus), 2 Date types (createTime, updateTime), and 6 block objects (secBasicInfo, sectestproject, secAllResults, secTestResults, secAppendix, secReferenceList, which respectively represent basic sample information, detection item information, detection result summary, detection result interpretation, appendix, and reference);
in another embodiment of the invention, the report template configuration module firstly provides a pull-down menu for the user to select the template frame, loads the frame structure in the form of HTML after selecting the frame, and provides the configuration of various basic information in the forms of text boxes, text fields, file fields and the like, wherein the basic information comprises company or hospital names, telephones, logos, report titles, detection item information, reference documents and the like, and in addition, the title names of tables of various sections are also configured;
in another embodiment of the present invention, the report creation sub-module first enters an HTML page, which is generally a sample information page, and this page displays various information of the sample, including basic information such as name, age, sex, and mobile phone number, clinical information such as disease type, disease history, medication history, censorship hospital, censorship department, censorship doctor, sampling time, and sample receiving time, and sample detection result information such as mutation detection, fusion, chromosome structure variation, TMB, MSI, PD-L1, etc.; in a 'template selection' pull-down menu, a user selects a template configured in advance, and then clicks 'report creation', so that one-click automatic generation of a report can be realized;
in the process, a background program queries and reads data in a MySQL relational database provided by a clinical and knowledge data storage submodule according to disease information, disease history, medication history and the like and by combining with a sample detection result, then medication conclusion, germ mutation site judgment, immune curative effect prediction and the like are carried out according to a set rule, and the obtained data are filled in corresponding positions of a report template one by one;
in another embodiment of the invention, the report data information storage submodule provides the structural information of the components, modules, layout blocks, frames and templates created by the unstructured MongoDB storage report template hierarchy construction module, stores the template data information generated by the report template configuration module configuration and the structure and data information of the report created by the report creation submodule; in order to facilitate the unified and centralized management of the frames, the templates and the reports, all the structural information and the data information of the templates and the reports are stored in the same Collection of the same database, and different frames, templates and reports are stored in different documents and are identified by different ids;
in another embodiment of the invention, the HTML version report auditing module can acquire the structure and data information of the report from the report data information storage submodule through the id field, display the report in an HTML page and provide an online editing and auditing function of the report information;
for example, some important information is not reflected in a report when a certain clinical report is created probably because the updating of a knowledge base is not timely, theoretically, two ways can be used, one is to update the knowledge base by returning to the beginning and then to create the report again, and the other is to edit and add through the HTML version report auditing module, supplement data in time and then have time to update the knowledge base by returning to the beginning;
in another embodiment of the invention, the Tex version report auditing module can read the text code from the Tex version report created and generated by the report creating sub-module and provide the online editing and auditing function of the Tex code;
because LaTex itself has some special/reserved characters, and the generated report data is likely to contain the characters, when the characters are compiled as a part of the code, errors may be caused, so that a PDF report cannot be generated normally, or even if the PDF report is generated, the report structure is disordered; or special characters have been resolved, but since the text content in a long form is too long, the form is enlarged or the data exceeds the form display, which are both problematic clinical PDF reports, but since the data itself is not problematic, optimization can only be achieved by editing the Tex code.
In another embodiment of the invention, the PDF report management module can manage the final clinical PDF report created and generated by the report creation sub-module, and a user can log in the system to view or download the report and also can feed back the report; in a real application scene, a hospital or a medical detection company needs to perform unified centralized management on sample information, a knowledge base and sample detection result data, and also needs to perform submission, sending and archive management on a finally generated clinical report, and the PDF report management module can realize all the functions.
In another embodiment of the invention, the technology can 1) realize persistent safe storage of sample information, sample detection results and knowledge data, 2) rapidly and individually customize clinical PDF report templates according to different fields, different companies, different projects and even different samples, 3) combine an automatic one-click report generation technology with a report multiple audit (HTML audit, Tex audit and the like) mechanism to rapidly and accurately generate expected clinical PDF reports, and 4) each intermediate version and final version report can be checked, edited and audited only by requiring specific system authority, thereby greatly ensuring the safety of reports and data.
In the technical scheme of the invention, firstly, the sample information, the detection result and the knowledge data are all stored in the structured MySQL database, which is not only beneficial to the persistent storage of all clinical relevant data information, but also can utilize the powerful function of the SQL query language to realize the automatic extraction of the target data and build a solid foundation for the accurate generation of the report data;
secondly, the report template is constructed by adopting a hierarchical structure of 'component-module-layout-frame-template', is created and managed by using Java object-oriented thought, and is stored in combination with a document storage mode of MongoDB to form report templates with different structures, so that the 'customizable' capability of the report template is greatly expanded, and the application field and the scene of the system are enriched;
further, the report may be created in a "three-step" manner: 1) calling target data in a MySQL database and a report template in the MongoDB, generating data of each version of a report according to rules, and storing the data in the MongoDB database; 2) the MongoDB report data is called, an HTML format report is dynamically generated, a page supports the editing and modifying operation of each section data of the report, and meanwhile, the editing operation of tex codes and the previewing function of a PDF report are provided, so that the final PDF report can be ensured no matter the accuracy of the data or the attractiveness of the report is ensured; 3) and generating a tex code according to the MongoDB report data, and calling XeLatex to realize the generation of the PDF format report. The second step can be set to "optional" so long as there is no problem with the report data generation rules and the tex framework design, thus enabling "two-step" creation of reports. Thus, report creation can be achieved only by a few click operations: 1) selecting a target sample and sample detection result data, 2) selecting a report template customized in advance, and 3) clicking a 'create report' button to realize automatic creation of a PDF report.
By the technical scheme, the clinical PDF report can be automatically, quickly and accurately generated, the productivity is improved, and meanwhile, the authority and the reliability of hospitals and medical detection companies are improved due to low report error rate.
Finally, the gene detection field mentioned in the examples is only one of the application fields of the technology of the present invention, and should not be regarded as the only application field of the present invention; the entity classes of each level structure of the report template mentioned in the embodiments are only a few examples of numerous examples, and do not represent all types, so any similar class obtained after the addition, deletion and modification operation on the entity class field should be regarded as the protection scope of the patent; the relational data MySQL and the non-relational database MongoDB mentioned in the embodiments are only examples, and the two databases can be used without representing the patent, and any case of only changing the database type should be regarded as the technical protection scope of the patent.
Claims (8)
1. An automated generation system of clinical PDF reports, characterized by: the system comprises a clinical and knowledge data storage submodule, a report template hierarchy construction module, a report template configuration module, a report creation submodule, a report data information storage submodule, an HTML version report auditing module, a Tex version report auditing module and a PDF version report management module which are sequentially connected;
the clinical and knowledge data storage submodule is used for storing various data such as sample information, sample detection result data, interpretation knowledge data and the like;
the report template level construction module develops a report template so as to realize the personalized requirements of different companies, different projects and even different samples on the report template;
the report template configuration module is used for filling data information which needs to be kept consistent in reports of the same company, the same project or the same sample type, and comprises report titles, unit logos, edition block titles and the like;
the report creating submodule is used for selecting sample information, selecting sample detection result data, selecting a report template, and then creating a PDF clinical report in a one-click mode;
the report data information storage submodule is used for storing the template, the corresponding report structure and the report data;
the HTML version report auditing module calls a report structure and data according to the report ID, displays the report structure and data in an HTML page and provides a data editing and auditing function;
the Tex version report auditing module calls a generated Tex version report according to the report ID and provides a data editing and auditing function and a preview function of corresponding PDF;
the PDF report management module provides unified management for the finally generated clinical PDF report.
2. The automated clinical PDF report generation system according to claim 1, wherein: the clinical and knowledge data storage sub-module adopts a relational database MySQL or a non-relational database MongoDB.
3. An automatic generation method of clinical PDF report is characterized in that: the method comprises the following steps:
the method comprises the following steps: creating a report template of a 'component-module-edition-frame-template' hierarchical framework by the report template hierarchical construction module;
step two: configuring a specific report template by the report template configuration module;
step three: the clinical and knowledge data storage submodule stores various data such as sample information, sample detection result data and interpretation knowledge data;
step four: calling sample information, detection result data, knowledge data and a report template through the report creating submodule, and creating a clinical PDF report;
step five: storing all levels of structures of the template, template data and report data through the report data information storage submodule;
step six: the report is audited through the HTML report auditing module and the Tex version report auditing module respectively;
step seven: the viewing, downloading and archiving of clinical PDF reports are realized through the PDF report management module.
4. The method of claim 3, wherein the method comprises: the template construction of the report template hierarchy construction module adopts Java object-oriented creation most basic structural components.
5. The method of claim 3, wherein the method comprises: the report template configuration module provides a pull-down menu for a user to select a template frame, loads a frame structure in an HTML form after the frame is selected, and provides configuration of various basic information in the forms of a text box, a text field, a file field and the like.
6. The method for automatically generating clinical PDF report according to any one of claim 3 or claim 4, characterized by: the report creating submodule firstly enters an HTML page for displaying sample information; in the drop-down menu, the user selects a template configured in advance, and then creates a report.
7. The method of claim 3, wherein the method comprises: and the HTML version report auditing module acquires the report structure and data information from the report data information storage submodule through the id field, displays the report structure and data information in an HTML page and provides an online editing and auditing function of the report information.
8. The method of claim 3, wherein the method comprises: the Tex version report auditing module reads a text code from the Tex version report created and generated by the report creating submodule and provides an online editing and auditing function of the Tex code.
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| CN111737953A (en) * | 2020-06-04 | 2020-10-02 | 国网天津市电力公司电力科学研究院 | Report document automation method easy for secondary development |
| CN112580321A (en) * | 2020-12-29 | 2021-03-30 | 山东爱新卓尔智慧医疗技术有限公司 | Inspection report automatic generation method and system based on dual-model designer |
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